Merge pull request #2 from yimmon/master

remove needless files

69 files changed, 0 insertions, 17535 deletions

diff --git a/kaldi_io/src/kaldi/base/io-funcs-inl.h b/kaldi_io/src/kaldi/base/io-funcs-inl.h
deleted file mode 100644
index e55458e..0000000
--- a/kaldi_io/src/kaldi/base/io-funcs-inl.h
+++ /dev/null
@@ -1,219 +0,0 @@
-// base/io-funcs-inl.h
-
-// Copyright 2009-2011  Microsoft Corporation;  Saarland University;
-//                      Jan Silovsky;   Yanmin Qian;  Johns Hopkins University (Author: Daniel Povey)
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-
-//  http://www.apache.org/licenses/LICENSE-2.0
-
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_BASE_IO_FUNCS_INL_H_
-#define KALDI_BASE_IO_FUNCS_INL_H_ 1
-
-// Do not include this file directly.  It is included by base/io-funcs.h
-
-#include <limits>
-#include <vector>
-
-namespace kaldi {
-
-// Template that covers integers.
-template<class T>  void WriteBasicType(std::ostream &os,
-                                       bool binary, T t) {
-  // Compile time assertion that this is not called with a wrong type.
-  KALDI_ASSERT_IS_INTEGER_TYPE(T);
-  if (binary) {
-    char len_c = (std::numeric_limits<T>::is_signed ? 1 :  -1)
-        * static_cast<char>(sizeof(t));
-    os.put(len_c);
-    os.write(reinterpret_cast<const char *>(&t), sizeof(t));
-  } else {
-    if (sizeof(t) == 1)
-      os << static_cast<int16>(t) << " ";
-    else
-      os << t << " ";
-  }
-  if (os.fail()) {
-    throw std::runtime_error("Write failure in WriteBasicType.");
-  }
-}
-
-// Template that covers integers.
-template<class T> inline void ReadBasicType(std::istream &is,
-                                            bool binary, T *t) {
-  KALDI_PARANOID_ASSERT(t != NULL);
-  // Compile time assertion that this is not called with a wrong type.
-  KALDI_ASSERT_IS_INTEGER_TYPE(T);
-  if (binary) {
-    int len_c_in = is.get();
-    if (len_c_in == -1)
-      KALDI_ERR << "ReadBasicType: encountered end of stream.";
-    char len_c = static_cast<char>(len_c_in), len_c_expected
-      = (std::numeric_limits<T>::is_signed ? 1 :  -1)
-      * static_cast<char>(sizeof(*t));
-    
-    if (len_c !=  len_c_expected) {
-      KALDI_ERR << "ReadBasicType: did not get expected integer type, "
-                << static_cast<int>(len_c)
-                << " vs. " << static_cast<int>(len_c_expected)
-                << ".  You can change this code to successfully"
-                << " read it later, if needed.";
-      // insert code here to read "wrong" type.  Might have a switch statement.
-    }
-    is.read(reinterpret_cast<char *>(t), sizeof(*t));
-  } else {
-    if (sizeof(*t) == 1) {
-      int16 i;
-      is >> i;
-      *t = i;
-    } else {
-      is >> *t;
-    }
-  }
-  if (is.fail()) {
-    KALDI_ERR << "Read failure in ReadBasicType, file position is "
-              << is.tellg() << ", next char is " << is.peek();
-  }
-}
-
-
-template<class T> inline void WriteIntegerVector(std::ostream &os, bool binary,
-                                                 const std::vector<T> &v) {
-  // Compile time assertion that this is not called with a wrong type.
-  KALDI_ASSERT_IS_INTEGER_TYPE(T);
-  if (binary) {
-    char sz = sizeof(T);  // this is currently just a check.
-    os.write(&sz, 1);
-    int32 vecsz = static_cast<int32>(v.size());
-    KALDI_ASSERT((size_t)vecsz == v.size());
-    os.write(reinterpret_cast<const char *>(&vecsz), sizeof(vecsz));
-    if (vecsz != 0) {
-      os.write(reinterpret_cast<const char *>(&(v[0])), sizeof(T)*vecsz);
-    }
-  } else {
-    // focus here is on prettiness of text form rather than
-    // efficiency of reading-in.
-    // reading-in is dominated by low-level operations anyway:
-    // for efficiency use binary.
-    os << "[ ";
-    typename std::vector<T>::const_iterator iter = v.begin(), end = v.end();
-    for (; iter != end; ++iter) {
-      if (sizeof(T) == 1)
-        os << static_cast<int16>(*iter) << " ";
-      else
-        os << *iter << " ";
-    }
-    os << "]\n";
-  }
-  if (os.fail()) {
-    throw std::runtime_error("Write failure in WriteIntegerType.");
-  }
-}
-
-
-template<class T> inline void ReadIntegerVector(std::istream &is,
-                                                bool binary,
-                                                std::vector<T> *v) {
-  KALDI_ASSERT_IS_INTEGER_TYPE(T);
-  KALDI_ASSERT(v != NULL);
-  if (binary) {
-    int sz = is.peek();
-    if (sz == sizeof(T)) {
-      is.get();
-    } else {  // this is currently just a check.
-      KALDI_ERR << "ReadIntegerVector: expected to see type of size "
-                << sizeof(T) << ", saw instead " << sz << ", at file position "
-                << is.tellg();
-    }
-    int32 vecsz;
-    is.read(reinterpret_cast<char *>(&vecsz), sizeof(vecsz));
-    if (is.fail() || vecsz < 0) goto bad;
-    v->resize(vecsz);
-    if (vecsz > 0) {
-      is.read(reinterpret_cast<char *>(&((*v)[0])), sizeof(T)*vecsz);
-    }
-  } else {
-    std::vector<T> tmp_v;  // use temporary so v doesn't use extra memory
-                           // due to resizing.
-    is >> std::ws;
-    if (is.peek() != static_cast<int>('[')) {
-      KALDI_ERR << "ReadIntegerVector: expected to see [, saw "
-                << is.peek() << ", at file position " << is.tellg();
-    }
-    is.get();  // consume the '['.
-    is >> std::ws;  // consume whitespace.
-    while (is.peek() != static_cast<int>(']')) {
-      if (sizeof(T) == 1) {  // read/write chars as numbers.
-        int16 next_t;
-        is >> next_t >> std::ws;
-        if (is.fail()) goto bad;
-        else
-            tmp_v.push_back((T)next_t);
-      } else {
-        T next_t;
-        is >> next_t >> std::ws;
-        if (is.fail()) goto bad;
-        else
-            tmp_v.push_back(next_t);
-      }
-    }
-    is.get();  // get the final ']'.
-    *v = tmp_v;  // could use std::swap to use less temporary memory, but this
-    // uses less permanent memory.
-  }
-  if (!is.fail()) return;
- bad:
-  KALDI_ERR << "ReadIntegerVector: read failure at file position "
-            << is.tellg();
-}
-
-// Initialize an opened stream for writing by writing an optional binary
-// header and modifying the floating-point precision.
-inline void InitKaldiOutputStream(std::ostream &os, bool binary) {
-  // This does not throw exceptions (does not check for errors).
-  if (binary) {
-    os.put('\0');
-    os.put('B');
-  }
-  // Note, in non-binary mode we may at some point want to mess with
-  // the precision a bit.
-  // 7 is a bit more than the precision of float..
-  if (os.precision() < 7)
-    os.precision(7);
-}
-
-/// Initialize an opened stream for reading by detecting the binary header and
-// setting the "binary" value appropriately.
-inline bool InitKaldiInputStream(std::istream &is, bool *binary) {
-  // Sets the 'binary' variable.
-  // Throws exception in the very unusual situation that stream
-  // starts with '\0' but not then 'B'.
-
-  if (is.peek() == '\0') {  // seems to be binary
-    is.get();
-    if (is.peek() != 'B') {
-      return false;
-    }
-    is.get();
-    *binary = true;
-    return true;
-  } else {
-    *binary = false;
-    return true;
-  }
-}
-
-}  // end namespace kaldi.
-
-#endif  // KALDI_BASE_IO_FUNCS_INL_H_
diff --git a/kaldi_io/src/kaldi/base/io-funcs.h b/kaldi_io/src/kaldi/base/io-funcs.h
deleted file mode 100644
index 2bc9da8..0000000
--- a/kaldi_io/src/kaldi/base/io-funcs.h
+++ /dev/null
@@ -1,231 +0,0 @@
-// base/io-funcs.h
-
-// Copyright 2009-2011  Microsoft Corporation;  Saarland University;
-//                      Jan Silovsky;   Yanmin Qian
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-
-//  http://www.apache.org/licenses/LICENSE-2.0
-
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_BASE_IO_FUNCS_H_
-#define KALDI_BASE_IO_FUNCS_H_
-
-// This header only contains some relatively low-level I/O functions.
-// The full Kaldi I/O declarations are in ../util/kaldi-io.h
-// and ../util/kaldi-table.h
-// They were put in util/ in order to avoid making the Matrix library
-// dependent on them.
-
-#include <cctype>
-#include <vector>
-#include <string>
-#include "base/kaldi-common.h"
-
-namespace kaldi {
-
-
-
-/*
-  This comment describes the Kaldi approach to I/O.  All objects can be written
-  and read in two modes: binary and text.  In addition we want to make the I/O
-  work if we redefine the typedef "BaseFloat" between floats and doubles.
-  We also want to have control over whitespace in text mode without affecting
-  the meaning of the file, for pretty-printing purposes.
-
-  Errors are handled by throwing an exception (std::runtime_error).
-
-  For integer and floating-point types (and boolean values):
-
-   WriteBasicType(std::ostream &, bool binary, const T&);
-   ReadBasicType(std::istream &, bool binary, T*);
-
-  and we expect these functions to be defined in such a way that they work when
-  the type T changes between float and double, so you can read float into double
-  and vice versa].  Note that for efficiency and space-saving reasons, the Vector
-  and Matrix classes do not use these functions [but they preserve the type
-  interchangeability in their own way]
-
-  For a class (or struct) C:
-  class C {
-  ..
-    Write(std::ostream &, bool binary, [possibly extra optional args for specific classes]) const;
-    Read(std::istream &, bool binary, [possibly extra optional args for specific classes]);
-  ..
-  }
-  NOTE: The only actual optional args we used are the "add" arguments in
-  Vector/Matrix classes, which specify whether we should sum the data already
-  in the class with the data being read.
-
-  For types which are typedef's involving stl classes, I/O is as follows:
-  typedef std::vector<std::pair<A, B> > MyTypedefName;
-
-  The user should define something like:
-
-   WriteMyTypedefName(std::ostream &, bool binary, const MyTypedefName &t);
-   ReadMyTypedefName(std::ostream &, bool binary, MyTypedefName *t);
-
-  The user would have to write these functions.
-
-  For a type std::vector<T>:
-
-   void WriteIntegerVector(std::ostream &os, bool binary, const std::vector<T> &v);
-   void ReadIntegerVector(std::istream &is, bool binary, std::vector<T> *v);
-
-  For other types, e.g. vectors of pairs, the user should create a routine of the
-  type WriteMyTypedefName.  This is to avoid introducing confusing templated functions;
-  we could easily create templated functions to handle most of these cases but they
-  would have to share the same name.
-
-  It also often happens that the user needs to write/read special tokens as part
-  of a file.  These might be class headers, or separators/identifiers in the class.
-  We provide special functions for manipulating these.  These special tokens must
-  be nonempty and must not contain any whitespace.
-
-    void WriteToken(std::ostream &os, bool binary, const char*);
-    void WriteToken(std::ostream &os, bool binary, const std::string & token);
-    int Peek(std::istream &is, bool binary);
-    void ReadToken(std::istream &is, bool binary, std::string *str);
-    void PeekToken(std::istream &is, bool binary, std::string *str);
-
-
-  WriteToken writes the token and one space (whether in binary or text mode).
-
-  Peek returns the first character of the next token, by consuming whitespace
-  (in text mode) and then returning the peek() character.  It returns -1 at EOF;
-  it doesn't throw.  It's useful if a class can have various forms based on
-  typedefs and virtual classes, and wants to know which version to read.
-
-  ReadToken allow the caller to obtain the next token.  PeekToken works just
-  like ReadToken, but seeks back to the beginning of the token.  A subsequent
-  call to ReadToken will read the same token again.  This is useful when
-  different object types are written to the same file; using PeekToken one can
-  decide which of the objects to read.
-
-  There is currently no special functionality for writing/reading strings (where the strings
-  contain data rather than "special tokens" that are whitespace-free and nonempty).  This is
-  because Kaldi is structured in such a way that strings don't appear, except as OpenFst symbol
-  table entries (and these have their own format).
-
-
-  NOTE: you should not call ReadIntegerType and WriteIntegerType with types,
-  such as int and size_t, that are machine-independent -- at least not
-  if you want your file formats to port between machines.  Use int32 and
-  int64 where necessary.  There is no way to detect this using compile-time
-  assertions because C++ only keeps track of the internal representation of
-  the type.
-*/
-
-/// \addtogroup io_funcs_basic
-/// @{
-
-
-/// WriteBasicType is the name of the write function for bool, integer types,
-/// and floating-point types. They all throw on error.
-template<class T> void WriteBasicType(std::ostream &os, bool binary, T t);
-
-/// ReadBasicType is the name of the read function for bool, integer types,
-/// and floating-point types. They all throw on error.
-template<class T> void ReadBasicType(std::istream &is, bool binary, T *t);
-
-
-// Declare specialization for bool.
-template<>
-void WriteBasicType<bool>(std::ostream &os, bool binary, bool b);
-
-template <>
-void ReadBasicType<bool>(std::istream &is, bool binary, bool *b);
-
-// Declare specializations for float and double.
-template<>
-void WriteBasicType<float>(std::ostream &os, bool binary, float f);
-
-template<>
-void WriteBasicType<double>(std::ostream &os, bool binary, double f);
-
-template<>
-void ReadBasicType<float>(std::istream &is, bool binary, float *f);
-
-template<>
-void ReadBasicType<double>(std::istream &is, bool binary, double *f);
-
-// Define ReadBasicType that accepts an "add" parameter to add to
-// the destination.  Caution: if used in Read functions, be careful
-// to initialize the parameters concerned to zero in the default
-// constructor.
-template<class T>
-inline void ReadBasicType(std::istream &is, bool binary, T *t, bool add) {
-  if (!add) {
-    ReadBasicType(is, binary, t);
-  } else {
-    T tmp = T(0);
-    ReadBasicType(is, binary, &tmp);
-    *t += tmp;
-  }
-}
-
-/// Function for writing STL vectors of integer types.
-template<class T> inline void WriteIntegerVector(std::ostream &os, bool binary,
-                                                 const std::vector<T> &v);
-
-/// Function for reading STL vector of integer types.
-template<class T> inline void ReadIntegerVector(std::istream &is, bool binary,
-                                                std::vector<T> *v);
-
-/// The WriteToken functions are for writing nonempty sequences of non-space
-/// characters. They are not for general strings.
-void WriteToken(std::ostream &os, bool binary, const char *token);
-void WriteToken(std::ostream &os, bool binary, const std::string & token);
-
-/// Peek consumes whitespace (if binary == false) and then returns the peek()
-/// value of the stream.
-int Peek(std::istream &is, bool binary);
-
-/// ReadToken gets the next token and puts it in str (exception on failure).
-void ReadToken(std::istream &is, bool binary, std::string *token);
-
-/// PeekToken will return the first character of the next token, or -1 if end of
-/// file.  It's the same as Peek(), except if the first character is '<' it will
-/// skip over it and will return the next character.  It will unget the '<' so
-/// the stream is where it was before you did PeekToken().
-int PeekToken(std::istream &is, bool binary);
-
-/// ExpectToken tries to read in the given token, and throws an exception
-/// on failure.
-void ExpectToken(std::istream &is, bool binary, const char *token);
-void ExpectToken(std::istream &is, bool binary, const std::string & token);
-
-/// ExpectPretty attempts to read the text in "token", but only in non-binary
-/// mode.  Throws exception on failure.  It expects an exact match except that
-/// arbitrary whitespace matches arbitrary whitespace.
-void ExpectPretty(std::istream &is, bool binary, const char *token);
-void ExpectPretty(std::istream &is, bool binary, const std::string & token);
-
-/// @} end "addtogroup io_funcs_basic"
-
-
-/// InitKaldiOutputStream initializes an opened stream for writing by writing an
-/// optional binary header and modifying the floating-point precision; it will
-/// typically not be called by users directly.
-inline void InitKaldiOutputStream(std::ostream &os, bool binary);
-
-/// InitKaldiInputStream initializes an opened stream for reading by detecting
-/// the binary header and setting the "binary" value appropriately;
-/// It will typically not be called by users directly.
-inline bool InitKaldiInputStream(std::istream &is, bool *binary);
-
-}  // end namespace kaldi.
-
-#include "base/io-funcs-inl.h"
-
-#endif  // KALDI_BASE_IO_FUNCS_H_
diff --git a/kaldi_io/src/kaldi/base/kaldi-common.h b/kaldi_io/src/kaldi/base/kaldi-common.h
deleted file mode 100644
index 33f6f31..0000000
--- a/kaldi_io/src/kaldi/base/kaldi-common.h
+++ /dev/null
@@ -1,41 +0,0 @@
-// base/kaldi-common.h
-
-// Copyright 2009-2011 Microsoft Corporation
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_BASE_KALDI_COMMON_H_
-#define KALDI_BASE_KALDI_COMMON_H_ 1
-
-#include <cstddef>
-#include <cstdlib>
-#include <cstring>  // C string stuff like strcpy
-#include <string>
-#include <sstream>
-#include <stdexcept>
-#include <cassert>
-#include <vector>
-#include <iostream>  
-#include <fstream>  
-
-#include "base/kaldi-utils.h"
-#include "base/kaldi-error.h"
-#include "base/kaldi-types.h"
-#include "base/io-funcs.h"
-#include "base/kaldi-math.h"
-
-#endif  // KALDI_BASE_KALDI_COMMON_H_
-
diff --git a/kaldi_io/src/kaldi/base/kaldi-error.h b/kaldi_io/src/kaldi/base/kaldi-error.h
deleted file mode 100644
index 8334e42..0000000
--- a/kaldi_io/src/kaldi/base/kaldi-error.h
+++ /dev/null
@@ -1,153 +0,0 @@
-// base/kaldi-error.h
-
-// Copyright 2009-2011  Microsoft Corporation;  Ondrej Glembek;  Lukas Burget;
-//                      Saarland University
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_BASE_KALDI_ERROR_H_
-#define KALDI_BASE_KALDI_ERROR_H_ 1
-
-#include <stdexcept>
-#include <string>
-#include <cstring>
-#include <sstream>
-#include <cstdio>
-
-#ifdef _MSC_VER
-#define NOEXCEPT(Predicate)
-#elif __cplusplus > 199711L || defined(__GXX_EXPERIMENTAL_CXX0X__)
-#define NOEXCEPT(Predicate) noexcept((Predicate))
-#else
-#define NOEXCEPT(Predicate)
-#endif
-
-#include "base/kaldi-types.h"
-#include "base/kaldi-utils.h"
-
-/* Important that this file does not depend on any other kaldi headers. */
-
-
-namespace kaldi {
-
-/// \addtogroup error_group
-/// @{
-
-/// This is set by util/parse-options.{h, cc} if you set --verbose = ? option
-extern int32 g_kaldi_verbose_level;
-
-/// This is set by util/parse-options.{h, cc} (from argv[0]) and used (if set)
-/// in error reporting code to display the name of the program (this is because
-/// in our scripts, we often mix together the stderr of many programs).  it is
-/// the base-name of the program (no directory), followed by ':' We don't use
-/// std::string, due to the static initialization order fiasco.
-extern const char *g_program_name;
-
-inline int32 GetVerboseLevel() { return g_kaldi_verbose_level; }
-
-/// This should be rarely used; command-line programs set the verbose level
-/// automatically from ParseOptions.
-inline void SetVerboseLevel(int32 i) { g_kaldi_verbose_level = i; }
-
-// Class KaldiLogMessage is invoked from the  KALDI_WARN, KALDI_VLOG and
-// KALDI_LOG macros. It prints the message to stderr.  Note: we avoid
-// using cerr, due to problems with thread safety.  fprintf is guaranteed
-// thread-safe.
-
-// class KaldiWarnMessage is invoked from the KALDI_WARN macro.
-class KaldiWarnMessage {
- public:
-  inline std::ostream &stream() { return ss; }
-  KaldiWarnMessage(const char *func, const char *file, int32 line);
-  ~KaldiWarnMessage()  { fprintf(stderr, "%s\n", ss.str().c_str()); }
- private:
-  std::ostringstream ss;
-};
-
-// class KaldiLogMessage is invoked from the KALDI_LOG macro.
-class KaldiLogMessage {
- public:
-  inline std::ostream &stream() { return ss; }
-  KaldiLogMessage(const char *func, const char *file, int32 line);
-  ~KaldiLogMessage() { fprintf(stderr, "%s\n", ss.str().c_str()); }
- private:
-  std::ostringstream ss;
-};
-
-// Class KaldiVlogMessage is invoked from the KALDI_VLOG macro.
-class KaldiVlogMessage {
- public:
-  KaldiVlogMessage(const char *func, const char *file, int32 line,
-                   int32 verbose_level);
-  inline std::ostream &stream() { return ss; }
-  ~KaldiVlogMessage() { fprintf(stderr, "%s\n", ss.str().c_str()); }
- private:
-  std::ostringstream ss;
-};
-
-
-// class KaldiErrorMessage is invoked from the KALDI_ERROR macro.
-// The destructor throws an exception.
-class KaldiErrorMessage {
- public:
-  KaldiErrorMessage(const char *func, const char *file, int32 line);
-  inline std::ostream &stream() { return ss; }
-  ~KaldiErrorMessage() NOEXCEPT(false);  // defined in kaldi-error.cc
- private:
-  std::ostringstream ss;
-};
-
-
-
-#ifdef _MSC_VER
-#define __func__ __FUNCTION__
-#endif
-
-#ifndef NDEBUG
-#define KALDI_ASSERT(cond) \
-  if (!(cond)) kaldi::KaldiAssertFailure_(__func__, __FILE__, __LINE__, #cond);
-#else
-#define KALDI_ASSERT(cond)
-#endif
-// also see KALDI_COMPILE_TIME_ASSERT, defined in base/kaldi-utils.h,
-// and KALDI_ASSERT_IS_INTEGER_TYPE and KALDI_ASSERT_IS_FLOATING_TYPE,
-// also defined there.
-#ifdef KALDI_PARANOID // some more expensive asserts only checked if this defined
-#define KALDI_PARANOID_ASSERT(cond) \
-  if (!(cond)) kaldi::KaldiAssertFailure_(__func__, __FILE__, __LINE__, #cond);
-#else
-#define KALDI_PARANOID_ASSERT(cond)
-#endif
-
-#define KALDI_ERR kaldi::KaldiErrorMessage(__func__, __FILE__, __LINE__).stream() 
-#define KALDI_WARN kaldi::KaldiWarnMessage(__func__, __FILE__, __LINE__).stream() 
-#define KALDI_LOG kaldi::KaldiLogMessage(__func__, __FILE__, __LINE__).stream()
-
-#define KALDI_VLOG(v) if (v <= kaldi::g_kaldi_verbose_level)     \
-           kaldi::KaldiVlogMessage(__func__, __FILE__, __LINE__, v).stream()
-
-inline bool IsKaldiError(const std::string &str) {
-  return(!strncmp(str.c_str(), "ERROR ", 6));
-}
-
-void KaldiAssertFailure_(const char *func, const char *file,
-                         int32 line, const char *cond_str);
-
-/// @} end "addtogroup error_group"
-
-}  // namespace kaldi
-
-#endif  // KALDI_BASE_KALDI_ERROR_H_
diff --git a/kaldi_io/src/kaldi/base/kaldi-math.h b/kaldi_io/src/kaldi/base/kaldi-math.h
deleted file mode 100644
index 4f60d00..0000000
--- a/kaldi_io/src/kaldi/base/kaldi-math.h
+++ /dev/null
@@ -1,346 +0,0 @@
-// base/kaldi-math.h
-
-// Copyright 2009-2011  Ondrej Glembek;  Microsoft Corporation;  Yanmin Qian;
-//                      Jan Silovsky;  Saarland University
-//
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_BASE_KALDI_MATH_H_
-#define KALDI_BASE_KALDI_MATH_H_ 1
-
-#ifdef _MSC_VER
-#include <float.h>
-#endif
-
-#include <cmath>
-#include <limits>
-#include <vector>
-
-#include "base/kaldi-types.h"
-#include "base/kaldi-common.h"
-
-
-#ifndef DBL_EPSILON
-#define DBL_EPSILON 2.2204460492503131e-16
-#endif
-#ifndef FLT_EPSILON
-#define FLT_EPSILON 1.19209290e-7f
-#endif
-
-#ifndef M_PI
-#  define M_PI 3.1415926535897932384626433832795
-#endif
-
-#ifndef M_SQRT2
-#  define M_SQRT2 1.4142135623730950488016887
-#endif
-
-
-#ifndef M_2PI
-#  define M_2PI 6.283185307179586476925286766559005
-#endif
-
-#ifndef M_SQRT1_2
-# define M_SQRT1_2 0.7071067811865475244008443621048490
-#endif
-
-#ifndef M_LOG_2PI
-#define M_LOG_2PI 1.8378770664093454835606594728112
-#endif
-
-#ifndef M_LN2
-#define M_LN2 0.693147180559945309417232121458
-#endif
-
-#ifdef _MSC_VER
-#  define KALDI_ISNAN _isnan
-#  define KALDI_ISINF(x) (!_isnan(x) && _isnan(x-x))
-#  define KALDI_ISFINITE _finite
-#else
-#  define KALDI_ISNAN std::isnan
-#  define KALDI_ISINF std::isinf
-#  define KALDI_ISFINITE(x) std::isfinite(x)
-#endif
-#if !defined(KALDI_SQR)
-# define KALDI_SQR(x) ((x) * (x))
-#endif
-
-namespace kaldi {
-
-// -infinity
-const float kLogZeroFloat = -std::numeric_limits<float>::infinity();
-const double kLogZeroDouble = -std::numeric_limits<double>::infinity();
-const BaseFloat kLogZeroBaseFloat = -std::numeric_limits<BaseFloat>::infinity();
-
-// Returns a random integer between 0 and RAND_MAX, inclusive
-int Rand(struct RandomState* state=NULL);
-
-// State for thread-safe random number generator
-struct RandomState {
-  RandomState();
-  unsigned seed;
-};
-
-// Returns a random integer between min and max inclusive.
-int32 RandInt(int32 min, int32 max, struct RandomState* state=NULL);
-
-bool WithProb(BaseFloat prob, struct RandomState* state=NULL); // Returns true with probability "prob",
-// with 0 <= prob <= 1 [we check this].
-// Internally calls Rand().  This function is carefully implemented so
-// that it should work even if prob is very small.
-
-/// Returns a random number strictly between 0 and 1.
-inline float RandUniform(struct RandomState* state = NULL) {
-  return static_cast<float>((Rand(state) + 1.0) / (RAND_MAX+2.0));
-}
-
-inline float RandGauss(struct RandomState* state = NULL) {
-  return static_cast<float>(sqrtf (-2 * logf(RandUniform(state)))
-                            * cosf(2*M_PI*RandUniform(state)));
-}
-
-// Returns poisson-distributed random number.  Uses Knuth's algorithm.
-// Take care: this takes time proportinal
-// to lambda.  Faster algorithms exist but are more complex.
-int32 RandPoisson(float lambda, struct RandomState* state=NULL);
-
-// Returns a pair of gaussian random numbers. Uses Box-Muller transform
-void RandGauss2(float *a, float *b, RandomState *state = NULL);
-void RandGauss2(double *a, double *b, RandomState *state = NULL);
-
-// Also see Vector<float,double>::RandCategorical().
-
-// This is a randomized pruning mechanism that preserves expectations,
-// that we typically use to prune posteriors.
-template<class Float>
-inline Float RandPrune(Float post, BaseFloat prune_thresh, struct RandomState* state=NULL) {
-  KALDI_ASSERT(prune_thresh >= 0.0);
-  if (post == 0.0 || std::abs(post) >= prune_thresh)
-    return post;
-  return (post >= 0 ? 1.0 : -1.0) *
-      (RandUniform(state) <= fabs(post)/prune_thresh ? prune_thresh : 0.0);
-}
-
-static const double kMinLogDiffDouble = std::log(DBL_EPSILON);  // negative!
-static const float kMinLogDiffFloat = std::log(FLT_EPSILON);  // negative!
-
-inline double LogAdd(double x, double y) {
-  double diff;
-  if (x < y) {
-    diff = x - y;
-    x = y;
-  } else {
-    diff = y - x;
-  }
-  // diff is negative.  x is now the larger one.
-
-  if (diff >= kMinLogDiffDouble) {
-    double res;
-#ifdef _MSC_VER
-    res = x + log(1.0 + exp(diff));
-#else
-    res = x + log1p(exp(diff));
-#endif
-    return res;
-  } else {
-    return x;  // return the larger one.
-  }
-}
-
-
-inline float LogAdd(float x, float y) {
-  float diff;
-  if (x < y) {
-    diff = x - y;
-    x = y;
-  } else {
-    diff = y - x;
-  }
-  // diff is negative.  x is now the larger one.
-
-  if (diff >= kMinLogDiffFloat) {
-    float res;
-#ifdef _MSC_VER
-    res = x + logf(1.0 + expf(diff));
-#else
-    res = x + log1pf(expf(diff));
-#endif
-    return res;
-  } else {
-    return x;  // return the larger one.
-  }
-}
-
-
-// returns exp(x) - exp(y).
-inline double LogSub(double x, double y) {
-  if (y >= x) {  // Throws exception if y>=x.
-    if (y == x)
-      return kLogZeroDouble;
-    else
-      KALDI_ERR << "Cannot subtract a larger from a smaller number.";
-  }
-
-  double diff = y - x;  // Will be negative.
-  double res = x + log(1.0 - exp(diff));
-
-  // res might be NAN if diff ~0.0, and 1.0-exp(diff) == 0 to machine precision
-  if (KALDI_ISNAN(res))
-    return kLogZeroDouble;
-  return res;
-}
-
-
-// returns exp(x) - exp(y).
-inline float LogSub(float x, float y) {
-  if (y >= x) {  // Throws exception if y>=x.
-    if (y == x)
-      return kLogZeroDouble;
-    else
-      KALDI_ERR << "Cannot subtract a larger from a smaller number.";
-  }
-
-  float diff = y - x;  // Will be negative.
-  float res = x + logf(1.0 - expf(diff));
-
-  // res might be NAN if diff ~0.0, and 1.0-exp(diff) == 0 to machine precision
-  if (KALDI_ISNAN(res))
-    return kLogZeroFloat;
-  return res;
-}
-
-/// return abs(a - b) <= relative_tolerance * (abs(a)+abs(b)).
-static inline bool ApproxEqual(float a, float b,
-                               float relative_tolerance = 0.001) {
-  // a==b handles infinities.
-  if (a==b) return true;
-  float diff = std::abs(a-b);
-  if (diff == std::numeric_limits<float>::infinity()
-      || diff != diff) return false; // diff is +inf or nan.
-  return (diff <= relative_tolerance*(std::abs(a)+std::abs(b))); 
-}
-
-/// assert abs(a - b) <= relative_tolerance * (abs(a)+abs(b))
-static inline void AssertEqual(float a, float b,
-                               float relative_tolerance = 0.001) {
-  // a==b handles infinities.
-  KALDI_ASSERT(ApproxEqual(a, b, relative_tolerance));
-}
-
-
-// RoundUpToNearestPowerOfTwo does the obvious thing. It crashes if n <= 0.
-int32 RoundUpToNearestPowerOfTwo(int32 n);
-
-template<class I> I  Gcd(I m, I n) {
-  if (m == 0 || n == 0) {
-    if (m == 0 && n == 0) {  // gcd not defined, as all integers are divisors.
-      KALDI_ERR << "Undefined GCD since m = 0, n = 0.";
-    }
-    return (m == 0 ? (n > 0 ? n : -n) : ( m > 0 ? m : -m));
-    // return absolute value of whichever is nonzero
-  }
-  // could use compile-time assertion
-  // but involves messing with complex template stuff.
-  KALDI_ASSERT(std::numeric_limits<I>::is_integer);
-  while (1) {
-    m %= n;
-    if (m == 0) return (n > 0 ? n : -n);
-    n %= m;
-    if (n == 0) return (m > 0 ? m : -m);
-  }
-}
-
-/// Returns the least common multiple of two integers.  Will
-/// crash unless the inputs are positive.
-template<class I> I  Lcm(I m, I n) {
-  KALDI_ASSERT(m > 0 && n > 0);
-  I gcd = Gcd(m, n);
-  return gcd * (m/gcd) * (n/gcd);
-}
-
-
-template<class I> void Factorize(I m, std::vector<I> *factors) {
-  // Splits a number into its prime factors, in sorted order from
-  // least to greatest,  with duplication.  A very inefficient
-  // algorithm, which is mainly intended for use in the
-  // mixed-radix FFT computation (where we assume most factors
-  // are small).
-  KALDI_ASSERT(factors != NULL);
-  KALDI_ASSERT(m >= 1);  // Doesn't work for zero or negative numbers.
-  factors->clear();
-  I small_factors[10] = { 2, 3, 5, 7, 11, 13, 17, 19, 23, 29 };
-
-  // First try small factors.
-  for (I i = 0; i < 10; i++) {
-    if (m == 1) return;  // We're done.
-    while (m % small_factors[i] == 0) {
-      m /= small_factors[i];
-      factors->push_back(small_factors[i]);
-    }
-  }
-  // Next try all odd numbers starting from 31.
-  for (I j = 31;; j += 2) {
-    if (m == 1) return;
-    while (m % j == 0) {
-      m /= j;
-      factors->push_back(j);
-    }
-  }
-}
-
-inline double Hypot(double x, double y) {  return hypot(x, y); }
-
-inline float Hypot(float x, float y) {  return hypotf(x, y); }
-
-#if !defined(_MSC_VER) || (_MSC_VER >= 1800)
-inline double Log1p(double x) {  return log1p(x); }
-
-inline float Log1p(float x) {  return log1pf(x); }
-#else
-inline double Log1p(double x) {
-    const double cutoff = 1.0e-08;
-    if (x < cutoff)
-        return x - 2 * x * x;
-    else 
-        return log(1.0 + x);
-}
-
-inline float Log1p(float x) {
-    const float cutoff = 1.0e-07;
-    if (x < cutoff)
-        return x - 2 * x * x;
-    else 
-        return log(1.0 + x);
-}
-#endif
-
-inline double Exp(double x) { return exp(x); }
-
-#ifndef KALDI_NO_EXPF
-inline float Exp(float x) { return expf(x); }
-#else
-inline float Exp(float x) { return exp(x); }
-#endif
-
-inline double Log(double x) { return log(x); }
-
-inline float Log(float x) { return logf(x); }
-
-
-}  // namespace kaldi
-
-
-#endif  // KALDI_BASE_KALDI_MATH_H_
diff --git a/kaldi_io/src/kaldi/base/kaldi-types.h b/kaldi_io/src/kaldi/base/kaldi-types.h
deleted file mode 100644
index 04354b2..0000000
--- a/kaldi_io/src/kaldi/base/kaldi-types.h
+++ /dev/null
@@ -1,64 +0,0 @@
-// base/kaldi-types.h
-
-// Copyright 2009-2011  Microsoft Corporation;  Saarland University;
-//                      Jan Silovsky;  Yanmin Qian
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_BASE_KALDI_TYPES_H_
-#define KALDI_BASE_KALDI_TYPES_H_ 1
-
-namespace kaldi {
-// TYPEDEFS ..................................................................
-#if (KALDI_DOUBLEPRECISION != 0)
-typedef double  BaseFloat;
-#else
-typedef float   BaseFloat;
-#endif
-}
-
-#ifdef _MSC_VER
-namespace kaldi {
-typedef unsigned __int16 uint16;
-typedef unsigned __int32 uint32;
-typedef __int16          int16;
-typedef __int32          int32;
-typedef __int64          int64;
-typedef unsigned __int64 uint64;
-typedef float          float32;
-typedef double        double64;
-}
-#include <basetsd.h>
-#define ssize_t SSIZE_T
-
-#else
-// we can do this a different way if some platform
-// we find in the future lacks stdint.h
-#include <stdint.h>
-
-namespace kaldi {
-typedef uint16_t        uint16;
-typedef uint32_t        uint32;
-typedef uint64_t        uint64;
-typedef int16_t         int16;
-typedef int32_t         int32;
-typedef int64_t         int64;
-typedef float           float32;
-typedef double         double64;
-}  // end namespace kaldi
-#endif
-
-#endif  // KALDI_BASE_KALDI_TYPES_H_
diff --git a/kaldi_io/src/kaldi/base/kaldi-utils.h b/kaldi_io/src/kaldi/base/kaldi-utils.h
deleted file mode 100644
index 1b2c893..0000000
--- a/kaldi_io/src/kaldi/base/kaldi-utils.h
+++ /dev/null
@@ -1,157 +0,0 @@
-// base/kaldi-utils.h
-
-// Copyright 2009-2011  Ondrej Glembek;  Microsoft Corporation;
-//                      Saarland University;  Karel Vesely;  Yanmin Qian
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_BASE_KALDI_UTILS_H_
-#define KALDI_BASE_KALDI_UTILS_H_ 1
-
-#include <limits>
-#include <string>
-
-#if defined(_MSC_VER)
-# define WIN32_LEAN_AND_MEAN
-# define NOMINMAX
-# include <windows.h>
-#endif
-
-#if defined(_MSC_VER)
-#pragma warning(disable: 4244 4056 4305 4800 4267 4996 4756 4661)
-#define __restrict__
-#endif
-
-#ifdef HAVE_POSIX_MEMALIGN
-#  define KALDI_MEMALIGN(align, size, pp_orig) \
-     (!posix_memalign(pp_orig, align, size) ? *(pp_orig) : NULL)
-#  define KALDI_MEMALIGN_FREE(x) free(x)
-#elif defined(HAVE_MEMALIGN)
-  /* Some systems have memalign() but no declaration for it */
-  void * memalign(size_t align, size_t size);
-#  define KALDI_MEMALIGN(align, size, pp_orig) \
-     (*(pp_orig) = memalign(align, size))
-#  define KALDI_MEMALIGN_FREE(x) free(x)
-#elif defined(_MSC_VER)
-#  define KALDI_MEMALIGN(align, size, pp_orig) \
-  (*(pp_orig) = _aligned_malloc(size, align))
-#  define KALDI_MEMALIGN_FREE(x) _aligned_free(x)
-#else
-#error Manual memory alignment is no longer supported
-#endif
-
-#ifdef __ICC
-#pragma warning(disable: 383)  // ICPC remark we don't want.
-#pragma warning(disable: 810)  // ICPC remark we don't want.
-#pragma warning(disable: 981)  // ICPC remark we don't want.
-#pragma warning(disable: 1418)  // ICPC remark we don't want.
-#pragma warning(disable: 444)  // ICPC remark we don't want.
-#pragma warning(disable: 869)  // ICPC remark we don't want.
-#pragma warning(disable: 1287)  // ICPC remark we don't want.
-#pragma warning(disable: 279)  // ICPC remark we don't want.
-#pragma warning(disable: 981)  // ICPC remark we don't want.
-#endif
-
-
-namespace kaldi {
-
-
-// CharToString prints the character in a human-readable form, for debugging.
-std::string CharToString(const char &c);
-
-
-inline int MachineIsLittleEndian() {
-  int check = 1;
-  return (*reinterpret_cast<char*>(&check) != 0);
-}
-
-// This function kaldi::Sleep() provides a portable way to sleep for a possibly fractional
-// number of seconds.  On Windows it's only accurate to microseconds.
-void Sleep(float seconds);
-
-}
-
-#define KALDI_SWAP8(a) { \
-  int t = ((char*)&a)[0]; ((char*)&a)[0]=((char*)&a)[7]; ((char*)&a)[7]=t;\
-      t = ((char*)&a)[1]; ((char*)&a)[1]=((char*)&a)[6]; ((char*)&a)[6]=t;\
-      t = ((char*)&a)[2]; ((char*)&a)[2]=((char*)&a)[5]; ((char*)&a)[5]=t;\
-      t = ((char*)&a)[3]; ((char*)&a)[3]=((char*)&a)[4]; ((char*)&a)[4]=t;}
-#define KALDI_SWAP4(a) { \
-  int t = ((char*)&a)[0]; ((char*)&a)[0]=((char*)&a)[3]; ((char*)&a)[3]=t;\
-      t = ((char*)&a)[1]; ((char*)&a)[1]=((char*)&a)[2]; ((char*)&a)[2]=t;}
-#define KALDI_SWAP2(a) { \
-  int t = ((char*)&a)[0]; ((char*)&a)[0]=((char*)&a)[1]; ((char*)&a)[1]=t;}
-
-
-// Makes copy constructor and operator= private.  Same as in compat.h of OpenFst
-// toolkit.  If using VS, for which this results in compilation errors, we
-// do it differently.
-
-#if defined(_MSC_VER)
-#define KALDI_DISALLOW_COPY_AND_ASSIGN(type) \
-  void operator = (const type&)
-#else
-#define KALDI_DISALLOW_COPY_AND_ASSIGN(type)    \
-  type(const type&);                  \
-  void operator = (const type&)
-#endif
-
-template<bool B> class KaldiCompileTimeAssert { };
-template<> class KaldiCompileTimeAssert<true> {
- public:
-  static inline void Check() { }  
-};
-
-#define KALDI_COMPILE_TIME_ASSERT(b) KaldiCompileTimeAssert<(b)>::Check()
-
-#define KALDI_ASSERT_IS_INTEGER_TYPE(I) \
-  KaldiCompileTimeAssert<std::numeric_limits<I>::is_specialized \
-                 && std::numeric_limits<I>::is_integer>::Check()
-
-#define KALDI_ASSERT_IS_FLOATING_TYPE(F) \
-  KaldiCompileTimeAssert<std::numeric_limits<F>::is_specialized \
-                && !std::numeric_limits<F>::is_integer>::Check()
-
-#ifdef _MSC_VER
-#include <stdio.h>
-#define unlink _unlink
-#else
-#include <unistd.h>
-#endif
-
-
-#ifdef _MSC_VER
-#define KALDI_STRCASECMP _stricmp
-#else
-#define KALDI_STRCASECMP strcasecmp
-#endif
-#ifdef _MSC_VER
-#  define KALDI_STRTOLL(cur_cstr, end_cstr) _strtoi64(cur_cstr, end_cstr, 10);
-#else
-#  define KALDI_STRTOLL(cur_cstr, end_cstr) strtoll(cur_cstr, end_cstr, 10);
-#endif
-
-#define KALDI_STRTOD(cur_cstr, end_cstr) strtod(cur_cstr, end_cstr)
-
-#ifdef _MSC_VER
-#  define KALDI_STRTOF(cur_cstr, end_cstr) \
-    static_cast<float>(strtod(cur_cstr, end_cstr));
-#else
-#  define KALDI_STRTOF(cur_cstr, end_cstr) strtof(cur_cstr, end_cstr);
-#endif
-
-#endif  // KALDI_BASE_KALDI_UTILS_H_
-
diff --git a/kaldi_io/src/kaldi/base/timer.h b/kaldi_io/src/kaldi/base/timer.h
deleted file mode 100644
index d93a461..0000000
--- a/kaldi_io/src/kaldi/base/timer.h
+++ /dev/null
@@ -1,83 +0,0 @@
-// base/timer.h
-
-// Copyright 2009-2011  Ondrej Glembek;  Microsoft Corporation
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-
-//  http://www.apache.org/licenses/LICENSE-2.0
-
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-#ifndef KALDI_BASE_TIMER_H_
-#define KALDI_BASE_TIMER_H_
-
-#include "base/kaldi-utils.h"
-// Note: Sleep(float secs) is included in base/kaldi-utils.h.
-
-
-#if defined(_MSC_VER) || defined(MINGW)
-
-namespace kaldi
-{
-
-class Timer {
- public:
-  Timer() { Reset(); }
-  void Reset() {
-    QueryPerformanceCounter(&time_start_);
-  }
-  double Elapsed() {
-    LARGE_INTEGER time_end;
-    LARGE_INTEGER freq;
-    QueryPerformanceCounter(&time_end);
-    if (QueryPerformanceFrequency(&freq) == 0) return 0.0;  // Hardware does not support this.
-    return ((double)time_end.QuadPart - (double)time_start_.QuadPart) /
-        ((double)freq.QuadPart);
-  }
- private:
-  LARGE_INTEGER time_start_;
-};
-}
-
-#else
-
-# include <sys/time.h>
-# include <unistd.h>
-namespace kaldi
-{
-class Timer
-{
- public:
-  Timer() { Reset(); }
-
-  void Reset() { gettimeofday(&this->time_start_, &time_zone_); }
-
-  /// Returns time in seconds.
-  double Elapsed() {
-    struct timeval time_end;
-    gettimeofday(&time_end, &time_zone_);
-    double t1, t2;
-    t1 =  (double)time_start_.tv_sec +
-        (double)time_start_.tv_usec/(1000*1000);
-    t2 =  (double)time_end.tv_sec + (double)time_end.tv_usec/(1000*1000);
-    return t2-t1;
-  }
-
- private:
-  struct timeval time_start_;
-  struct timezone time_zone_;
-};
-}
-
-#endif
-
-
-#endif
diff --git a/kaldi_io/src/kaldi/hmm/hmm-topology.h b/kaldi_io/src/kaldi/hmm/hmm-topology.h
deleted file mode 100644
index 53ca427..0000000
--- a/kaldi_io/src/kaldi/hmm/hmm-topology.h
+++ /dev/null
@@ -1,172 +0,0 @@
-// hmm/hmm-topology.h
-
-// Copyright 2009-2011  Microsoft Corporation
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_HMM_HMM_TOPOLOGY_H_
-#define KALDI_HMM_HMM_TOPOLOGY_H_
-
-#include "base/kaldi-common.h"
-#include "tree/context-dep.h"
-#include "util/const-integer-set.h"
-
-
-namespace kaldi {
-
-
-/// \addtogroup hmm_group
-/// @{
-
-/*
- // The following would be the text form for the "normal" HMM topology.
- // Note that the first state is the start state, and the final state,
- // which must have no output transitions and must be nonemitting, has
- // an exit probability of one (no other state can have nonzero exit
- // probability; you can treat the transition probability to the final
- // state as an exit probability).
- // Note also that it's valid to omit the "<PdfClass>" entry of the <State>, which
- // will mean we won't have a pdf on that state [non-emitting state].  This is equivalent
- // to setting the <PdfClass> to -1.  We do this normally just for the final state.
- // The Topology object can have multiple <TopologyEntry> blocks.
- // This is useful if there are multiple types of topology in the system.
-
- <Topology>
- <TopologyEntry>
- <ForPhones> 1 2 3 4 5 6 7 8 </ForPhones>
- <State> 0 <PdfClass> 0
- <Transition> 0 0.5
- <Transition> 1 0.5
- </State>
- <State> 1 <PdfClass> 1
- <Transition> 1 0.5
- <Transition> 2 0.5
- </State>
- <State> 2 <PdfClass> 2
- <Transition> 2 0.5
- <Transition> 3 0.5
- <Final> 0.5
- </State>
- <State> 3
- </State> 
- </TopologyEntry>
- </Topology>
-*/
-
-// kNoPdf is used where pdf_class or pdf would be used, to indicate,
-// none is there.  Mainly useful in skippable models, but also used
-// for end states.
-// A caveat with nonemitting states is that their out-transitions
-// are not trainable, due to technical issues with the way
-// we decided to accumulate the stats.  Any transitions arising from (*)
-// HMM states with "kNoPdf" as the label are second-class transitions,
-// They do not have "transition-states" or "transition-ids" associated
-// with them.  They are used to create the FST version of the
-// HMMs, where they lead to epsilon arcs.
-// (*) "arising from" is a bit of a technical term here, due to the way
-// (if reorder == true), we put the transition-id associated with the
-// outward arcs of the state, on the input transition to the state.
-
-/// A constant used in the HmmTopology class as the \ref pdf_class "pdf-class"
-/// kNoPdf, which is used when a HMM-state is nonemitting (has no associated
-/// PDF).
-
-static const int32 kNoPdf = -1;
-
-/// A class for storing topology information for phones.  See  \ref hmm for context.
-/// This object is sometimes accessed in a file by itself, but more often
-/// as a class member of the Transition class (this is for convenience to reduce
-/// the number of files programs have to access).
-
-class HmmTopology {
- public:
-  /// A structure defined inside HmmTopology to represent a HMM state.
-  struct HmmState {
-    /// The \ref pdf_class pdf-class, typically 0, 1 or 2 (the same as the HMM-state index),
-    /// but may be different to enable us to hardwire sharing of state, and may be
-    /// equal to \ref kNoPdf == -1 in order to specify nonemitting states (unusual).
-    int32 pdf_class;
-
-    /// A list of transitions.  The first member of each pair is the index of
-    /// the next HmmState, and the second is the default transition probability
-    /// (before training).
-    std::vector<std::pair<int32, BaseFloat> > transitions;
-
-    explicit HmmState(int32 p): pdf_class(p) { }
-
-    bool operator == (const HmmState &other) const {
-      return (pdf_class == other.pdf_class && transitions == other.transitions);
-    }
-    
-    HmmState(): pdf_class(-1) { }
-  };
-
-  /// TopologyEntry is a typedef that represents the topology of
-  /// a single (prototype) state.
-  typedef std::vector<HmmState> TopologyEntry;
-
-  void Read(std::istream &is, bool binary);
-  void Write(std::ostream &os, bool binary) const;
-
-  // Checks that the object is valid, and throw exception otherwise.
-  void Check();
-
-
-  /// Returns the topology entry (i.e. vector of HmmState) for this phone;
-  /// will throw exception if phone not covered by the topology.
-  const TopologyEntry &TopologyForPhone(int32 phone) const;
-
-  /// Returns the number of \ref pdf_class "pdf-classes" for this phone;
-  /// throws exception if phone not covered by this topology.
-  int32 NumPdfClasses(int32 phone) const;
-
-  /// Returns a reference to a sorted, unique list of phones covered by
-  /// the topology (these phones will be positive integers, and usually
-  /// contiguous and starting from one but the toolkit doesn't assume
-  /// they are contiguous).
-  const std::vector<int32> &GetPhones() const { return phones_; };
-
-  /// Outputs a vector of int32, indexed by phone, that gives the
-  /// number of \ref pdf_class pdf-classes for the phones; this is
-  /// used by tree-building code such as BuildTree().
-  void GetPhoneToNumPdfClasses(std::vector<int32> *phone2num_pdf_classes) const;
-
-  HmmTopology() {}
-
-  bool operator == (const HmmTopology &other) const {
-    return phones_ == other.phones_ && phone2idx_ == other.phone2idx_
-        && entries_ == other.entries_;
-  }
-  // Allow default assignment operator and copy constructor.
- private:
-  std::vector<int32> phones_;  // list of all phones we have topology for.  Sorted, uniq.  no epsilon (zero) phone.
-  std::vector<int32> phone2idx_;  // map from phones to indexes into the entries vector (or -1 for not present).
-  std::vector<TopologyEntry> entries_;
-};
-
-
-/// This function returns a HmmTopology object giving a normal 3-state topology,
-/// covering all phones in the list "phones".  This is mainly of use in testing
-/// code.
-HmmTopology GetDefaultTopology(const std::vector<int32> &phones);
-
-/// @} end "addtogroup hmm_group"
-
-
-} // end namespace kaldi
-
-
-#endif
diff --git a/kaldi_io/src/kaldi/hmm/hmm-utils.h b/kaldi_io/src/kaldi/hmm/hmm-utils.h
deleted file mode 100644
index 240f706..0000000
--- a/kaldi_io/src/kaldi/hmm/hmm-utils.h
+++ /dev/null
@@ -1,295 +0,0 @@
-// hmm/hmm-utils.h
-
-// Copyright 2009-2011  Microsoft Corporation
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_HMM_HMM_UTILS_H_
-#define KALDI_HMM_HMM_UTILS_H_
-
-#include "hmm/hmm-topology.h"
-#include "hmm/transition-model.h"
-#include "lat/kaldi-lattice.h"
-
-namespace kaldi {
-
-
-/// \defgroup hmm_group_graph Classes and functions for creating FSTs from HMMs
-/// \ingroup hmm_group
-/// @{
-
-/// Configuration class for the GetHTransducer() function; see
-/// \ref hmm_graph_config for context.
-struct HTransducerConfig {
-  /// Transition log-prob scale, see \ref hmm_scale.
-  /// Note this doesn't apply to self-loops; GetHTransducer() does
-  /// not include self-loops.
-  BaseFloat transition_scale;
-
-  /// if true, we are constructing time-reversed FST: phone-seqs in ilabel_info
-  /// are backwards, and we want to output a backwards version of the HMM
-  /// corresponding to each phone.  If reverse == true,
-  bool reverse;
-
-  /// This variable is only looked at if reverse == true.  If reverse == true
-  /// and push_weights == true, then we push the weights in the reversed FSTs we create for each
-  /// phone HMM.  This is only safe if the HMMs are probabilistic (i.e. not discriminatively
-  bool push_weights;
-
-  /// delta used if we do push_weights [only relevant if reverse == true
-  /// and push_weights == true].
-  BaseFloat push_delta;
-
-  HTransducerConfig():
-      transition_scale(1.0),
-      reverse(false),
-      push_weights(true),
-      push_delta(0.001)
-  { }
-
-  // Note-- this Register registers the easy-to-register options
-  // but not the "sym_type" which is an enum and should be handled
-  // separately in main().
-  void Register (OptionsItf *po) {
-    po->Register("transition-scale", &transition_scale,
-                 "Scale of transition probs (relative to LM)");
-    po->Register("reverse", &reverse,
-                 "Set true to build time-reversed FST.");
-    po->Register("push-weights", &push_weights,
-                 "Push weights (only applicable if reverse == true)");
-    po->Register("push-delta", &push_delta,
-                 "Delta used in pushing weights (only applicable if "
-                 "reverse && push-weights");
-  }
-};
-
-
-struct HmmCacheHash {
-  int operator () (const std::pair<int32, std::vector<int32> >&p) const {
-    VectorHasher<int32> v;
-    int32 prime = 103049;
-    return prime*p.first + v(p.second);
-  }
-};
-
-/// HmmCacheType is a map from (central-phone, sequence of pdf-ids) to FST, used
-/// as cache in GetHmmAsFst, as an optimization.
-typedef unordered_map<std::pair<int32, std::vector<int32> >,
-                      fst::VectorFst<fst::StdArc>*,
-                      HmmCacheHash> HmmCacheType;
-
-
-/// Called by GetHTransducer() and probably will not need to be called directly;
-/// it creates the FST corresponding to the phone.  Does not include self-loops;
-/// you have to call AddSelfLoops() for that.  Result owned by caller.
-/// Returns an acceptor (i.e. ilabels, olabels identical) with transition-ids
-/// as the symbols.
-/// For documentation in context, see \ref hmm_graph_get_hmm_as_fst
-///   @param context_window  A vector representing the phonetic context; see
-///            \ref tree_window "here" for explanation.
-///   @param ctx_dep The object that contains the phonetic decision-tree
-///   @param trans_model The transition-model object, which provides
-///         the mappings to transition-ids and also the transition
-///         probabilities.
-///   @param config Configuration object, see \ref HTransducerConfig.
-///   @param cache Object used as a lookaside buffer to save computation;
-///       if it finds that the object it needs is already there, it will
-///       just return a pointer value from "cache"-- not that this means
-///       you have to be careful not to delete things twice.
-
-fst::VectorFst<fst::StdArc> *GetHmmAsFst(
-    std::vector<int32> context_window,
-    const ContextDependencyInterface &ctx_dep,
-    const TransitionModel &trans_model,
-    const HTransducerConfig &config,
-    HmmCacheType *cache = NULL);
-
-/// Included mainly as a form of documentation, not used in any other code
-/// currently.  Creates the FST with self-loops, and with fewer options.
-fst::VectorFst<fst::StdArc>*
-GetHmmAsFstSimple(std::vector<int32> context_window,
-                  const ContextDependencyInterface &ctx_dep,
-                  const TransitionModel &trans_model,
-                  BaseFloat prob_scale);
-
-
-/**
-  * Returns the H tranducer; result owned by caller.
-  * See \ref hmm_graph_get_h_transducer.  The H transducer has on the
-  * input transition-ids, and also possibly some disambiguation symbols, which
-  * will be put in disambig_syms.  The output side contains the identifiers that
-  * are indexes into "ilabel_info" (these represent phones-in-context or
-  * disambiguation symbols).  The ilabel_info vector allows GetHTransducer to map
-  * from symbols to phones-in-context (i.e. phonetic context windows).  Any
-  * singleton symbols in the ilabel_info vector which are not phones, will be
-  * treated as disambiguation symbols.  [Not all recipes use these].  The output
-  * "disambig_syms_left" will be set to a list of the disambiguation symbols on
-  * the input of the transducer (i.e. same symbol type as whatever is on the
-  * input of the transducer
-  */
-fst::VectorFst<fst::StdArc>*
-GetHTransducer (const std::vector<std::vector<int32> > &ilabel_info,
-                const ContextDependencyInterface &ctx_dep,
-                const TransitionModel &trans_model,
-                const HTransducerConfig &config,
-                std::vector<int32> *disambig_syms_left);
-
-/**
-  * GetIlabelMapping produces a mapping that's similar to HTK's logical-to-physical
-  * model mapping (i.e. the xwrd.clustered.mlist files).   It groups together
-  * "logical HMMs" (i.e. in our world, phonetic context windows) that share the
-  * same sequence of transition-ids.   This can be used in an
-  * optional graph-creation step that produces a remapped form of CLG that can be
-  * more productively determinized and minimized.  This is used in the command-line program
-  * make-ilabel-transducer.cc.
-  * @param ilabel_info_old [in] The original \ref tree_ilabel "ilabel_info" vector
-  * @param ctx_dep [in] The tree
-  * @param trans_model [in] The transition-model object
-  * @param old2new_map [out] The output; this vector, which is of size equal to the
-  *       number of new labels, is a mapping to the old labels such that we could
-  *       create a vector ilabel_info_new such that
-  *       ilabel_info_new[i] == ilabel_info_old[old2new_map[i]]
-  */
-void GetIlabelMapping (const std::vector<std::vector<int32> > &ilabel_info_old,
-                       const ContextDependencyInterface &ctx_dep,
-                       const TransitionModel &trans_model,
-                       std::vector<int32> *old2new_map);
-
-
-
-/**
-  * For context, see \ref hmm_graph_add_self_loops.  Expands an FST that has been
-  * built without self-loops, and adds the self-loops (it also needs to modify
-  * the probability of the non-self-loop ones, as the graph without self-loops
-  * was created in such a way that it was stochastic).  Note that the
-  * disambig_syms will be empty in some recipes (e.g.  if you already removed
-  * the disambiguation symbols).
-  * @param trans_model [in] Transition model
-  * @param disambig_syms [in] Sorted, uniq list of disambiguation symbols, required
-  *       if the graph contains disambiguation symbols but only needed for sanity checks.
-  * @param self_loop_scale [in] Transition-probability scale for self-loops; c.f.
-  *                    \ref hmm_scale
-  * @param reorder [in] If true, reorders the transitions (see \ref hmm_reorder).
-  * @param  fst [in, out] The FST to be modified.
-  */
-void AddSelfLoops(const TransitionModel &trans_model,
-                  const std::vector<int32> &disambig_syms,  // used as a check only.
-                  BaseFloat self_loop_scale,
-                  bool reorder,  // true->dan-style, false->lukas-style.
-                  fst::VectorFst<fst::StdArc> *fst);
-
-/**
-  * Adds transition-probs, with the supplied
-  * scales (see \ref hmm_scale), to the graph.
-  * Useful if you want to create a graph without transition probs, then possibly
-  * train the model (including the transition probs) but keep the graph fixed,
-  * and add back in the transition probs.  It assumes the fst has transition-ids
-  * on it.  It is not an error if the FST has no states (nothing will be done).
-  * @param trans_model [in] The transition model
-  * @param disambig_syms [in] A list of disambiguation symbols, required if the
-  *                       graph has disambiguation symbols on its input but only
-  *                       used for checks.
-  * @param transition_scale [in] A scale on transition-probabilities apart from
-  *                      those involving self-loops; see \ref hmm_scale.
-  * @param self_loop_scale [in] A scale on self-loop transition probabilities;
-  *                      see \ref hmm_scale.
-  * @param  fst [in, out] The FST to be modified.
-  */
-void AddTransitionProbs(const TransitionModel &trans_model,
-                        const std::vector<int32> &disambig_syms,
-                        BaseFloat transition_scale,
-                        BaseFloat self_loop_scale,
-                        fst::VectorFst<fst::StdArc> *fst);
-
-/**
-   This is as AddSelfLoops(), but operates on a Lattice, where
-   it affects the graph part of the weight (the first element
-   of the pair). */
-void AddTransitionProbs(const TransitionModel &trans_model,
-                        BaseFloat transition_scale,
-                        BaseFloat self_loop_scale,
-                        Lattice *lat);
-
-
-/// Returns a transducer from pdfs plus one (input) to  transition-ids (output).
-/// Currenly of use only for testing.
-fst::VectorFst<fst::StdArc>*
-GetPdfToTransitionIdTransducer(const TransitionModel &trans_model);
-
-/// Converts all transition-ids in the FST to pdfs plus one.
-/// Placeholder: not implemented yet!
-void ConvertTransitionIdsToPdfs(const TransitionModel &trans_model,
-                                const std::vector<int32> &disambig_syms,
-                                fst::VectorFst<fst::StdArc> *fst);
-
-/// @} end "defgroup hmm_group_graph"
-
-/// \addtogroup hmm_group
-/// @{
-
-/// SplitToPhones splits up the TransitionIds in "alignment" into their
-/// individual phones (one vector per instance of a phone).  At output,
-/// the sum of the sizes of the vectors in split_alignment will be the same
-/// as the corresponding sum for "alignment".  The function returns
-/// true on success.  If the alignment appears to be incomplete, e.g.
-/// not ending at the end-state of a phone, it will still break it up into
-/// phones but it will return false.  For more serious errors it will
-/// die or throw an exception.
-/// This function works out by itself whether the graph was created
-/// with "reordering" (dan-style graph), and just does the right thing.
-
-bool SplitToPhones(const TransitionModel &trans_model,
-                   const std::vector<int32> &alignment,
-                   std::vector<std::vector<int32> > *split_alignment);
-
-/// ConvertAlignment converts an alignment that was created using one
-/// model, to another model.  They must use a compatible topology (so we
-/// know the state alignments of the new model).
-/// It returns false if it could not be split to phones (probably
-/// because the alignment was partial), but for other kinds of
-/// error that are more likely a coding error, it will throw
-/// an exception.
-bool ConvertAlignment(const TransitionModel &old_trans_model,
-                      const TransitionModel &new_trans_model,
-                      const ContextDependencyInterface &new_ctx_dep,
-                      const std::vector<int32> &old_alignment,
-                      const std::vector<int32> *phone_map,  // may be NULL
-                      std::vector<int32> *new_alignment);
-
-// ConvertPhnxToProns is only needed in bin/phones-to-prons.cc and
-// isn't closely related with HMMs, but we put it here as there isn't
-// any other obvious place for it and it needs to be tested.
-// This function takes a phone-sequence with word-start and word-end
-// markers in it, and a word-sequence, and outputs the pronunciations
-// "prons"... the format of "prons" is, each element is a vector,
-// where the first element is the word (or zero meaning no word, e.g.
-// for optional silence introduced by the lexicon), and the remaining
-// elements are the phones in the word's pronunciation.
-// It returns false if it encounters a problem of some kind, e.g.
-// if the phone-sequence doesn't seem to have the right number of
-// words in it.
-bool ConvertPhnxToProns(const std::vector<int32> &phnx,
-                        const std::vector<int32> &words,
-                        int32 word_start_sym,
-                        int32 word_end_sym,
-                        std::vector<std::vector<int32> > *prons);
-
-/// @} end "addtogroup hmm_group"
-
-} // end namespace kaldi
-
-
-#endif
diff --git a/kaldi_io/src/kaldi/hmm/posterior.h b/kaldi_io/src/kaldi/hmm/posterior.h
deleted file mode 100644
index be73be9..0000000
--- a/kaldi_io/src/kaldi/hmm/posterior.h
+++ /dev/null
@@ -1,214 +0,0 @@
-// hmm/posterior.h
-
-// Copyright 2009-2011     Microsoft Corporation
-//           2013-2014     Johns Hopkins University (author: Daniel Povey)
-//                2014     Guoguo Chen
-
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_HMM_POSTERIOR_H_
-#define KALDI_HMM_POSTERIOR_H_
-
-#include "base/kaldi-common.h"
-#include "tree/context-dep.h"
-#include "util/const-integer-set.h"
-#include "util/kaldi-table.h"
-#include "hmm/transition-model.h"
-
-
-namespace kaldi {
-
-
-/// \addtogroup posterior_group
-/// @{
-
-/// Posterior is a typedef for storing acoustic-state (actually, transition-id)
-/// posteriors over an utterance.  The "int32" is a transition-id, and the BaseFloat
-/// is a probability (typically between zero and one).
-typedef std::vector<std::vector<std::pair<int32, BaseFloat> > > Posterior;
-
-/// GaussPost is a typedef for storing Gaussian-level posteriors for an utterance.
-/// the "int32" is a transition-id, and the Vector<BaseFloat> is a vector of
-/// Gaussian posteriors.
-/// WARNING: We changed "int32" from transition-id to pdf-id, and the change is
-/// applied for all programs using GaussPost. This is for efficiency purpose. We
-/// also changed the name slightly from GauPost to GaussPost to reduce the
-/// chance that the change will go un-noticed in downstream code.
-typedef std::vector<std::vector<std::pair<int32, Vector<BaseFloat> > > > GaussPost;
-
-
-// PosteriorHolder is a holder for Posterior, which is
-// std::vector<std::vector<std::pair<int32, BaseFloat> > >
-// This is used for storing posteriors of transition id's for an
-// utterance.
-class PosteriorHolder {
- public:
-  typedef Posterior T;
-
-  PosteriorHolder() { }
-
-  static bool Write(std::ostream &os, bool binary, const T &t);
-  
-  void Clear() { Posterior tmp; std::swap(tmp, t_); }
-
-  // Reads into the holder.
-  bool Read(std::istream &is);
-  
-  // Kaldi objects always have the stream open in binary mode for
-  // reading.
-  static bool IsReadInBinary() { return true; }
-
-  const T &Value() const { return t_; }
-  
- private:
-  KALDI_DISALLOW_COPY_AND_ASSIGN(PosteriorHolder);
-  T t_;
-};
-
-
-// GaussPostHolder is a holder for GaussPost, which is
-// std::vector<std::vector<std::pair<int32, Vector<BaseFloat> > > >
-// This is used for storing posteriors of transition id's for an
-// utterance.
-class GaussPostHolder {
- public:
-  typedef GaussPost T;
-
-  GaussPostHolder() { }
-
-  static bool Write(std::ostream &os, bool binary, const T &t);  
-
-  void Clear() {  GaussPost tmp;  std::swap(tmp, t_); }
-
-  // Reads into the holder.
-  bool Read(std::istream &is);
-  
-  // Kaldi objects always have the stream open in binary mode for
-  // reading.
-  static bool IsReadInBinary() { return true; }
-
-  const T &Value() const { return t_; }
-  
- private:
-  KALDI_DISALLOW_COPY_AND_ASSIGN(GaussPostHolder);
-  T t_;
-};
-
-
-// Posterior is a typedef: vector<vector<pair<int32, BaseFloat> > >,
-// representing posteriors over (typically) transition-ids for an
-// utterance.
-typedef TableWriter<PosteriorHolder> PosteriorWriter;
-typedef SequentialTableReader<PosteriorHolder> SequentialPosteriorReader;
-typedef RandomAccessTableReader<PosteriorHolder> RandomAccessPosteriorReader;
-
-
-// typedef std::vector<std::vector<std::pair<int32, Vector<BaseFloat> > > > GaussPost;
-typedef TableWriter<GaussPostHolder> GaussPostWriter;
-typedef SequentialTableReader<GaussPostHolder> SequentialGaussPostReader;
-typedef RandomAccessTableReader<GaussPostHolder> RandomAccessGaussPostReader;
-
-
-/// Scales the BaseFloat (weight) element in the posterior entries.
-void ScalePosterior(BaseFloat scale, Posterior *post);
-
-/// Returns the total of all the weights in "post".
-BaseFloat TotalPosterior(const Posterior &post);
-
-/// Returns true if the two lists of pairs have no common .first element.
-bool PosteriorEntriesAreDisjoint(
-    const std::vector<std::pair<int32, BaseFloat> > &post_elem1,
-    const std::vector<std::pair<int32, BaseFloat> > &post_elem2);
-
-
-/// Merge two sets of posteriors, which must have the same length.  If "merge"
-/// is true, it will make a common entry whenever there are duplicated entries,
-/// adding up the weights.  If "drop_frames" is true, for frames where the
-/// two sets of posteriors were originally disjoint, makes no entries for that
-/// frame (relates to frame dropping, or drop_frames, see Vesely et al, ICASSP
-/// 2013).  Returns the number of frames for which the two posteriors were
-/// disjoint (i.e. no common transition-ids or whatever index we are using).
-int32 MergePosteriors(const Posterior &post1,
-                      const Posterior &post2,
-                      bool merge,
-                      bool drop_frames,
-                      Posterior *post);
-
-/// Given a vector of log-likelihoods (typically of Gaussians in a GMM
-/// but could be of pdf-ids), a number gselect >= 1 and a minimum posterior
-/// 0 <= min_post < 1, it gets the posterior for each element of log-likes
-/// by applying Softmax(), then prunes the posteriors using "gselect" and
-/// "min_post" (keeping at least one), and outputs the result into
-/// "post_entry", sorted from greatest to least posterior.
-/// Returns the total log-likelihood (the output of calling ApplySoftMax()
-/// on a copy of log_likes).
-BaseFloat VectorToPosteriorEntry(
-    const VectorBase<BaseFloat> &log_likes,
-    int32 num_gselect,
-    BaseFloat min_post,
-    std::vector<std::pair<int32, BaseFloat> > *post_entry);
-
-/// Convert an alignment to a posterior (with a scale of 1.0 on
-/// each entry).
-void AlignmentToPosterior(const std::vector<int32> &ali,
-                          Posterior *post);
-
-/// Sorts posterior entries so that transition-ids with same pdf-id are next to
-/// each other.
-void SortPosteriorByPdfs(const TransitionModel &tmodel,
-                         Posterior *post);
-
-
-/// Converts a posterior over transition-ids to be a posterior
-/// over pdf-ids.
-void ConvertPosteriorToPdfs(const TransitionModel &tmodel,
-                            const Posterior &post_in,
-                            Posterior *post_out);
-
-/// Converts a posterior over transition-ids to be a posterior
-/// over phones.
-void ConvertPosteriorToPhones(const TransitionModel &tmodel,
-                              const Posterior &post_in,
-                              Posterior *post_out);
-
-/// Weight any silence phones in the posterior (i.e. any phones
-/// in the set "silence_set" by scale "silence_scale".
-/// The interface was changed in Feb 2014 to do the modification
-/// "in-place" rather than having separate input and output.
-void WeightSilencePost(const TransitionModel &trans_model,
-                       const ConstIntegerSet<int32> &silence_set,
-                       BaseFloat silence_scale,
-                       Posterior *post);
-
-/// This is similar to WeightSilencePost, except that on each frame it
-/// works out the amount by which the overall posterior would be reduced,
-/// and scales down everything on that frame by the same amount.  It
-/// has the effect that frames that are mostly silence get down-weighted.
-/// The interface was changed in Feb 2014 to do the modification
-/// "in-place" rather than having separate input and output.
-void WeightSilencePostDistributed(const TransitionModel &trans_model,
-                                  const ConstIntegerSet<int32> &silence_set,
-                                  BaseFloat silence_scale,
-                                  Posterior *post);
-
-/// @} end "addtogroup posterior_group"
-
-
-} // end namespace kaldi
-
-
-#endif
diff --git a/kaldi_io/src/kaldi/hmm/transition-model.h b/kaldi_io/src/kaldi/hmm/transition-model.h
deleted file mode 100644
index ccc4f11..0000000
--- a/kaldi_io/src/kaldi/hmm/transition-model.h
+++ /dev/null
@@ -1,345 +0,0 @@
-// hmm/transition-model.h
-
-// Copyright 2009-2012  Microsoft Corporation
-//                      Johns Hopkins University (author: Guoguo Chen)
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_HMM_TRANSITION_MODEL_H_
-#define KALDI_HMM_TRANSITION_MODEL_H_
-
-#include "base/kaldi-common.h"
-#include "tree/context-dep.h"
-#include "util/const-integer-set.h"
-#include "fst/fst-decl.h" // forward declarations.
-#include "hmm/hmm-topology.h"
-#include "itf/options-itf.h"
-
-namespace kaldi {
-
-/// \addtogroup hmm_group
-/// @{
-
-// The class TransitionModel is a repository for the transition probabilities.
-// It also handles certain integer mappings.
-// The basic model is as follows.  Each phone has a HMM topology defined in
-// hmm-topology.h.  Each HMM-state of each of these phones has a number of
-// transitions (and final-probs) out of it.  Each HMM-state defined in the
-// HmmTopology class has an associated "pdf_class".  This gets replaced with
-// an actual pdf-id via the tree.  The transition model associates the
-// transition probs with the (phone, HMM-state, pdf-id).  We associate with
-// each such triple a transition-state.  Each
-// transition-state has a number of associated probabilities to estimate;
-// this depends on the number of transitions/final-probs in the topology for
-// that (phone, HMM-state).  Each probability has an associated transition-index.
-// We associate with each (transition-state, transition-index) a unique transition-id.
-// Each individual probability estimated by the transition-model is asociated with a
-// transition-id.
-//
-// List of the various types of quantity referred to here and what they mean:
-//           phone:  a phone index (1, 2, 3 ...)
-//       HMM-state:  a number (0, 1, 2...) that indexes TopologyEntry (see hmm-topology.h)
-//          pdf-id:  a number output by the Compute function of ContextDependency (it
-//                   indexes pdf's).  Zero-based.
-// transition-state:  the states for which we estimate transition probabilities for transitions
-//                    out of them.  In some topologies, will map one-to-one with pdf-ids.
-//                    One-based, since it appears on FSTs.
-// transition-index:  identifier of a transition (or final-prob) in the HMM.  Indexes the
-//                    "transitions" vector in HmmTopology::HmmState.  [if it is out of range,
-//                    equal to transitions.size(), it refers to the final-prob.]
-//                    Zero-based.
-//   transition-id:   identifier of a unique parameter of the TransitionModel.
-//                    Associated with a (transition-state, transition-index) pair.
-//                    One-based, since it appears on FSTs.
-//
-// List of the possible mappings TransitionModel can do:
-//             (phone, HMM-state, pdf-id) -> transition-state
-//   (transition-state, transition-index) -> transition-id
-//  Reverse mappings:
-//                        transition-id -> transition-state
-//                        transition-id -> transition-index
-//                     transition-state -> phone
-//                     transition-state -> HMM-state
-//                     transition-state -> pdf-id
-//
-// The main things the TransitionModel object can do are:
-//    Get initialized (need ContextDependency and HmmTopology objects).
-//    Read/write.
-//    Update [given a vector of counts indexed by transition-id].
-//    Do the various integer mappings mentioned above.
-//    Get the probability (or log-probability) associated with a particular transition-id.
-
-
-// Note: this was previously called TransitionUpdateConfig.
-struct MleTransitionUpdateConfig {
-  BaseFloat floor;
-  BaseFloat mincount;
-  bool share_for_pdfs; // If true, share all transition parameters that have the same pdf.
-  MleTransitionUpdateConfig(BaseFloat floor = 0.01,
-                            BaseFloat mincount = 5.0,
-                            bool share_for_pdfs = false):
-      floor(floor), mincount(mincount), share_for_pdfs(share_for_pdfs) {}
-  
-  void Register (OptionsItf *po) {
-    po->Register("transition-floor", &floor,
-                 "Floor for transition probabilities");
-    po->Register("transition-min-count", &mincount,
-                 "Minimum count required to update transitions from a state");
-    po->Register("share-for-pdfs", &share_for_pdfs,
-                 "If true, share all transition parameters where the states "
-                 "have the same pdf.");
-  }
-};
-
-struct MapTransitionUpdateConfig {
-  BaseFloat tau;
-  bool share_for_pdfs; // If true, share all transition parameters that have the same pdf.
-  MapTransitionUpdateConfig(): tau(5.0), share_for_pdfs(false) { }
-
-  void Register (OptionsItf *po) {
-    po->Register("transition-tau", &tau, "Tau value for MAP estimation of transition "
-                 "probabilities.");
-    po->Register("share-for-pdfs", &share_for_pdfs,
-                 "If true, share all transition parameters where the states "
-                 "have the same pdf.");
-  }
-};
-
-class TransitionModel {
-
- public:
-  /// Initialize the object [e.g. at the start of training].
-  /// The class keeps a copy of the HmmTopology object, but not
-  /// the ContextDependency object.
-  TransitionModel(const ContextDependency &ctx_dep,
-                  const HmmTopology &hmm_topo);
-
-
-  /// Constructor that takes no arguments: typically used prior to calling Read.
-  TransitionModel() { }
-
-  void Read(std::istream &is, bool binary);  // note, no symbol table: topo object always read/written w/o symbols.
-  void Write(std::ostream &os, bool binary) const;
-
-
-  /// return reference to HMM-topology object.
-  const HmmTopology &GetTopo() const { return topo_; }
-
-  /// \name Integer mapping functions
-  /// @{
-
-  int32 TripleToTransitionState(int32 phone, int32 hmm_state, int32 pdf) const;
-  int32 PairToTransitionId(int32 trans_state, int32 trans_index) const;
-  int32 TransitionIdToTransitionState(int32 trans_id) const;
-  int32 TransitionIdToTransitionIndex(int32 trans_id) const;
-  int32 TransitionStateToPhone(int32 trans_state) const;
-  int32 TransitionStateToHmmState(int32 trans_state) const;
-  int32 TransitionStateToPdf(int32 trans_state) const;
-  int32 SelfLoopOf(int32 trans_state) const;  // returns the self-loop transition-id, or zero if
-  // this state doesn't have a self-loop.
-
-  inline int32 TransitionIdToPdf(int32 trans_id) const;
-  int32 TransitionIdToPhone(int32 trans_id) const;
-  int32 TransitionIdToPdfClass(int32 trans_id) const;
-  int32 TransitionIdToHmmState(int32 trans_id) const;
-
-  /// @}
-
-  bool IsFinal(int32 trans_id) const;  // returns true if this trans_id goes to the final state
-  // (which is bound to be nonemitting).
-  bool IsSelfLoop(int32 trans_id) const;  // return true if this trans_id corresponds to a self-loop.
-
-  /// Returns the total number of transition-ids (note, these are one-based).
-  inline int32 NumTransitionIds() const { return id2state_.size()-1; }
-
-  /// Returns the number of transition-indices for a particular transition-state.
-  /// Note: "Indices" is the plural of "index".   Index is not the same as "id",
-  /// here.  A transition-index is a zero-based offset into the transitions
-  /// out of a particular transition state.
-  int32 NumTransitionIndices(int32 trans_state) const;
-
-  /// Returns the total number of transition-states (note, these are one-based).
-  int32 NumTransitionStates() const { return triples_.size(); }
-
-  // NumPdfs() actually returns the highest-numbered pdf we ever saw, plus one.
-  // In normal cases this should equal the number of pdfs in the system, but if you
-  // initialized this object with fewer than all the phones, and it happens that
-  // an unseen phone has the highest-numbered pdf, this might be different.
-  int32 NumPdfs() const { return num_pdfs_; }
-
-  // This loops over the triples and finds the highest phone index present. If
-  // the FST symbol table for the phones is created in the expected way, i.e.:
-  // starting from 1 (<eps> is 0) and numbered contiguously till the last phone,
-  // this will be the total number of phones.
-  int32 NumPhones() const;
-
-  /// Returns a sorted, unique list of phones.
-  const std::vector<int32> &GetPhones() const { return topo_.GetPhones(); }
-
-  // Transition-parameter-getting functions:
-  BaseFloat GetTransitionProb(int32 trans_id) const;
-  BaseFloat GetTransitionLogProb(int32 trans_id) const;
-
-  // The following functions are more specialized functions for getting
-  // transition probabilities, that are provided for convenience.
-
-  /// Returns the log-probability of a particular non-self-loop transition
-  /// after subtracting the probability mass of the self-loop and renormalizing;
-  /// will crash if called on a self-loop.  Specifically:
-  /// for non-self-loops it returns the log of that prob divided by (1 minus
-  /// self-loop-prob-for-that-state).
-  BaseFloat GetTransitionLogProbIgnoringSelfLoops(int32 trans_id) const;
-
-  /// Returns the log-prob of the non-self-loop probability
-  /// mass for this transition state. (you can get the self-loop prob, if a self-loop
-  /// exists, by calling GetTransitionLogProb(SelfLoopOf(trans_state)).
-  BaseFloat GetNonSelfLoopLogProb(int32 trans_state) const;
-
-  /// Does Maximum Likelihood estimation.  The stats are counts/weights, indexed
-  /// by transition-id.  This was previously called Update().
-  void MleUpdate(const Vector<double> &stats, 
-                 const MleTransitionUpdateConfig &cfg,
-                 BaseFloat *objf_impr_out,
-                 BaseFloat *count_out);
-
-  /// Does Maximum A Posteriori (MAP) estimation.  The stats are counts/weights,
-  /// indexed by transition-id.
-  void MapUpdate(const Vector<double> &stats, 
-                 const MapTransitionUpdateConfig &cfg,
-                 BaseFloat *objf_impr_out,
-                 BaseFloat *count_out);
-  
-  /// Print will print the transition model in a human-readable way, for purposes of human
-  /// inspection.  The "occs" are optional (they are indexed by pdf-id).
-  void Print(std::ostream &os,
-             const std::vector<std::string> &phone_names,
-             const Vector<double> *occs = NULL);
-
-
-  void InitStats(Vector<double> *stats) const { stats->Resize(NumTransitionIds()+1); }
-
-  void Accumulate(BaseFloat prob, int32 trans_id, Vector<double> *stats) const {
-    KALDI_ASSERT(trans_id <= NumTransitionIds());
-    (*stats)(trans_id) += prob;
-    // This is trivial and doesn't require class members, but leaves us more open
-    // to design changes than doing it manually.
-  }
-
-  /// returns true if all the integer class members are identical (but does not
-  /// compare the transition probabilities.
-  bool Compatible(const TransitionModel &other) const;
-  
- private:
-  void MleUpdateShared(const Vector<double> &stats,
-                       const MleTransitionUpdateConfig &cfg,
-                       BaseFloat *objf_impr_out, BaseFloat *count_out);
-  void MapUpdateShared(const Vector<double> &stats,
-                       const MapTransitionUpdateConfig &cfg,
-                       BaseFloat *objf_impr_out, BaseFloat *count_out);
-  void ComputeTriples(const ContextDependency &ctx_dep);  // called from constructor.  initializes triples_.
-  void ComputeDerived();  // called from constructor and Read function: computes state2id_ and id2state_.
-  void ComputeDerivedOfProbs();  // computes quantities derived from log-probs (currently just
-  // non_self_loop_log_probs_; called whenever log-probs change.
-  void InitializeProbs();  // called from constructor.
-  void Check() const;
-
-  struct Triple {
-    int32 phone;
-    int32 hmm_state;
-    int32 pdf;
-    Triple() { }
-    Triple(int32 phone, int32 hmm_state, int32 pdf):
-        phone(phone), hmm_state(hmm_state), pdf(pdf) { }
-    bool operator < (const Triple &other) const {
-      if (phone < other.phone) return true;
-      else if (phone > other.phone) return false;
-      else if (hmm_state < other.hmm_state) return true;
-      else if (hmm_state > other.hmm_state) return false;
-      else return pdf < other.pdf;
-    }
-    bool operator == (const Triple &other) const {
-      return (phone == other.phone && hmm_state == other.hmm_state
-              && pdf == other.pdf);
-    }
-  };
-
-  HmmTopology topo_;
-
-  /// Triples indexed by transition state minus one;
-  /// the triples are in sorted order which allows us to do the reverse mapping from
-  /// triple to transition state
-  std::vector<Triple> triples_;
-  
-  /// Gives the first transition_id of each transition-state; indexed by
-  /// the transition-state.  Array indexed 1..num-transition-states+1 (the last one
-  /// is needed so we can know the num-transitions of the last transition-state.
-  std::vector<int32> state2id_;
-
-  /// For each transition-id, the corresponding transition
-  /// state (indexed by transition-id).
-  std::vector<int32> id2state_;
-
-  /// For each transition-id, the corresponding log-prob.  Indexed by transition-id.
-  Vector<BaseFloat> log_probs_;
-
-  /// For each transition-state, the log of (1 - self-loop-prob).  Indexed by
-  /// transition-state.
-  Vector<BaseFloat> non_self_loop_log_probs_;
-
-  /// This is actually one plus the highest-numbered pdf we ever got back from the
-  /// tree (but the tree numbers pdfs contiguously from zero so this is the number
-  /// of pdfs).
-  int32 num_pdfs_;
-
-
-  DISALLOW_COPY_AND_ASSIGN(TransitionModel);
-
-};
-
-inline int32 TransitionModel::TransitionIdToPdf(int32 trans_id) const {
-  // If a lot of time is spent here we may create an extra array
-  // to handle this.
-  KALDI_ASSERT(static_cast<size_t>(trans_id) < id2state_.size() &&
-               "Likely graph/model mismatch (graph built from wrong model?)");
-  int32 trans_state = id2state_[trans_id];
-  return triples_[trans_state-1].pdf;
-}
-
-/// Works out which pdfs might correspond to the given phones.  Will return true
-/// if these pdfs correspond *just* to these phones, false if these pdfs are also
-/// used by other phones.
-/// @param trans_model [in] Transition-model used to work out this information
-/// @param phones [in] A sorted, uniq vector that represents a set of phones
-/// @param pdfs [out] Will be set to a sorted, uniq list of pdf-ids that correspond
-///                   to one of this set of phones.
-/// @return  Returns true if all of the pdfs output to "pdfs" correspond to phones from
-///          just this set (false if they may be shared with phones outside this set).
-bool GetPdfsForPhones(const TransitionModel &trans_model,
-                      const std::vector<int32> &phones,
-                      std::vector<int32> *pdfs);
-
-/// Works out which phones might correspond to the given pdfs. Similar to the
-/// above GetPdfsForPhones(, ,)
-bool GetPhonesForPdfs(const TransitionModel &trans_model,
-                      const std::vector<int32> &pdfs,
-                      std::vector<int32> *phones);
-/// @}
-
-
-} // end namespace kaldi
-
-
-#endif
diff --git a/kaldi_io/src/kaldi/hmm/tree-accu.h b/kaldi_io/src/kaldi/hmm/tree-accu.h
deleted file mode 100644
index d571762..0000000
--- a/kaldi_io/src/kaldi/hmm/tree-accu.h
+++ /dev/null
@@ -1,69 +0,0 @@
-// hmm/tree-accu.h
-
-// Copyright 2009-2011 Microsoft Corporation
-//                2013 Johns Hopkins University (author: Daniel Povey)
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-
-//  http://www.apache.org/licenses/LICENSE-2.0
-
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-#ifndef KALDI_HMM_TREE_ACCU_H_
-#define KALDI_HMM_TREE_ACCU_H_
-
-#include <cctype>  // For isspace.
-#include <limits>
-#include "base/kaldi-common.h"
-#include "hmm/transition-model.h"
-#include "tree/clusterable-classes.h"
-#include "tree/build-tree-questions.h" // needed for this typedef:
-// typedef std::vector<std::pair<EventVector, Clusterable*> > BuildTreeStatsType;
-
-namespace kaldi {
-
-/// \ingroup tree_group_top
-/// @{
-
-
-/// Accumulates the stats needed for training context-dependency trees (in the
-/// "normal" way).  It adds to 'stats' the stats obtained from this file.  Any
-/// new GaussClusterable* pointers in "stats" will be allocated with "new".
-
-void AccumulateTreeStats(const TransitionModel &trans_model,
-                         BaseFloat var_floor,
-                         int N,  // context window size.
-                         int P,  // central position.
-                         const std::vector<int32> &ci_phones,  // sorted
-                         const std::vector<int32> &alignment,
-                         const Matrix<BaseFloat> &features,
-                         const std::vector<int32> *phone_map, // or NULL
-                         std::map<EventType, GaussClusterable*> *stats);
-
-
-
-/*** Read a mapping from one phone set to another.  The phone map file has lines
- of the form <old-phone> <new-phone>, where both entries are integers, usually
- nonzero (but this is not enforced).  This program will crash if the input is
- invalid, e.g. there are multiple inconsistent entries for the same old phone.
- The output vector "phone_map" will be indexed by old-phone and will contain
- the corresponding new-phone, or -1 for any entry that was not defined. */
- 
-void ReadPhoneMap(std::string phone_map_rxfilename,
-                  std::vector<int32> *phone_map);
-
-
-
-/// @}
-
-}  // end namespace kaldi.
-
-#endif
diff --git a/kaldi_io/src/kaldi/itf/clusterable-itf.h b/kaldi_io/src/kaldi/itf/clusterable-itf.h
deleted file mode 100644
index 7ef9ae0..0000000
--- a/kaldi_io/src/kaldi/itf/clusterable-itf.h
+++ /dev/null
@@ -1,97 +0,0 @@
-// itf/clusterable-itf.h
-
-// Copyright 2009-2011     Microsoft Corporation;  Go Vivace Inc.
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-
-#ifndef KALDI_ITF_CLUSTERABLE_ITF_H_
-#define KALDI_ITF_CLUSTERABLE_ITF_H_ 1
-
-#include <string>
-#include "base/kaldi-common.h"
-
-namespace kaldi {
-
-
-/** \addtogroup clustering_group
- @{
-  A virtual class for clusterable objects; see \ref clustering for an
-  explanation if its function.
-*/
-
-
-
-class Clusterable {
- public:
-  /// \name Functions that must be overridden
-  /// @{
-
-  /// Return a copy of this object.
-  virtual Clusterable *Copy() const = 0;
-  /// Return the objective function associated with the stats
-  /// [assuming ML estimation]
-  virtual BaseFloat Objf() const = 0;
-  /// Return the normalizer (typically, count) associated with the stats
-  virtual BaseFloat Normalizer() const = 0;
-  /// Set stats to empty.
-  virtual void SetZero() = 0;
-  /// Add other stats.
-  virtual void Add(const Clusterable &other) = 0;
-  /// Subtract other stats.
-  virtual void Sub(const Clusterable &other) = 0;
-  /// Scale the stats by a positive number f [not mandatory to supply this].
-  virtual void Scale(BaseFloat f) {
-    KALDI_ERR << "This Clusterable object does not implement Scale().";
-  }
-
-  /// Return a string that describes the inherited type. 
-  virtual std::string Type() const = 0;
-
-  /// Write data to stream.
-  virtual void Write(std::ostream &os, bool binary) const = 0;
-
-  /// Read data from a stream and return the corresponding object (const
-  /// function; it's a class member because we need access to the vtable
-  /// so generic code can read derived types).
-  virtual Clusterable* ReadNew(std::istream &os, bool binary) const = 0;
-
-  virtual ~Clusterable() {}
-
-  /// @}
-
-  /// \name Functions that have default implementations
-  /// @{
-
-  // These functions have default implementations (but may be overridden for
-  // speed). Implementatons in tree/clusterable-classes.cc
-
-  /// Return the objective function of the combined object this + other.
-  virtual BaseFloat ObjfPlus(const Clusterable &other) const;
-  /// Return the objective function of the subtracted object this - other.
-  virtual BaseFloat ObjfMinus(const Clusterable &other) const;
-  /// Return the objective function decrease from merging the two
-  /// clusters, negated to be a positive number (or zero).
-  virtual BaseFloat Distance(const Clusterable &other) const;
-  /// @}
-
-};
-/// @} end of "ingroup clustering_group"
-
-}  // end namespace kaldi
-
-#endif  // KALDI_ITF_CLUSTERABLE_ITF_H_
-
diff --git a/kaldi_io/src/kaldi/itf/context-dep-itf.h b/kaldi_io/src/kaldi/itf/context-dep-itf.h
deleted file mode 100644
index 6a0bd0f..0000000
--- a/kaldi_io/src/kaldi/itf/context-dep-itf.h
+++ /dev/null
@@ -1,80 +0,0 @@
-// itf/context-dep-itf.h
-
-// Copyright 2009-2011     Microsoft Corporation;  Go Vivace Inc.
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-
-#ifndef KALDI_ITF_CONTEXT_DEP_ITF_H_
-#define KALDI_ITF_CONTEXT_DEP_ITF_H_
-#include "base/kaldi-common.h"
-
-namespace kaldi {
-/// @ingroup tree_group
-/// @{
-
-/// context-dep-itf.h provides a link between
-/// the tree-building code in ../tree/, and the FST code in ../fstext/
-/// (particularly, ../fstext/context-dep.h).  It is an abstract
-/// interface that describes an object that can map from a
-/// phone-in-context to a sequence of integer leaf-ids.
-class ContextDependencyInterface {
- public:
-  /// ContextWidth() returns the value N (e.g. 3 for triphone models) that says how many phones
-  ///   are considered for computing context.
-  virtual int ContextWidth() const = 0;
-
-  /// Central position P of the phone context, in 0-based numbering, e.g. P = 1 for typical
-  /// triphone system.  We have to see if we can do without this function.
-  virtual int CentralPosition() const = 0;
-
-  /// The "new" Compute interface.  For typical topologies,
-  /// pdf_class would be 0, 1, 2.
-  /// Returns success or failure; outputs the pdf-id.
-  ///
-  /// "Compute" is the main function of this interface, that takes a
-  /// sequence of N phones (and it must be N phones), possibly
-  /// including epsilons (symbol id zero) but only at positions other
-  /// than P [these represent unknown phone context due to end or
-  /// begin of sequence].  We do not insist that Compute must always
-  /// output (into stateseq) a nonempty sequence of states, but we
-  /// anticipate that stateseq will alyway be nonempty at output in
-  /// typical use cases.  "Compute" returns false if expansion somehow
-  /// failed.  Normally the calling code should raise an exception if
-  /// this happens.  We can define a different interface later in
-  /// order to handle other kinds of information-- the underlying
-  /// data-structures from event-map.h are very flexible.
-  virtual bool Compute(const std::vector<int32> &phoneseq, int32 pdf_class,
-                       int32 *pdf_id) const = 0;
-
-
-
-  /// NumPdfs() returns the number of acoustic pdfs (they are numbered 0.. NumPdfs()-1).
-  virtual int32 NumPdfs() const = 0;
-
-  virtual ~ContextDependencyInterface() {};
-  ContextDependencyInterface() {}
-
-  /// Returns pointer to new object which is copy of current one.
-  virtual ContextDependencyInterface *Copy() const = 0;
- private:
-  KALDI_DISALLOW_COPY_AND_ASSIGN(ContextDependencyInterface);
-};
-/// @}
-}  // namespace Kaldi
-
-
-#endif
diff --git a/kaldi_io/src/kaldi/itf/decodable-itf.h b/kaldi_io/src/kaldi/itf/decodable-itf.h
deleted file mode 100644
index ba4d765..0000000
--- a/kaldi_io/src/kaldi/itf/decodable-itf.h
+++ /dev/null
@@ -1,123 +0,0 @@
-// itf/decodable-itf.h
-
-// Copyright 2009-2011  Microsoft Corporation;  Saarland University;
-//                      Mirko Hannemann;  Go Vivace Inc.;
-//                2013  Johns Hopkins University (author: Daniel Povey)
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_ITF_DECODABLE_ITF_H_
-#define KALDI_ITF_DECODABLE_ITF_H_ 1
-#include "base/kaldi-common.h"
-
-namespace kaldi {
-/// @ingroup Interfaces
-/// @{
-
-
-/**
-    DecodableInterface provides a link between the (acoustic-modeling and
-    feature-processing) code and the decoder.  The idea is to make this
-    interface as small as possible, and to make it as agnostic as possible about
-    the form of the acoustic model (e.g. don't assume the probabilities are a
-    function of just a vector of floats), and about the decoder (e.g. don't
-    assume it accesses frames in strict left-to-right order).  For normal
-    models, without on-line operation, the "decodable" sub-class will just be a
-    wrapper around a matrix of features and an acoustic model, and it will
-    answer the question 'what is the acoustic likelihood for this index and this
-    frame?'.
-
-    For online decoding, where the features are coming in in real time, it is
-    important to understand the IsLastFrame() and NumFramesReady() functions.
-    There are two ways these are used: the old online-decoding code, in ../online/,
-    and the new online-decoding code, in ../online2/.  In the old online-decoding
-    code, the decoder would do:
-    \code{.cc}
-    for (int frame = 0; !decodable.IsLastFrame(frame); frame++) {
-      // Process this frame
-    }
-    \endcode
-   and the the call to IsLastFrame would block if the features had not arrived yet.
-   The decodable object would have to know when to terminate the decoding.  This
-   online-decoding mode is still supported, it is what happens when you call, for
-   example, LatticeFasterDecoder::Decode().
-
-   We realized that this "blocking" mode of decoding is not very convenient
-   because it forces the program to be multi-threaded and makes it complex to
-   control endpointing.  In the "new" decoding code, you don't call (for example)
-   LatticeFasterDecoder::Decode(), you call LatticeFasterDecoder::InitDecoding(),
-   and then each time you get more features, you provide them to the decodable
-   object, and you call LatticeFasterDecoder::AdvanceDecoding(), which does
-   something like this:
-   \code{.cc}
-   while (num_frames_decoded_ < decodable.NumFramesReady()) {
-     // Decode one more frame [increments num_frames_decoded_]
-   }
-   \endcode
-   So the decodable object never has IsLastFrame() called.  For decoding where
-   you are starting with a matrix of features, the NumFramesReady() function will
-   always just return the number of frames in the file, and IsLastFrame() will
-   return true for the last frame.
-
-   For truly online decoding, the "old" online decodable objects in ../online/ have a
-   "blocking" IsLastFrame() and will crash if you call NumFramesReady().
-   The "new" online decodable objects in ../online2/ return the number of frames
-   currently accessible if you call NumFramesReady().  You will likely not need
-   to call IsLastFrame(), but we implement it to only return true for the last
-   frame of the file once we've decided to terminate decoding.
-*/
-
-class DecodableInterface {
- public:
-  /// Returns the log likelihood, which will be negated in the decoder.
-  /// The "frame" starts from zero.  You should verify that IsLastFrame(frame-1)
-  /// returns false before calling this.
-  virtual BaseFloat LogLikelihood(int32 frame, int32 index) = 0;
-
-  /// Returns true if this is the last frame.  Frames are zero-based, so the
-  /// first frame is zero.  IsLastFrame(-1) will return false, unless the file
-  /// is empty (which is a case that I'm not sure all the code will handle, so
-  /// be careful).  Caution: the behavior of this function in an online setting
-  /// is being changed somewhat.  In future it may return false in cases where
-  /// we haven't yet decided to terminate decoding, but later true if we decide
-  /// to terminate decoding.  The plan in future is to rely more on
-  /// NumFramesReady(), and in future, IsLastFrame() would always return false
-  /// in an online-decoding setting, and would only return true in a
-  /// decoding-from-matrix setting where we want to allow the last delta or LDA
-  /// features to be flushed out for compatibility with the baseline setup.
-  virtual bool IsLastFrame(int32 frame) const = 0;
-  
-  /// The call NumFramesReady() will return the number of frames currently available
-  /// for this decodable object.  This is for use in setups where you don't want the
-  /// decoder to block while waiting for input.  This is newly added as of Jan 2014,
-  /// and I hope, going forward, to rely on this mechanism more than IsLastFrame to
-  /// know when to stop decoding.
-  virtual int32 NumFramesReady() const {
-    KALDI_ERR << "NumFramesReady() not implemented for this decodable type.";
-    return -1;
-  }
-
-  /// Returns the number of states in the acoustic model
-  /// (they will be indexed one-based, i.e. from 1 to NumIndices();
-  /// this is for compatibility with OpenFst.
-  virtual int32 NumIndices() const = 0;
-  
-  virtual ~DecodableInterface() {}
-};
-/// @}
-}  // namespace Kaldi
-
-#endif  // KALDI_ITF_DECODABLE_ITF_H_
diff --git a/kaldi_io/src/kaldi/itf/online-feature-itf.h b/kaldi_io/src/kaldi/itf/online-feature-itf.h
deleted file mode 100644
index dafcd8a..0000000
--- a/kaldi_io/src/kaldi/itf/online-feature-itf.h
+++ /dev/null
@@ -1,105 +0,0 @@
-// itf/online-feature-itf.h
-
-// Copyright    2013  Johns Hopkins University (author: Daniel Povey)
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_ITF_ONLINE_FEATURE_ITF_H_
-#define KALDI_ITF_ONLINE_FEATURE_ITF_H_ 1
-#include "base/kaldi-common.h"
-#include "matrix/matrix-lib.h"
-
-namespace kaldi {
-/// @ingroup Interfaces
-/// @{
-
-/**
-   OnlineFeatureInterface is an interface for online feature processing (it is
-   also usable in the offline setting, but currently we're not using it for
-   that).  This is for use in the online2/ directory, and it supersedes the
-   interface in ../online/online-feat-input.h.  We have a slighty different
-   model that puts more control in the hands of the calling thread, and won't
-   involve waiting on semaphores in the decoding thread.
-
-   This interface only specifies how the object *outputs* the features.
-   How it obtains the features, e.g. from a previous object or objects of type
-   OnlineFeatureInterface, is not specified in the interface and you will
-   likely define new constructors or methods in the derived type to do that.
-
-   You should appreciate that this interface is designed to allow random
-   access to features, as long as they are ready.  That is, the user
-   can call GetFrame for any frame less than NumFramesReady(), and when
-   implementing a child class you must not make assumptions about the
-   order in which the user makes these calls.
-*/
-   
-class OnlineFeatureInterface {
- public:
-  virtual int32 Dim() const = 0; /// returns the feature dimension.
-  
-  /// Returns the total number of frames, since the start of the utterance, that
-  /// are now available.  In an online-decoding context, this will likely
-  /// increase with time as more data becomes available.
-  virtual int32 NumFramesReady() const = 0;
-
-  /// Returns true if this is the last frame.  Frame indices are zero-based, so the
-  /// first frame is zero.  IsLastFrame(-1) will return false, unless the file
-  /// is empty (which is a case that I'm not sure all the code will handle, so
-  /// be careful).  This function may return false for some frame if
-  /// we haven't yet decided to terminate decoding, but later true if we decide
-  /// to terminate decoding.  This function exists mainly to correctly handle
-  /// end effects in feature extraction, and is not a mechanism to determine how
-  /// many frames are in the decodable object (as it used to be, and for backward
-  /// compatibility, still is, in the Decodable interface).
-  virtual bool IsLastFrame(int32 frame) const = 0;
-  
-  /// Gets the feature vector for this frame.  Before calling this for a given
-  /// frame, it is assumed that you called NumFramesReady() and it returned a
-  /// number greater than "frame".  Otherwise this call will likely crash with
-  /// an assert failure.  This function is not declared const, in case there is
-  /// some kind of caching going on, but most of the time it shouldn't modify
-  /// the class.
-  virtual void GetFrame(int32 frame, VectorBase<BaseFloat> *feat) = 0;
-
-  /// Virtual destructor.  Note: constructors that take another member of
-  /// type OnlineFeatureInterface are not expected to take ownership of
-  /// that pointer; the caller needs to keep track of that manually.
-  virtual ~OnlineFeatureInterface() { }  
-};
-
-
-/// Add a virtual class for "source" features such as MFCC or PLP or pitch
-/// features.
-class OnlineBaseFeature: public OnlineFeatureInterface {
- public:
-  /// This would be called from the application, when you get more wave data.
-  /// Note: the sampling_rate is typically only provided so the code can assert
-  /// that it matches the sampling rate expected in the options.
-  virtual void AcceptWaveform(BaseFloat sampling_rate,
-                              const VectorBase<BaseFloat> &waveform) = 0;
-
-  /// InputFinished() tells the class you won't be providing any
-  /// more waveform.  This will help flush out the last few frames
-  /// of delta or LDA features (it will typically affect the return value
-  /// of IsLastFrame.
-  virtual void InputFinished() = 0;
-};
-
-
-/// @}
-}  // namespace Kaldi
-
-#endif  // KALDI_ITF_ONLINE_FEATURE_ITF_H_
diff --git a/kaldi_io/src/kaldi/itf/optimizable-itf.h b/kaldi_io/src/kaldi/itf/optimizable-itf.h
deleted file mode 100644
index 1b8f54b..0000000
--- a/kaldi_io/src/kaldi/itf/optimizable-itf.h
+++ /dev/null
@@ -1,51 +0,0 @@
-// itf/optimizable-itf.h
-
-// Copyright 2009-2011  Go Vivace Inc.;  Microsoft Corporation;  Georg Stemmer
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-#ifndef KALDI_ITF_OPTIMIZABLE_ITF_H_
-#define KALDI_ITF_OPTIMIZABLE_ITF_H_
-
-#include "base/kaldi-common.h"
-#include "matrix/matrix-lib.h"
-
-namespace kaldi {
-/// @ingroup Interfaces
-/// @{
-
-/// OptimizableInterface provides
-/// a virtual class for optimizable objects.
-/// E.g. a class that computed a likelihood function and
-/// its gradient using some parameter
-/// that has to be optimized on data
-/// could inherit from it.
-template<class Real>
-class OptimizableInterface {
- public:
-  /// computes gradient for a parameter params and returns it
-  /// in gradient_out
-  virtual void ComputeGradient(const Vector<Real> &params,
-                               Vector<Real> *gradient_out) = 0;
-  /// computes the function value for a parameter params
-  /// and returns it
-  virtual Real ComputeValue(const Vector<Real> &params) = 0;
-
-  virtual ~OptimizableInterface() {}
-};
-/// @} end of "Interfaces"
-} // end namespace kaldi
-
-#endif
diff --git a/kaldi_io/src/kaldi/itf/options-itf.h b/kaldi_io/src/kaldi/itf/options-itf.h
deleted file mode 100644
index 204f46d..0000000
--- a/kaldi_io/src/kaldi/itf/options-itf.h
+++ /dev/null
@@ -1,49 +0,0 @@
-// itf/options-itf.h
-
-// Copyright 2013  Tanel Alumae, Tallinn University of Technology
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_ITF_OPTIONS_ITF_H_
-#define KALDI_ITF_OPTIONS_ITF_H_ 1
-#include "base/kaldi-common.h"
-
-namespace kaldi {
-
-class OptionsItf {
- public:
-  
-  virtual void Register(const std::string &name,
-                bool *ptr, const std::string &doc) = 0; 
-  virtual void Register(const std::string &name,
-                int32 *ptr, const std::string &doc) = 0; 
-  virtual void Register(const std::string &name,
-                uint32 *ptr, const std::string &doc) = 0; 
-  virtual void Register(const std::string &name,
-                float *ptr, const std::string &doc) = 0; 
-  virtual void Register(const std::string &name,
-                double *ptr, const std::string &doc) = 0; 
-  virtual void Register(const std::string &name,
-                std::string *ptr, const std::string &doc) = 0; 
-  
-  virtual ~OptionsItf() {}
-};
-
-}  // namespace Kaldi
-
-#endif  // KALDI_ITF_OPTIONS_ITF_H_
-
-
diff --git a/kaldi_io/src/kaldi/matrix/cblas-wrappers.h b/kaldi_io/src/kaldi/matrix/cblas-wrappers.h
deleted file mode 100644
index ebec0a3..0000000
--- a/kaldi_io/src/kaldi/matrix/cblas-wrappers.h
+++ /dev/null
@@ -1,491 +0,0 @@
-// matrix/cblas-wrappers.h
-
-// Copyright 2012  Johns Hopkins University (author: Daniel Povey);
-//                 Haihua Xu; Wei Shi
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-
-//  http://www.apache.org/licenses/LICENSE-2.0
-
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-#ifndef KALDI_MATRIX_CBLAS_WRAPPERS_H_
-#define KALDI_MATRIX_CBLAS_WRAPPERS_H_ 1
-
-
-#include <limits>
-#include "matrix/sp-matrix.h"
-#include "matrix/kaldi-vector.h"
-#include "matrix/kaldi-matrix.h"
-#include "matrix/matrix-functions.h"
-
-// Do not include this file directly.  It is to be included
-// by .cc files in this directory.
-
-namespace kaldi {
-
-
-inline void cblas_Xcopy(const int N, const float *X, const int incX, float *Y,
-                        const int incY) {
-  cblas_scopy(N, X, incX, Y, incY);
-}
-
-inline void cblas_Xcopy(const int N, const double *X, const int incX, double *Y,
-                        const int incY) {
-  cblas_dcopy(N, X, incX, Y, incY);
-}
-
-
-inline float cblas_Xasum(const int N, const float *X, const int incX) {
-  return cblas_sasum(N, X, incX);
-}
-
-inline double cblas_Xasum(const int N, const double *X, const int incX) {
-  return cblas_dasum(N, X, incX);
-}
-
-inline void cblas_Xrot(const int N, float *X, const int incX, float *Y,
-                       const int incY, const float c, const float s) {
-  cblas_srot(N, X, incX, Y, incY, c, s);
-}
-inline void cblas_Xrot(const int N, double *X, const int incX, double *Y,
-                       const int incY, const double c, const double s) {
-  cblas_drot(N, X, incX, Y, incY, c, s);
-}
-inline float cblas_Xdot(const int N, const float *const X,
-                        const int incX, const float *const Y,
-                        const int incY) {
-  return cblas_sdot(N, X, incX, Y, incY);
-}
-inline double cblas_Xdot(const int N, const double *const X,
-                        const int incX, const double *const Y,
-                        const int incY) {
-  return cblas_ddot(N, X, incX, Y, incY);
-}
-inline void cblas_Xaxpy(const int N, const float alpha, const float *X,
-                        const int incX, float *Y, const int incY) {
-  cblas_saxpy(N, alpha, X, incX, Y, incY);
-}
-inline void cblas_Xaxpy(const int N, const double alpha, const double *X,
-                        const int incX, double *Y, const int incY) {
-  cblas_daxpy(N, alpha, X, incX, Y, incY);
-}
-inline void cblas_Xscal(const int N, const float alpha, float *data,
-                        const int inc) {
-  cblas_sscal(N, alpha, data, inc);
-}
-inline void cblas_Xscal(const int N, const double alpha, double *data, 
-                        const int inc) {
-  cblas_dscal(N, alpha, data, inc);
-}
-inline void cblas_Xspmv(const float alpha, const int num_rows, const float *Mdata,
-                        const float *v, const int v_inc,
-                        const float beta, float *y, const int y_inc) {
-  cblas_sspmv(CblasRowMajor, CblasLower, num_rows, alpha, Mdata, v, v_inc, beta, y, y_inc);
-}
-inline void cblas_Xspmv(const double alpha, const int num_rows, const double *Mdata,
-                        const double *v, const int v_inc,
-                        const double beta, double *y, const int y_inc) {
-  cblas_dspmv(CblasRowMajor, CblasLower, num_rows, alpha, Mdata, v, v_inc, beta, y, y_inc);
-}
-inline void cblas_Xtpmv(MatrixTransposeType trans, const float *Mdata,
-                        const int num_rows, float *y, const int y_inc) {
-  cblas_stpmv(CblasRowMajor, CblasLower, static_cast<CBLAS_TRANSPOSE>(trans),
-              CblasNonUnit, num_rows, Mdata, y, y_inc);
-}
-inline void cblas_Xtpmv(MatrixTransposeType trans, const double *Mdata,
-                        const int num_rows, double *y, const int y_inc) {
-  cblas_dtpmv(CblasRowMajor, CblasLower, static_cast<CBLAS_TRANSPOSE>(trans),
-              CblasNonUnit, num_rows, Mdata, y, y_inc);
-}
-
-
-inline void cblas_Xtpsv(MatrixTransposeType trans, const float *Mdata,
-                        const int num_rows, float *y, const int y_inc) {
-  cblas_stpsv(CblasRowMajor, CblasLower, static_cast<CBLAS_TRANSPOSE>(trans),
-              CblasNonUnit, num_rows, Mdata, y, y_inc);
-}
-inline void cblas_Xtpsv(MatrixTransposeType trans, const double *Mdata,
-                        const int num_rows, double *y, const int y_inc) {
-  cblas_dtpsv(CblasRowMajor, CblasLower, static_cast<CBLAS_TRANSPOSE>(trans),
-              CblasNonUnit, num_rows, Mdata, y, y_inc);
-}
-
-// x = alpha * M * y + beta * x
-inline void cblas_Xspmv(MatrixIndexT dim, float alpha, const float *Mdata,
-                        const float *ydata, MatrixIndexT ystride,
-                        float beta, float *xdata, MatrixIndexT xstride) {
-  cblas_sspmv(CblasRowMajor, CblasLower, dim, alpha, Mdata,
-              ydata, ystride, beta, xdata, xstride);
-}
-inline void cblas_Xspmv(MatrixIndexT dim, double alpha, const double *Mdata,
-                        const double *ydata, MatrixIndexT ystride,
-                        double beta, double *xdata, MatrixIndexT xstride) {
-  cblas_dspmv(CblasRowMajor, CblasLower, dim, alpha, Mdata,
-              ydata, ystride, beta, xdata, xstride);
-}
-
-// Implements  A += alpha * (x y'  + y x'); A is symmetric matrix.
-inline void cblas_Xspr2(MatrixIndexT dim, float alpha, const float *Xdata,
-                        MatrixIndexT incX, const float *Ydata, MatrixIndexT incY,
-                          float *Adata) {
-  cblas_sspr2(CblasRowMajor, CblasLower, dim, alpha, Xdata,
-              incX, Ydata, incY, Adata);
-}
-inline void cblas_Xspr2(MatrixIndexT dim, double alpha, const double *Xdata,
-                        MatrixIndexT incX, const double *Ydata, MatrixIndexT incY,
-                        double *Adata) {
-  cblas_dspr2(CblasRowMajor, CblasLower, dim, alpha, Xdata,
-              incX, Ydata, incY, Adata);
-}
-
-// Implements  A += alpha * (x x'); A is symmetric matrix.
-inline void cblas_Xspr(MatrixIndexT dim, float alpha, const float *Xdata,
-                       MatrixIndexT incX, float *Adata) {
-  cblas_sspr(CblasRowMajor, CblasLower, dim, alpha, Xdata, incX, Adata);
-}
-inline void cblas_Xspr(MatrixIndexT dim, double alpha, const double *Xdata,
-                       MatrixIndexT incX, double *Adata) {
-  cblas_dspr(CblasRowMajor, CblasLower, dim, alpha, Xdata, incX, Adata);
-}
-
-// sgemv,dgemv: y = alpha M x + beta y.
-inline void cblas_Xgemv(MatrixTransposeType trans, MatrixIndexT num_rows,
-                        MatrixIndexT num_cols, float alpha, const float *Mdata,
-                        MatrixIndexT stride, const float *xdata,
-                        MatrixIndexT incX, float beta, float *ydata, MatrixIndexT incY) {
-  cblas_sgemv(CblasRowMajor, static_cast<CBLAS_TRANSPOSE>(trans), num_rows,
-              num_cols, alpha, Mdata, stride, xdata, incX, beta, ydata, incY);
-}
-inline void cblas_Xgemv(MatrixTransposeType trans, MatrixIndexT num_rows,
-                        MatrixIndexT num_cols, double alpha, const double *Mdata,
-                        MatrixIndexT stride, const double *xdata,
-                        MatrixIndexT incX, double beta, double *ydata, MatrixIndexT incY) {
-  cblas_dgemv(CblasRowMajor, static_cast<CBLAS_TRANSPOSE>(trans), num_rows,
-              num_cols, alpha, Mdata, stride, xdata, incX, beta, ydata, incY);
-}
-
-// sgbmv, dgmmv: y = alpha M x +  + beta * y.
-inline void cblas_Xgbmv(MatrixTransposeType trans, MatrixIndexT num_rows,
-                        MatrixIndexT num_cols, MatrixIndexT num_below,
-                        MatrixIndexT num_above, float alpha, const float *Mdata,
-                        MatrixIndexT stride, const float *xdata,
-                        MatrixIndexT incX, float beta, float *ydata, MatrixIndexT incY) {
-  cblas_sgbmv(CblasRowMajor, static_cast<CBLAS_TRANSPOSE>(trans), num_rows,
-              num_cols, num_below, num_above, alpha, Mdata, stride, xdata,
-              incX, beta, ydata, incY);
-}
-inline void cblas_Xgbmv(MatrixTransposeType trans, MatrixIndexT num_rows,
-                        MatrixIndexT num_cols, MatrixIndexT num_below,
-                        MatrixIndexT num_above, double alpha, const double *Mdata,
-                        MatrixIndexT stride, const double *xdata,
-                        MatrixIndexT incX, double beta, double *ydata, MatrixIndexT incY) {
-  cblas_dgbmv(CblasRowMajor, static_cast<CBLAS_TRANSPOSE>(trans), num_rows,
-              num_cols, num_below, num_above, alpha, Mdata, stride, xdata,
-              incX, beta, ydata, incY);
-}
-
-
-template<typename Real>
-inline void Xgemv_sparsevec(MatrixTransposeType trans, MatrixIndexT num_rows,
-                            MatrixIndexT num_cols, Real alpha, const Real *Mdata,
-                            MatrixIndexT stride, const Real *xdata,
-                            MatrixIndexT incX, Real beta, Real *ydata,
-                            MatrixIndexT incY) {
-  if (trans == kNoTrans) {
-    if (beta != 1.0) cblas_Xscal(num_rows, beta, ydata, incY);
-    for (MatrixIndexT i = 0; i < num_cols; i++) {
-      Real x_i = xdata[i * incX];
-      if (x_i == 0.0) continue;
-      // Add to ydata, the i'th column of M, times alpha * x_i
-      cblas_Xaxpy(num_rows, x_i * alpha, Mdata + i, stride, ydata, incY);
-    }    
-  } else {
-    if (beta != 1.0) cblas_Xscal(num_cols, beta, ydata, incY);
-    for (MatrixIndexT i = 0; i < num_rows; i++) {
-      Real x_i = xdata[i * incX];
-      if (x_i == 0.0) continue;
-      // Add to ydata, the i'th row of M, times alpha * x_i
-      cblas_Xaxpy(num_cols, x_i * alpha,
-                  Mdata + (i * stride), 1, ydata, incY);
-    }
-  }
-}
-
-inline void cblas_Xgemm(const float alpha,
-                        MatrixTransposeType transA,
-                        const float *Adata,
-                        MatrixIndexT a_num_rows, MatrixIndexT a_num_cols, MatrixIndexT a_stride,
-                        MatrixTransposeType transB, 
-                        const float *Bdata, MatrixIndexT b_stride,
-                        const float beta,
-                        float *Mdata, 
-                        MatrixIndexT num_rows, MatrixIndexT num_cols,MatrixIndexT stride) {
-  cblas_sgemm(CblasRowMajor, static_cast<CBLAS_TRANSPOSE>(transA), 
-              static_cast<CBLAS_TRANSPOSE>(transB),
-              num_rows, num_cols, transA == kNoTrans ? a_num_cols : a_num_rows,
-              alpha, Adata, a_stride, Bdata, b_stride,
-              beta, Mdata, stride); 
-}
-inline void cblas_Xgemm(const double alpha,
-                        MatrixTransposeType transA,
-                        const double *Adata,
-                        MatrixIndexT a_num_rows, MatrixIndexT a_num_cols, MatrixIndexT a_stride,
-                        MatrixTransposeType transB, 
-                        const double *Bdata, MatrixIndexT b_stride,
-                        const double beta,
-                        double *Mdata, 
-                        MatrixIndexT num_rows, MatrixIndexT num_cols,MatrixIndexT stride) {
-  cblas_dgemm(CblasRowMajor, static_cast<CBLAS_TRANSPOSE>(transA), 
-              static_cast<CBLAS_TRANSPOSE>(transB),
-              num_rows, num_cols, transA == kNoTrans ? a_num_cols : a_num_rows,
-              alpha, Adata, a_stride, Bdata, b_stride,
-              beta, Mdata, stride); 
-}
-
-
-inline void cblas_Xsymm(const float alpha,
-                        MatrixIndexT sz,
-                        const float *Adata,MatrixIndexT a_stride,
-                        const float *Bdata,MatrixIndexT b_stride,
-                        const float beta,
-                        float *Mdata, MatrixIndexT stride) {
-  cblas_ssymm(CblasRowMajor, CblasLeft, CblasLower, sz, sz, alpha, Adata,
-              a_stride, Bdata, b_stride, beta, Mdata, stride);
-}
-inline void cblas_Xsymm(const double alpha,
-                        MatrixIndexT sz,
-                        const double *Adata,MatrixIndexT a_stride,
-                        const double *Bdata,MatrixIndexT b_stride,
-                        const double beta,
-                        double *Mdata, MatrixIndexT stride) {
-  cblas_dsymm(CblasRowMajor, CblasLeft, CblasLower, sz, sz, alpha, Adata,
-              a_stride, Bdata, b_stride, beta, Mdata, stride);
-}
-// ger: M += alpha x y^T.
-inline void cblas_Xger(MatrixIndexT num_rows, MatrixIndexT num_cols, float alpha,
-                       const float *xdata, MatrixIndexT incX, const float *ydata,
-                       MatrixIndexT incY, float *Mdata, MatrixIndexT stride) {
-  cblas_sger(CblasRowMajor, num_rows, num_cols, alpha, xdata, 1, ydata, 1,
-             Mdata, stride);
-}
-inline void cblas_Xger(MatrixIndexT num_rows, MatrixIndexT num_cols, double alpha,
-                       const double *xdata, MatrixIndexT incX, const double *ydata,
-                       MatrixIndexT incY, double *Mdata, MatrixIndexT stride) {
-  cblas_dger(CblasRowMajor, num_rows, num_cols, alpha, xdata, 1, ydata, 1,
-             Mdata, stride);
-}
-
-// syrk: symmetric rank-k update.
-// if trans==kNoTrans, then C = alpha A A^T + beta C
-// else C = alpha A^T A + beta C.
-// note: dim_c is dim(C), other_dim_a is the "other" dimension of A, i.e.
-// num-cols(A) if kNoTrans, or num-rows(A) if kTrans.
-// We only need the row-major and lower-triangular option of this, and this
-// is hard-coded.
-inline void cblas_Xsyrk (
-    const MatrixTransposeType trans, const MatrixIndexT dim_c,
-    const MatrixIndexT other_dim_a, const float alpha, const float *A,
-    const MatrixIndexT a_stride, const float beta, float *C,
-    const MatrixIndexT c_stride) {
-  cblas_ssyrk(CblasRowMajor, CblasLower, static_cast<CBLAS_TRANSPOSE>(trans),
-              dim_c, other_dim_a, alpha, A, a_stride, beta, C, c_stride);
-}
-
-inline void cblas_Xsyrk(
-    const MatrixTransposeType trans, const MatrixIndexT dim_c,
-    const MatrixIndexT other_dim_a, const double alpha, const double *A,
-    const MatrixIndexT a_stride, const double beta, double *C,
-    const MatrixIndexT c_stride) {
-  cblas_dsyrk(CblasRowMajor, CblasLower, static_cast<CBLAS_TRANSPOSE>(trans),
-              dim_c, other_dim_a, alpha, A, a_stride, beta, C, c_stride);
-}
-
-/// matrix-vector multiply using a banded matrix; we always call this
-/// with b = 1 meaning we're multiplying by a diagonal matrix.  This is used for
-/// elementwise multiplication.  We miss some of the arguments out of this
-/// wrapper.
-inline void cblas_Xsbmv1(
-    const MatrixIndexT dim,
-    const double *A,
-    const double alpha,
-    const double *x,
-    const double beta,
-    double *y) {
-  cblas_dsbmv(CblasRowMajor, CblasLower, dim, 0, alpha, A,
-              1, x, 1, beta, y, 1);
-}
-
-inline void cblas_Xsbmv1(
-    const MatrixIndexT dim,
-    const float *A,
-    const float alpha,
-    const float *x,
-    const float beta,
-    float *y) {
-  cblas_ssbmv(CblasRowMajor, CblasLower, dim, 0, alpha, A,
-              1, x, 1, beta, y, 1);
-}
-
-
-/// This is not really a wrapper for CBLAS as CBLAS does not have this; in future we could
-/// extend this somehow.
-inline void mul_elements(
-    const MatrixIndexT dim,
-    const double *a,
-    double *b) { // does b *= a, elementwise.
-  double c1, c2, c3, c4;
-  MatrixIndexT i;
-  for (i = 0; i + 4 <= dim; i += 4) {
-    c1 = a[i] * b[i];
-    c2 = a[i+1] * b[i+1];
-    c3 = a[i+2] * b[i+2];
-    c4 = a[i+3] * b[i+3];
-    b[i] = c1;
-    b[i+1] = c2;
-    b[i+2] = c3;
-    b[i+3] = c4;
-  }
-  for (; i < dim; i++)
-    b[i] *= a[i];
-}
-
-inline void mul_elements(
-    const MatrixIndexT dim,
-    const float *a,
-    float *b) { // does b *= a, elementwise.
-  float c1, c2, c3, c4;
-  MatrixIndexT i;
-  for (i = 0; i + 4 <= dim; i += 4) {
-    c1 = a[i] * b[i];
-    c2 = a[i+1] * b[i+1];
-    c3 = a[i+2] * b[i+2];
-    c4 = a[i+3] * b[i+3];
-    b[i] = c1;
-    b[i+1] = c2;
-    b[i+2] = c3;
-    b[i+3] = c4;
-  }
-  for (; i < dim; i++)
-    b[i] *= a[i];
-}
-
-
-
-// add clapack here
-#if !defined(HAVE_ATLAS)
-inline void clapack_Xtptri(KaldiBlasInt *num_rows, float *Mdata, KaldiBlasInt *result) {
-  stptri_(const_cast<char *>("U"), const_cast<char *>("N"), num_rows, Mdata, result);
-}
-inline void clapack_Xtptri(KaldiBlasInt *num_rows, double *Mdata, KaldiBlasInt *result) {
-  dtptri_(const_cast<char *>("U"), const_cast<char *>("N"), num_rows, Mdata, result);
-}
-// 
-inline void clapack_Xgetrf2(KaldiBlasInt *num_rows, KaldiBlasInt *num_cols, 
-                            float *Mdata, KaldiBlasInt *stride, KaldiBlasInt *pivot, 
-                            KaldiBlasInt *result) {
-  sgetrf_(num_rows, num_cols, Mdata, stride, pivot, result);
-}
-inline void clapack_Xgetrf2(KaldiBlasInt *num_rows, KaldiBlasInt *num_cols, 
-                            double *Mdata, KaldiBlasInt *stride, KaldiBlasInt *pivot, 
-                            KaldiBlasInt *result) {
-  dgetrf_(num_rows, num_cols, Mdata, stride, pivot, result);
-}
-
-// 
-inline void clapack_Xgetri2(KaldiBlasInt *num_rows, float *Mdata, KaldiBlasInt *stride,
-                           KaldiBlasInt *pivot, float *p_work, 
-                           KaldiBlasInt *l_work, KaldiBlasInt *result) {
-  sgetri_(num_rows, Mdata, stride, pivot, p_work, l_work, result);
-}
-inline void clapack_Xgetri2(KaldiBlasInt *num_rows, double *Mdata, KaldiBlasInt *stride,
-                           KaldiBlasInt *pivot, double *p_work, 
-                           KaldiBlasInt *l_work, KaldiBlasInt *result) {
-  dgetri_(num_rows, Mdata, stride, pivot, p_work, l_work, result);
-}
-//
-inline void clapack_Xgesvd(char *v, char *u, KaldiBlasInt *num_cols,
-                           KaldiBlasInt *num_rows, float *Mdata, KaldiBlasInt *stride,
-                           float *sv, float *Vdata, KaldiBlasInt *vstride,
-                           float *Udata, KaldiBlasInt *ustride, float *p_work,
-                           KaldiBlasInt *l_work, KaldiBlasInt *result) {
-  sgesvd_(v, u,
-          num_cols, num_rows, Mdata, stride,
-          sv, Vdata, vstride, Udata, ustride, 
-          p_work, l_work, result); 
-}
-inline void clapack_Xgesvd(char *v, char *u, KaldiBlasInt *num_cols,
-                           KaldiBlasInt *num_rows, double *Mdata, KaldiBlasInt *stride,
-                           double *sv, double *Vdata, KaldiBlasInt *vstride,
-                           double *Udata, KaldiBlasInt *ustride, double *p_work,
-                           KaldiBlasInt *l_work, KaldiBlasInt *result) {
-  dgesvd_(v, u,
-          num_cols, num_rows, Mdata, stride,
-          sv, Vdata, vstride, Udata, ustride,
-          p_work, l_work, result); 
-}
-//
-void inline clapack_Xsptri(KaldiBlasInt *num_rows, float *Mdata, 
-                           KaldiBlasInt *ipiv, float *work, KaldiBlasInt *result) {
-  ssptri_(const_cast<char *>("U"), num_rows, Mdata, ipiv, work, result);
-}
-void inline clapack_Xsptri(KaldiBlasInt *num_rows, double *Mdata, 
-                           KaldiBlasInt *ipiv, double *work, KaldiBlasInt *result) {
-  dsptri_(const_cast<char *>("U"), num_rows, Mdata, ipiv, work, result);
-}
-//
-void inline clapack_Xsptrf(KaldiBlasInt *num_rows, float *Mdata,
-                           KaldiBlasInt *ipiv, KaldiBlasInt *result) {
-  ssptrf_(const_cast<char *>("U"), num_rows, Mdata, ipiv, result);
-}
-void inline clapack_Xsptrf(KaldiBlasInt *num_rows, double *Mdata,
-                           KaldiBlasInt *ipiv, KaldiBlasInt *result) {
-  dsptrf_(const_cast<char *>("U"), num_rows, Mdata, ipiv, result);
-}
-#else
-inline void clapack_Xgetrf(MatrixIndexT num_rows, MatrixIndexT num_cols,
-                           float *Mdata, MatrixIndexT stride, 
-                           int *pivot, int *result) {
-  *result = clapack_sgetrf(CblasColMajor, num_rows, num_cols,
-                              Mdata, stride, pivot);
-}
-
-inline void clapack_Xgetrf(MatrixIndexT num_rows, MatrixIndexT num_cols,
-                           double *Mdata, MatrixIndexT stride, 
-                           int *pivot, int *result) {
-  *result = clapack_dgetrf(CblasColMajor, num_rows, num_cols,
-                              Mdata, stride, pivot);
-}
-//
-inline int clapack_Xtrtri(int num_rows, float *Mdata, MatrixIndexT stride) {
-  return  clapack_strtri(CblasColMajor, CblasUpper, CblasNonUnit, num_rows,
-                              Mdata, stride);
-}
-
-inline int clapack_Xtrtri(int num_rows, double *Mdata, MatrixIndexT stride) {
-  return  clapack_dtrtri(CblasColMajor, CblasUpper, CblasNonUnit, num_rows,
-                              Mdata, stride);
-}
-//
-inline void clapack_Xgetri(MatrixIndexT num_rows, float *Mdata, MatrixIndexT stride,
-                      int *pivot, int *result) {
-  *result = clapack_sgetri(CblasColMajor, num_rows, Mdata, stride, pivot);
-}
-inline void clapack_Xgetri(MatrixIndexT num_rows, double *Mdata, MatrixIndexT stride,
-                      int *pivot, int *result) {
-  *result = clapack_dgetri(CblasColMajor, num_rows, Mdata, stride, pivot);
-}
-#endif
-
-}
-// namespace kaldi
-
-#endif
diff --git a/kaldi_io/src/kaldi/matrix/compressed-matrix.h b/kaldi_io/src/kaldi/matrix/compressed-matrix.h
deleted file mode 100644
index 746cab3..0000000
--- a/kaldi_io/src/kaldi/matrix/compressed-matrix.h
+++ /dev/null
@@ -1,179 +0,0 @@
-// matrix/compressed-matrix.h
-
-// Copyright 2012  Johns Hopkins University (author: Daniel Povey)
-//                 Frantisek Skala, Wei Shi
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_MATRIX_COMPRESSED_MATRIX_H_
-#define KALDI_MATRIX_COMPRESSED_MATRIX_H_ 1
-
-#include "kaldi-matrix.h"
-
-namespace kaldi {
-
-/// \addtogroup matrix_group
-/// @{
-
-/// This class does lossy compression of a matrix.  It only
-/// supports copying to-from a KaldiMatrix.  For large matrices,
-/// each element is compressed into about one byte, but there
-/// is a little overhead on top of that (globally, and also per
-/// column).
-
-/// The basic idea is for each column (in the normal configuration)
-/// we work out the values at the 0th, 25th, 50th and 100th percentiles
-/// and store them as 16-bit integers; we then encode each value in
-/// the column as a single byte, in 3 separate ranges with different
-/// linear encodings (0-25th, 25-50th, 50th-100th).
-/// If the matrix has 8 rows or fewer, we simply store all values as
-/// uint16.
-
-class CompressedMatrix {
- public:
-  CompressedMatrix(): data_(NULL) { }
-
-  ~CompressedMatrix() { Destroy(); }
-  
-  template<typename Real>
-  CompressedMatrix(const MatrixBase<Real> &mat): data_(NULL) { CopyFromMat(mat); }
-
-  /// Initializer that can be used to select part of an existing
-  /// CompressedMatrix without un-compressing and re-compressing (note: unlike
-  /// similar initializers for class Matrix, it doesn't point to the same memory
-  /// location).
-  CompressedMatrix(const CompressedMatrix &mat,
-                   const MatrixIndexT row_offset,
-                   const MatrixIndexT num_rows,
-                   const MatrixIndexT col_offset,
-                   const MatrixIndexT num_cols);
-
-  void *Data() const { return this->data_; }
-
-  /// This will resize *this and copy the contents of mat to *this.
-  template<typename Real>
-  void CopyFromMat(const MatrixBase<Real> &mat);
-
-  CompressedMatrix(const CompressedMatrix &mat);
-
-  CompressedMatrix &operator = (const CompressedMatrix &mat); // assignment operator.
-
-  template<typename Real>
-  CompressedMatrix &operator = (const MatrixBase<Real> &mat); // assignment operator.
-  
-  /// Copies contents to matrix.  Note: mat must have the correct size,
-  /// CopyToMat no longer attempts to resize it.
-  template<typename Real>
-  void CopyToMat(MatrixBase<Real> *mat) const;
-
-  void Write(std::ostream &os, bool binary) const;
-  
-  void Read(std::istream &is, bool binary);
-
-  /// Returns number of rows (or zero for emtpy matrix).
-  inline MatrixIndexT NumRows() const { return (data_ == NULL) ? 0 :
-      (*reinterpret_cast<GlobalHeader*>(data_)).num_rows; }
-
-  /// Returns number of columns (or zero for emtpy matrix).
-  inline MatrixIndexT NumCols() const { return (data_ == NULL) ? 0 :
-      (*reinterpret_cast<GlobalHeader*>(data_)).num_cols; }
-
-  /// Copies row #row of the matrix into vector v.
-  /// Note: v must have same size as #cols.
-  template<typename Real>
-  void CopyRowToVec(MatrixIndexT row, VectorBase<Real> *v) const;
-
-  /// Copies column #col of the matrix into vector v.
-  /// Note: v must have same size as #rows.
-  template<typename Real>
-  void CopyColToVec(MatrixIndexT col, VectorBase<Real> *v) const;
-
-  /// Copies submatrix of compressed matrix into matrix dest.
-  /// Submatrix starts at row row_offset and column column_offset and its size
-  /// is defined by size of provided matrix dest
-  template<typename Real>
-  void CopyToMat(int32 row_offset,
-                 int32 column_offset,
-                 MatrixBase<Real> *dest) const;
-
-  void Swap(CompressedMatrix *other) { std::swap(data_, other->data_); }
-  
-  friend class Matrix<float>;
-  friend class Matrix<double>;
- private:
-
-  // allocates data using new [], ensures byte alignment
-  // sufficient for float.
-  static void *AllocateData(int32 num_bytes);
-
-  // the "format" will be 1 for the original format where each column has a
-  // PerColHeader, and 2 for the format now used for matrices with 8 or fewer
-  // rows, where everything is represented as 16-bit integers.
-  struct GlobalHeader {
-    int32 format;
-    float min_value;
-    float range;
-    int32 num_rows;
-    int32 num_cols;
-  };
-
-  static MatrixIndexT DataSize(const GlobalHeader &header);
-
-  struct PerColHeader {
-    uint16 percentile_0;
-    uint16 percentile_25;
-    uint16 percentile_75;
-    uint16 percentile_100;
-  };
-
-  template<typename Real>
-  static void CompressColumn(const GlobalHeader &global_header,
-                             const Real *data, MatrixIndexT stride,
-                             int32 num_rows, PerColHeader *header,
-                             unsigned char *byte_data);
-  template<typename Real>
-  static void ComputeColHeader(const GlobalHeader &global_header,
-                               const Real *data, MatrixIndexT stride,
-                               int32 num_rows, PerColHeader *header);
-
-  static inline uint16 FloatToUint16(const GlobalHeader &global_header,
-                                     float value);
-
-  static inline float Uint16ToFloat(const GlobalHeader &global_header,
-                                    uint16 value);
-  static inline unsigned char FloatToChar(float p0, float p25,
-                                          float p75, float p100,
-                                          float value);
-  static inline float CharToFloat(float p0, float p25,
-                                  float p75, float p100,
-                                  unsigned char value);
-  
-  void Destroy();
-  
-  void *data_; // first GlobalHeader, then PerColHeader (repeated), then
-  // the byte data for each column (repeated).  Note: don't intersperse
-  // the byte data with the PerColHeaders, because of alignment issues.
-
-};
-
-
-/// @} end of \addtogroup matrix_group
-
-
-}  // namespace kaldi
-
-
-#endif  // KALDI_MATRIX_COMPRESSED_MATRIX_H_
diff --git a/kaldi_io/src/kaldi/matrix/jama-eig.h b/kaldi_io/src/kaldi/matrix/jama-eig.h
deleted file mode 100644
index c7278bc..0000000
--- a/kaldi_io/src/kaldi/matrix/jama-eig.h
+++ /dev/null
@@ -1,924 +0,0 @@
-// matrix/jama-eig.h
-
-// Copyright 2009-2011 Microsoft Corporation 
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-
-//  http://www.apache.org/licenses/LICENSE-2.0
-
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-// This file consists of a port and modification of materials from
-//   JAMA: A Java Matrix Package
-// under the following notice: This software is a cooperative product of
-// The MathWorks and the National Institute of Standards and Technology (NIST)
-// which has been released to the public.  This notice and the original code are
-// available at http://math.nist.gov/javanumerics/jama/domain.notice
-
-
-
-#ifndef KALDI_MATRIX_JAMA_EIG_H_
-#define KALDI_MATRIX_JAMA_EIG_H_ 1
-
-#include "matrix/kaldi-matrix.h"
-
-namespace kaldi {
-
-// This class is not to be used externally.  See the Eig function in the Matrix
-// class in kaldi-matrix.h.  This is the external interface.
-
-template<typename Real> class EigenvalueDecomposition {
-  // This class is based on the EigenvalueDecomposition class from the JAMA
-  // library (version 1.0.2).
- public:
-  EigenvalueDecomposition(const MatrixBase<Real> &A);
-
-  ~EigenvalueDecomposition();  // free memory.
-
-  void GetV(MatrixBase<Real> *V_out) {  // V is what we call P externally; it's the matrix of
-    // eigenvectors.
-    KALDI_ASSERT(V_out->NumRows() == static_cast<MatrixIndexT>(n_)
-                 && V_out->NumCols() == static_cast<MatrixIndexT>(n_));
-    for (int i = 0; i < n_; i++)
-      for (int j = 0; j < n_; j++)
-        (*V_out)(i, j) = V(i, j);  // V(i, j) is member function.
-  }
-  void GetRealEigenvalues(VectorBase<Real> *r_out) {
-    // returns real part of eigenvalues.
-    KALDI_ASSERT(r_out->Dim() == static_cast<MatrixIndexT>(n_));
-    for (int i = 0; i < n_; i++)
-      (*r_out)(i) = d_[i];
-  }
-  void GetImagEigenvalues(VectorBase<Real> *i_out) {
-    // returns imaginary part of eigenvalues.
-    KALDI_ASSERT(i_out->Dim() == static_cast<MatrixIndexT>(n_));
-    for (int i = 0; i < n_; i++)
-      (*i_out)(i) = e_[i];
-  }
- private:
-
-  inline Real &H(int r, int c) { return H_[r*n_ + c]; }
-  inline Real &V(int r, int c) { return V_[r*n_ + c]; }
-
-  // complex division
-  inline static void cdiv(Real xr, Real xi, Real yr, Real yi, Real *cdivr, Real *cdivi) {
-    Real r, d;
-    if (std::abs(yr) > std::abs(yi)) {
-      r = yi/yr;
-      d = yr + r*yi;
-      *cdivr = (xr + r*xi)/d;
-      *cdivi = (xi - r*xr)/d;
-    } else {
-      r = yr/yi;
-      d = yi + r*yr;
-      *cdivr = (r*xr + xi)/d;
-      *cdivi = (r*xi - xr)/d;
-    }
-  }
-
-  // Nonsymmetric reduction from Hessenberg to real Schur form.
-  void Hqr2 ();
-
-
-  int n_;  // matrix dimension.
-
-  Real *d_, *e_;  // real and imaginary parts of eigenvalues.
-  Real *V_;  // the eigenvectors (P in our external notation)
-  Real *H_;  // the nonsymmetric Hessenberg form.
-  Real *ort_;  // working storage for nonsymmetric algorithm.
-
-  // Symmetric Householder reduction to tridiagonal form.
-  void Tred2 ();
-
-  // Symmetric tridiagonal QL algorithm.
-  void Tql2 ();
-
-  // Nonsymmetric reduction to Hessenberg form.
-  void Orthes ();
-
-};
-
-template class EigenvalueDecomposition<float>;  // force instantiation.
-template class EigenvalueDecomposition<double>;  // force instantiation.
-
-template<typename Real> void  EigenvalueDecomposition<Real>::Tred2() {
-  //  This is derived from the Algol procedures tred2 by
-  //  Bowdler, Martin, Reinsch, and Wilkinson, Handbook for
-  //  Auto. Comp., Vol.ii-Linear Algebra, and the corresponding
-  //  Fortran subroutine in EISPACK.
-
-  for (int j = 0; j < n_; j++) {
-    d_[j] = V(n_-1, j);
-  }
-
-  // Householder reduction to tridiagonal form.
-
-  for (int i = n_-1; i > 0; i--) {
-
-    // Scale to avoid under/overflow.
-
-    Real scale = 0.0;
-    Real h = 0.0;
-    for (int k = 0; k < i; k++) {
-      scale = scale + std::abs(d_[k]);
-    }
-    if (scale == 0.0) {
-      e_[i] = d_[i-1];
-      for (int j = 0; j < i; j++) {
-        d_[j] = V(i-1, j);
-        V(i, j) = 0.0;
-        V(j, i) = 0.0;
-      }
-    } else {
-
-      // Generate Householder vector.
-
-      for (int k = 0; k < i; k++) {
-        d_[k] /= scale;
-        h += d_[k] * d_[k];
-      }
-      Real f = d_[i-1];
-      Real g = std::sqrt(h);
-      if (f > 0) {
-        g = -g;
-      }
-      e_[i] = scale * g;
-      h = h - f * g;
-      d_[i-1] = f - g;
-      for (int j = 0; j < i; j++) {
-        e_[j] = 0.0;
-      }
-
-      // Apply similarity transformation to remaining columns.
-
-      for (int j = 0; j < i; j++) {
-        f = d_[j];
-        V(j, i) = f;
-        g =e_[j] + V(j, j) * f;
-        for (int k = j+1; k <= i-1; k++) {
-          g += V(k, j) * d_[k];
-          e_[k] += V(k, j) * f;
-        }
-        e_[j] = g;
-      }
-      f = 0.0;
-      for (int j = 0; j < i; j++) {
-        e_[j] /= h;
-        f += e_[j] * d_[j];
-      }
-      Real hh = f / (h + h);
-      for (int j = 0; j < i; j++) {
-        e_[j] -= hh * d_[j];
-      }
-      for (int j = 0; j < i; j++) {
-        f = d_[j];
-        g = e_[j];
-        for (int k = j; k <= i-1; k++) {
-          V(k, j) -= (f * e_[k] + g * d_[k]);
-        }
-        d_[j] = V(i-1, j);
-        V(i, j) = 0.0;
-      }
-    }
-    d_[i] = h;
-  }
-
-  // Accumulate transformations.
-
-  for (int i = 0; i < n_-1; i++) {
-    V(n_-1, i) = V(i, i);
-    V(i, i) = 1.0;
-    Real h = d_[i+1];
-    if (h != 0.0) {
-      for (int k = 0; k <= i; k++) {
-        d_[k] = V(k, i+1) / h;
-      }
-      for (int j = 0; j <= i; j++) {
-        Real g = 0.0;
-        for (int k = 0; k <= i; k++) {
-          g += V(k, i+1) * V(k, j);
-        }
-        for (int k = 0; k <= i; k++) {
-          V(k, j) -= g * d_[k];
-        }
-      }
-    }
-    for (int k = 0; k <= i; k++) {
-      V(k, i+1) = 0.0;
-    }
-  }
-  for (int j = 0; j < n_; j++) {
-    d_[j] = V(n_-1, j);
-    V(n_-1, j) = 0.0;
-  }
-  V(n_-1, n_-1) = 1.0;
-   e_[0] = 0.0;
-}
-
-template<typename Real> void EigenvalueDecomposition<Real>::Tql2() {
-  //  This is derived from the Algol procedures tql2, by
-  //  Bowdler, Martin, Reinsch, and Wilkinson, Handbook for
-  //  Auto. Comp., Vol.ii-Linear Algebra, and the corresponding
-  //  Fortran subroutine in EISPACK.
-
-  for (int i = 1; i < n_; i++) {
-     e_[i-1] = e_[i];
-  }
-   e_[n_-1] = 0.0;
-
-  Real f = 0.0;
-  Real tst1 = 0.0;
-  Real eps = std::numeric_limits<Real>::epsilon();
-  for (int l = 0; l < n_; l++) {
-
-    // Find small subdiagonal element
-
-    tst1 = std::max(tst1, std::abs(d_[l]) + std::abs(e_[l]));
-    int m = l;
-    while (m < n_) {
-      if (std::abs(e_[m]) <= eps*tst1) {
-        break;
-      }
-      m++;
-    }
-
-    // If m == l, d_[l] is an eigenvalue,
-    // otherwise, iterate.
-
-    if (m > l) {
-      int iter = 0;
-      do {
-        iter = iter + 1;  // (Could check iteration count here.)
-
-        // Compute implicit shift
-
-        Real g = d_[l];
-        Real p = (d_[l+1] - g) / (2.0 *e_[l]);
-        Real r = Hypot(p, static_cast<Real>(1.0));  // This is a Kaldi version of hypot that works with templates.
-        if (p < 0) {
-          r = -r;
-        }
-        d_[l] =e_[l] / (p + r);
-        d_[l+1] =e_[l] * (p + r);
-        Real dl1 = d_[l+1];
-        Real h = g - d_[l];
-        for (int i = l+2; i < n_; i++) {
-          d_[i] -= h;
-        }
-        f = f + h;
-
-        // Implicit QL transformation.
-
-        p = d_[m];
-        Real c = 1.0;
-        Real c2 = c;
-        Real c3 = c;
-        Real el1 =e_[l+1];
-        Real s = 0.0;
-        Real s2 = 0.0;
-        for (int i = m-1; i >= l; i--) {
-          c3 = c2;
-          c2 = c;
-          s2 = s;
-          g = c *e_[i];
-          h = c * p;
-          r = Hypot(p, e_[i]);  // This is a Kaldi version of Hypot that works with templates.
-          e_[i+1] = s * r;
-          s =e_[i] / r;
-          c = p / r;
-          p = c * d_[i] - s * g;
-          d_[i+1] = h + s * (c * g + s * d_[i]);
-
-          // Accumulate transformation.
-
-          for (int k = 0; k < n_; k++) {
-            h = V(k, i+1);
-            V(k, i+1) = s * V(k, i) + c * h;
-            V(k, i) = c * V(k, i) - s * h;
-          }
-        }
-        p = -s * s2 * c3 * el1 *e_[l] / dl1;
-        e_[l] = s * p;
-        d_[l] = c * p;
-
-        // Check for convergence.
-
-      } while (std::abs(e_[l]) > eps*tst1);
-    }
-    d_[l] = d_[l] + f;
-    e_[l] = 0.0;
-  }
-
-  // Sort eigenvalues and corresponding vectors.
-
-  for (int i = 0; i < n_-1; i++) {
-    int k = i;
-    Real p = d_[i];
-    for (int j = i+1; j < n_; j++) {
-      if (d_[j] < p) {
-        k = j;
-        p = d_[j];
-      }
-    }
-    if (k != i) {
-      d_[k] = d_[i];
-      d_[i] = p;
-      for (int j = 0; j < n_; j++) {
-        p = V(j, i);
-        V(j, i) = V(j, k);
-        V(j, k) = p;
-      }
-    }
-  }
-}
-
-template<typename Real>
-void EigenvalueDecomposition<Real>::Orthes() {
-
-  //  This is derived from the Algol procedures orthes and ortran,
-  //  by Martin and Wilkinson, Handbook for Auto. Comp.,
-  //  Vol.ii-Linear Algebra, and the corresponding
-  //  Fortran subroutines in EISPACK.
-
-  int low = 0;
-  int high = n_-1;
-
-  for (int m = low+1; m <= high-1; m++) {
-
-    // Scale column.
-
-    Real scale = 0.0;
-    for (int i = m; i <= high; i++) {
-      scale = scale + std::abs(H(i, m-1));
-    }
-    if (scale != 0.0) {
-
-      // Compute Householder transformation.
-
-      Real h = 0.0;
-      for (int i = high; i >= m; i--) {
-        ort_[i] = H(i, m-1)/scale;
-        h += ort_[i] * ort_[i];
-      }
-      Real g = std::sqrt(h);
-      if (ort_[m] > 0) {
-        g = -g;
-      }
-      h = h - ort_[m] * g;
-      ort_[m] = ort_[m] - g;
-
-      // Apply Householder similarity transformation
-      // H = (I-u*u'/h)*H*(I-u*u')/h)
-
-      for (int j = m; j < n_; j++) {
-        Real f = 0.0;
-        for (int i = high; i >= m; i--) {
-          f += ort_[i]*H(i, j);
-        }
-        f = f/h;
-        for (int i = m; i <= high; i++) {
-          H(i, j) -= f*ort_[i];
-        }
-      }
-
-      for (int i = 0; i <= high; i++) {
-        Real f = 0.0;
-        for (int j = high; j >= m; j--) {
-          f += ort_[j]*H(i, j);
-        }
-        f = f/h;
-        for (int j = m; j <= high; j++) {
-          H(i, j) -= f*ort_[j];
-        }
-      }
-      ort_[m] = scale*ort_[m];
-      H(m, m-1) = scale*g;
-    }
-  }
-
-  // Accumulate transformations (Algol's ortran).
-
-  for (int i = 0; i < n_; i++) {
-    for (int j = 0; j < n_; j++) {
-      V(i, j) = (i == j ? 1.0 : 0.0);
-    }
-  }
-
-  for (int m = high-1; m >= low+1; m--) {
-    if (H(m, m-1) != 0.0) {
-      for (int i = m+1; i <= high; i++) {
-        ort_[i] = H(i, m-1);
-      }
-      for (int j = m; j <= high; j++) {
-        Real g = 0.0;
-        for (int i = m; i <= high; i++) {
-          g += ort_[i] * V(i, j);
-        }
-        // Double division avoids possible underflow
-        g = (g / ort_[m]) / H(m, m-1);
-        for (int i = m; i <= high; i++) {
-          V(i, j) += g * ort_[i];
-        }
-      }
-    }
-  }
-}
-
-template<typename Real> void  EigenvalueDecomposition<Real>::Hqr2() {
-  //  This is derived from the Algol procedure hqr2,
-  //  by Martin and Wilkinson, Handbook for Auto. Comp.,
-  //  Vol.ii-Linear Algebra, and the corresponding
-  //  Fortran subroutine in EISPACK.
-
-  int nn = n_;
-  int n = nn-1;
-  int low = 0;
-  int high = nn-1;
-  Real eps = std::numeric_limits<Real>::epsilon();
-  Real exshift = 0.0;
-  Real p = 0, q = 0, r = 0, s = 0, z=0, t, w, x, y;
-
-  // Store roots isolated by balanc and compute matrix norm
-
-  Real norm = 0.0;
-  for (int i = 0; i < nn; i++) {
-    if (i < low || i > high) {
-      d_[i] = H(i, i);
-      e_[i] = 0.0;
-    }
-    for (int j = std::max(i-1, 0); j < nn; j++) {
-      norm = norm + std::abs(H(i, j));
-    }
-  }
-
-  // Outer loop over eigenvalue index
-
-  int iter = 0;
-  while (n >= low) {
-
-    // Look for single small sub-diagonal element
-
-    int l = n;
-    while (l > low) {
-      s = std::abs(H(l-1, l-1)) + std::abs(H(l, l));
-      if (s == 0.0) {
-        s = norm;
-      }
-      if (std::abs(H(l, l-1)) < eps * s) {
-        break;
-      }
-      l--;
-    }
-
-    // Check for convergence
-    // One root found
-
-    if (l == n) {
-      H(n, n) = H(n, n) + exshift;
-      d_[n] = H(n, n);
-      e_[n] = 0.0;
-      n--;
-      iter = 0;
-
-      // Two roots found
-
-    } else if (l == n-1) {
-      w = H(n, n-1) * H(n-1, n);
-      p = (H(n-1, n-1) - H(n, n)) / 2.0;
-      q = p * p + w;
-      z = std::sqrt(std::abs(q));
-      H(n, n) = H(n, n) + exshift;
-      H(n-1, n-1) = H(n-1, n-1) + exshift;
-      x = H(n, n);
-
-      // Real pair
-
-      if (q >= 0) {
-        if (p >= 0) {
-          z = p + z;
-        } else {
-          z = p - z;
-        }
-        d_[n-1] = x + z;
-        d_[n] = d_[n-1];
-        if (z != 0.0) {
-          d_[n] = x - w / z;
-        }
-        e_[n-1] = 0.0;
-        e_[n] = 0.0;
-        x = H(n, n-1);
-        s = std::abs(x) + std::abs(z);
-        p = x / s;
-        q = z / s;
-        r = std::sqrt(p * p+q * q);
-        p = p / r;
-        q = q / r;
-
-        // Row modification
-
-        for (int j = n-1; j < nn; j++) {
-          z = H(n-1, j);
-          H(n-1, j) = q * z + p * H(n, j);
-          H(n, j) = q * H(n, j) - p * z;
-        }
-
-        // Column modification
-
-        for (int i = 0; i <= n; i++) {
-          z = H(i, n-1);
-          H(i, n-1) = q * z + p * H(i, n);
-          H(i, n) = q * H(i, n) - p * z;
-        }
-
-        // Accumulate transformations
-
-        for (int i = low; i <= high; i++) {
-          z = V(i, n-1);
-          V(i, n-1) = q * z + p * V(i, n);
-          V(i, n) = q * V(i, n) - p * z;
-        }
-
-        // Complex pair
-
-      } else {
-        d_[n-1] = x + p;
-        d_[n] = x + p;
-        e_[n-1] = z;
-        e_[n] = -z;
-      }
-      n = n - 2;
-      iter = 0;
-
-      // No convergence yet
-
-    } else {
-
-      // Form shift
-
-      x = H(n, n);
-      y = 0.0;
-      w = 0.0;
-      if (l < n) {
-        y = H(n-1, n-1);
-        w = H(n, n-1) * H(n-1, n);
-      }
-
-      // Wilkinson's original ad hoc shift
-
-      if (iter == 10) {
-        exshift += x;
-        for (int i = low; i <= n; i++) {
-          H(i, i) -= x;
-        }
-        s = std::abs(H(n, n-1)) + std::abs(H(n-1, n-2));
-        x = y = 0.75 * s;
-        w = -0.4375 * s * s;
-      }
-
-      // MATLAB's new ad hoc shift
-
-      if (iter == 30) {
-        s = (y - x) / 2.0;
-        s = s * s + w;
-        if (s > 0) {
-          s = std::sqrt(s);
-          if (y < x) {
-            s = -s;
-          }
-          s = x - w / ((y - x) / 2.0 + s);
-          for (int i = low; i <= n; i++) {
-            H(i, i) -= s;
-          }
-          exshift += s;
-          x = y = w = 0.964;
-        }
-      }
-
-      iter = iter + 1;   // (Could check iteration count here.)
-
-      // Look for two consecutive small sub-diagonal elements
-
-      int m = n-2;
-      while (m >= l) {
-        z = H(m, m);
-        r = x - z;
-        s = y - z;
-        p = (r * s - w) / H(m+1, m) + H(m, m+1);
-        q = H(m+1, m+1) - z - r - s;
-        r = H(m+2, m+1);
-        s = std::abs(p) + std::abs(q) + std::abs(r);
-        p = p / s;
-        q = q / s;
-        r = r / s;
-        if (m == l) {
-          break;
-        }
-        if (std::abs(H(m, m-1)) * (std::abs(q) + std::abs(r)) <
-            eps * (std::abs(p) * (std::abs(H(m-1, m-1)) + std::abs(z) +
-                                  std::abs(H(m+1, m+1))))) {
-          break;
-        }
-        m--;
-      }
-
-      for (int i = m+2; i <= n; i++) {
-        H(i, i-2) = 0.0;
-        if (i > m+2) {
-          H(i, i-3) = 0.0;
-        }
-      }
-
-      // Double QR step involving rows l:n and columns m:n
-
-      for (int k = m; k <= n-1; k++) {
-        bool notlast = (k != n-1);
-        if (k != m) {
-          p = H(k, k-1);
-          q = H(k+1, k-1);
-          r = (notlast ? H(k+2, k-1) : 0.0);
-          x = std::abs(p) + std::abs(q) + std::abs(r);
-          if (x != 0.0) {
-            p = p / x;
-            q = q / x;
-            r = r / x;
-          }
-        }
-        if (x == 0.0) {
-          break;
-        }
-        s = std::sqrt(p * p + q * q + r * r);
-        if (p < 0) {
-          s = -s;
-        }
-        if (s != 0) {
-          if (k != m) {
-            H(k, k-1) = -s * x;
-          } else if (l != m) {
-            H(k, k-1) = -H(k, k-1);
-          }
-          p = p + s;
-          x = p / s;
-          y = q / s;
-          z = r / s;
-          q = q / p;
-          r = r / p;
-
-          // Row modification
-
-          for (int j = k; j < nn; j++) {
-            p = H(k, j) + q * H(k+1, j);
-            if (notlast) {
-              p = p + r * H(k+2, j);
-              H(k+2, j) = H(k+2, j) - p * z;
-            }
-            H(k, j) = H(k, j) - p * x;
-            H(k+1, j) = H(k+1, j) - p * y;
-          }
-
-          // Column modification
-
-          for (int i = 0; i <= std::min(n, k+3); i++) {
-            p = x * H(i, k) + y * H(i, k+1);
-            if (notlast) {
-              p = p + z * H(i, k+2);
-              H(i, k+2) = H(i, k+2) - p * r;
-            }
-            H(i, k) = H(i, k) - p;
-            H(i, k+1) = H(i, k+1) - p * q;
-          }
-
-          // Accumulate transformations
-
-          for (int i = low; i <= high; i++) {
-            p = x * V(i, k) + y * V(i, k+1);
-            if (notlast) {
-              p = p + z * V(i, k+2);
-              V(i, k+2) = V(i, k+2) - p * r;
-            }
-            V(i, k) = V(i, k) - p;
-            V(i, k+1) = V(i, k+1) - p * q;
-          }
-        }  // (s != 0)
-      }  // k loop
-    }  // check convergence
-  }  // while (n >= low)
-
-  // Backsubstitute to find vectors of upper triangular form
-
-  if (norm == 0.0) {
-    return;
-  }
-
-  for (n = nn-1; n >= 0; n--) {
-    p = d_[n];
-    q = e_[n];
-
-    // Real vector
-
-    if (q == 0) {
-      int l = n;
-      H(n, n) = 1.0;
-      for (int i = n-1; i >= 0; i--) {
-        w = H(i, i) - p;
-        r = 0.0;
-        for (int j = l; j <= n; j++) {
-          r = r + H(i, j) * H(j, n);
-        }
-        if (e_[i] < 0.0) {
-          z = w;
-          s = r;
-        } else {
-          l = i;
-          if (e_[i] == 0.0) {
-            if (w != 0.0) {
-              H(i, n) = -r / w;
-            } else {
-              H(i, n) = -r / (eps * norm);
-            }
-
-            // Solve real equations
-
-          } else {
-            x = H(i, i+1);
-            y = H(i+1, i);
-            q = (d_[i] - p) * (d_[i] - p) +e_[i] *e_[i];
-            t = (x * s - z * r) / q;
-            H(i, n) = t;
-            if (std::abs(x) > std::abs(z)) {
-              H(i+1, n) = (-r - w * t) / x;
-            } else {
-              H(i+1, n) = (-s - y * t) / z;
-            }
-          }
-
-          // Overflow control
-
-          t = std::abs(H(i, n));
-          if ((eps * t) * t > 1) {
-            for (int j = i; j <= n; j++) {
-              H(j, n) = H(j, n) / t;
-            }
-          }
-        }
-      }
-
-      // Complex vector
-
-    } else if (q < 0) {
-      int l = n-1;
-
-      // Last vector component imaginary so matrix is triangular
-
-      if (std::abs(H(n, n-1)) > std::abs(H(n-1, n))) {
-        H(n-1, n-1) = q / H(n, n-1);
-        H(n-1, n) = -(H(n, n) - p) / H(n, n-1);
-      } else {
-        Real cdivr, cdivi;
-        cdiv(0.0, -H(n-1, n), H(n-1, n-1)-p, q, &cdivr, &cdivi);
-        H(n-1, n-1) = cdivr;
-        H(n-1, n) = cdivi;
-      }
-      H(n, n-1) = 0.0;
-      H(n, n) = 1.0;
-      for (int i = n-2; i >= 0; i--) {
-        Real ra, sa, vr, vi;
-        ra = 0.0;
-        sa = 0.0;
-        for (int j = l; j <= n; j++) {
-          ra = ra + H(i, j) * H(j, n-1);
-          sa = sa + H(i, j) * H(j, n);
-        }
-        w = H(i, i) - p;
-
-        if (e_[i] < 0.0) {
-          z = w;
-          r = ra;
-          s = sa;
-        } else {
-          l = i;
-          if (e_[i] == 0) {
-            Real cdivr, cdivi;
-            cdiv(-ra, -sa, w, q, &cdivr, &cdivi);
-            H(i, n-1) = cdivr;
-            H(i, n) = cdivi;
-          } else {
-            Real cdivr, cdivi;
-            // Solve complex equations
-
-            x = H(i, i+1);
-            y = H(i+1, i);
-            vr = (d_[i] - p) * (d_[i] - p) +e_[i] *e_[i] - q * q;
-            vi = (d_[i] - p) * 2.0 * q;
-            if (vr == 0.0 && vi == 0.0) {
-              vr = eps * norm * (std::abs(w) + std::abs(q) +
-                                 std::abs(x) + std::abs(y) + std::abs(z));
-            }
-            cdiv(x*r-z*ra+q*sa, x*s-z*sa-q*ra, vr, vi, &cdivr, &cdivi);
-            H(i, n-1) = cdivr;
-            H(i, n) = cdivi;
-            if (std::abs(x) > (std::abs(z) + std::abs(q))) {
-              H(i+1, n-1) = (-ra - w * H(i, n-1) + q * H(i, n)) / x;
-              H(i+1, n) = (-sa - w * H(i, n) - q * H(i, n-1)) / x;
-            } else {
-              cdiv(-r-y*H(i, n-1), -s-y*H(i, n), z, q, &cdivr, &cdivi);
-              H(i+1, n-1) = cdivr;
-              H(i+1, n) = cdivi;
-            }
-          }
-
-          // Overflow control
-
-          t = std::max(std::abs(H(i, n-1)), std::abs(H(i, n)));
-          if ((eps * t) * t > 1) {
-            for (int j = i; j <= n; j++) {
-              H(j, n-1) = H(j, n-1) / t;
-              H(j, n) = H(j, n) / t;
-            }
-          }
-        }
-      }
-    }
-  }
-
-  // Vectors of isolated roots
-
-  for (int i = 0; i < nn; i++) {
-    if (i < low || i > high) {
-      for (int j = i; j < nn; j++) {
-        V(i, j) = H(i, j);
-      }
-    }
-  }
-
-  // Back transformation to get eigenvectors of original matrix
-
-  for (int j = nn-1; j >= low; j--) {
-    for (int i = low; i <= high; i++) {
-      z = 0.0;
-      for (int k = low; k <= std::min(j, high); k++) {
-        z = z + V(i, k) * H(k, j);
-      }
-      V(i, j) = z;
-    }
-  }
-}
-
-template<typename Real>
-EigenvalueDecomposition<Real>::EigenvalueDecomposition(const MatrixBase<Real> &A) {
-  KALDI_ASSERT(A.NumCols() == A.NumRows() && A.NumCols() >= 1);
-  n_ = A.NumRows();
-  V_ = new Real[n_*n_];
-  d_ = new Real[n_];
-  e_ = new Real[n_];
-  H_ = NULL;
-  ort_ = NULL;
-  if (A.IsSymmetric(0.0)) {
-
-    for (int i = 0; i < n_; i++)
-      for (int j = 0; j < n_; j++)
-        V(i, j) = A(i, j);  // Note that V(i, j) is a member function; A(i, j) is an operator
-    // of the matrix A.
-    // Tridiagonalize.
-    Tred2();
-
-    // Diagonalize.
-    Tql2();
-  } else {
-    H_ = new Real[n_*n_];
-    ort_ = new Real[n_];
-    for (int i = 0; i < n_; i++)
-      for (int j = 0; j < n_; j++)
-        H(i, j) = A(i, j);  // as before: H is member function, A(i, j) is operator of matrix.
-
-    // Reduce to Hessenberg form.
-    Orthes();
-
-    // Reduce Hessenberg to real Schur form.
-    Hqr2();
-  }
-}
-
-template<typename Real>
-EigenvalueDecomposition<Real>::~EigenvalueDecomposition() {
-  delete [] d_;
-  delete [] e_;
-  delete [] V_;
-  if (H_) delete [] H_;
-  if (ort_) delete [] ort_;
-}
-
-// see function MatrixBase<Real>::Eig in kaldi-matrix.cc
-
-
-} // namespace kaldi
-
-#endif // KALDI_MATRIX_JAMA_EIG_H_
diff --git a/kaldi_io/src/kaldi/matrix/jama-svd.h b/kaldi_io/src/kaldi/matrix/jama-svd.h
deleted file mode 100644
index 8304dac..0000000
--- a/kaldi_io/src/kaldi/matrix/jama-svd.h
+++ /dev/null
@@ -1,531 +0,0 @@
-// matrix/jama-svd.h
-
-// Copyright 2009-2011 Microsoft Corporation
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-// This file consists of a port and modification of materials from
-//   JAMA: A Java Matrix Package
-// under the following notice: This software is a cooperative product of
-// The MathWorks and the National Institute of Standards and Technology (NIST)
-// which has been released to the public.  This notice and the original code are
-// available at http://math.nist.gov/javanumerics/jama/domain.notice
-
-
-#ifndef KALDI_MATRIX_JAMA_SVD_H_
-#define KALDI_MATRIX_JAMA_SVD_H_ 1
-
-
-#include "matrix/kaldi-matrix.h"
-#include "matrix/sp-matrix.h"
-#include "matrix/cblas-wrappers.h"
-
-namespace kaldi {
-
-#if defined(HAVE_ATLAS) || defined(USE_KALDI_SVD)
-// using ATLAS as our math library, which doesn't have SVD -> need
-// to implement it.
-
-// This routine is a modified form of jama_svd.h which is part of the TNT distribution.
-// (originally comes from JAMA).
-
-/** Singular Value Decomposition.
- * <P>
- * For an m-by-n matrix A with m >= n, the singular value decomposition is
- * an m-by-n orthogonal matrix U, an n-by-n diagonal matrix S, and
- * an n-by-n orthogonal matrix V so that A = U*S*V'.
- * <P>
- * The singular values, sigma[k] = S(k, k), are ordered so that
- * sigma[0] >= sigma[1] >= ... >= sigma[n-1].
- * <P>
- * The singular value decompostion always exists, so the constructor will
- * never fail.  The matrix condition number and the effective numerical
- * rank can be computed from this decomposition.
-
- * <p>
- *     (Adapted from JAMA, a Java Matrix Library, developed by jointly
- *     by the Mathworks and NIST; see  http://math.nist.gov/javanumerics/jama).
- */
-
-
-template<typename Real>
-bool MatrixBase<Real>::JamaSvd(VectorBase<Real> *s_in,
-                               MatrixBase<Real> *U_in,
-                               MatrixBase<Real> *V_in) {  //  Destructive!
-  KALDI_ASSERT(s_in != NULL && U_in != this && V_in != this);
-  int wantu = (U_in != NULL), wantv = (V_in != NULL);
-  Matrix<Real> Utmp, Vtmp;
-  MatrixBase<Real> &U = (U_in ? *U_in : Utmp), &V = (V_in ? *V_in : Vtmp);
-  VectorBase<Real> &s = *s_in;
-
-  int m = num_rows_, n = num_cols_;
-  KALDI_ASSERT(m>=n && m != 0 && n != 0);
-  if (wantu) KALDI_ASSERT((int)U.num_rows_ == m && (int)U.num_cols_ == n);
-  if (wantv) KALDI_ASSERT((int)V.num_rows_ == n && (int)V.num_cols_ == n);
-  KALDI_ASSERT((int)s.Dim() == n);  // n<=m so n is min.
-
-  int nu = n;
-  U.SetZero();  // make sure all zero.
-  Vector<Real> e(n);
-  Vector<Real> work(m);
-  MatrixBase<Real> &A(*this);
-  Real *adata = A.Data(), *workdata = work.Data(), *edata = e.Data(),
-      *udata = U.Data(), *vdata = V.Data();
-  int astride = static_cast<int>(A.Stride()),
-      ustride = static_cast<int>(U.Stride()),
-      vstride = static_cast<int>(V.Stride());
-  int i = 0, j = 0, k = 0;
-
-  // Reduce A to bidiagonal form, storing the diagonal elements
-  // in s and the super-diagonal elements in e.
-
-  int nct = std::min(m-1, n);
-  int nrt = std::max(0, std::min(n-2, m));
-  for (k = 0; k < std::max(nct, nrt); k++) {
-    if (k < nct) {
-
-      // Compute the transformation for the k-th column and
-      // place the k-th diagonal in s(k).
-      // Compute 2-norm of k-th column without under/overflow.
-      s(k) = 0;
-      for (i = k; i < m; i++) {
-        s(k) = hypot(s(k), A(i, k));
-      }
-      if (s(k) != 0.0) {
-        if (A(k, k) < 0.0) {
-          s(k) = -s(k);
-        }
-        for (i = k; i < m; i++) {
-          A(i, k) /= s(k);
-        }
-        A(k, k) += 1.0;
-      }
-      s(k) = -s(k);
-    }
-    for (j = k+1; j < n; j++) {
-      if ((k < nct) && (s(k) != 0.0))  {
-
-        // Apply the transformation.
-
-        Real t = cblas_Xdot(m - k, adata + astride*k + k, astride,
-                            adata + astride*k + j, astride);
-        /*for (i = k; i < m; i++) {
-          t += adata[i*astride + k]*adata[i*astride + j];  //   A(i, k)*A(i, j); // 3
-          }*/
-        t = -t/A(k, k);
-        cblas_Xaxpy(m - k, t, adata + k*astride + k, astride,
-                    adata + k*astride + j, astride);
-        /*for (i = k; i < m; i++) {
-          adata[i*astride + j] += t*adata[i*astride + k];  // A(i, j) += t*A(i, k); // 5
-          }*/
-      }
-
-      // Place the k-th row of A into e for the
-      // subsequent calculation of the row transformation.
-
-      e(j) = A(k, j);
-    }
-    if (wantu & (k < nct)) {
-
-      // Place the transformation in U for subsequent back
-      // multiplication.
-
-      for (i = k; i < m; i++) {
-        U(i, k) = A(i, k);
-      }
-    }
-    if (k < nrt) {
-
-      // Compute the k-th row transformation and place the
-      // k-th super-diagonal in e(k).
-      // Compute 2-norm without under/overflow.
-      e(k) = 0;
-      for (i = k+1; i < n; i++) {
-        e(k) = hypot(e(k), e(i));
-      }
-      if (e(k) != 0.0) {
-        if (e(k+1) < 0.0) {
-          e(k) = -e(k);
-        }
-        for (i = k+1; i < n; i++) {
-          e(i) /= e(k);
-        }
-        e(k+1) += 1.0;
-      }
-      e(k) = -e(k);
-      if ((k+1 < m) & (e(k) != 0.0)) {
-
-        // Apply the transformation.
-
-        for (i = k+1; i < m; i++) {
-          work(i) = 0.0;
-        }
-        for (j = k+1; j < n; j++) {
-          for (i = k+1; i < m; i++) {
-            workdata[i] += edata[j] * adata[i*astride + j];  // work(i) += e(j)*A(i, j); // 5
-          }
-        }
-        for (j = k+1; j < n; j++) {
-          Real t(-e(j)/e(k+1));
-          cblas_Xaxpy(m - (k+1), t, workdata + (k+1), 1,
-                      adata + (k+1)*astride + j, astride);
-          /*
-          for (i = k+1; i < m; i++) {
-            adata[i*astride + j] += t*workdata[i];  // A(i, j) += t*work(i); // 5
-            }*/
-        }
-      }
-      if (wantv) {
-
-        // Place the transformation in V for subsequent
-        // back multiplication.
-
-        for (i = k+1; i < n; i++) {
-          V(i, k) = e(i);
-        }
-      }
-    }
-  }
-
-  // Set up the final bidiagonal matrix or order p.
-
-  int p = std::min(n, m+1);
-  if (nct < n) {
-    s(nct) = A(nct, nct);
-  }
-  if (m < p) {
-    s(p-1) = 0.0;
-  }
-  if (nrt+1 < p) {
-    e(nrt) = A(nrt, p-1);
-  }
-  e(p-1) = 0.0;
-
-  // If required, generate U.
-
-  if (wantu) {
-    for (j = nct; j < nu; j++) {
-      for (i = 0; i < m; i++) {
-        U(i, j) = 0.0;
-      }
-      U(j, j) = 1.0;
-    }
-    for (k = nct-1; k >= 0; k--) {
-      if (s(k) != 0.0) {
-        for (j = k+1; j < nu; j++) {
-          Real t = cblas_Xdot(m - k, udata + k*ustride + k, ustride, udata + k*ustride + j, ustride);
-          //for (i = k; i < m; i++) {
-          //  t += udata[i*ustride + k]*udata[i*ustride + j];  // t += U(i, k)*U(i, j); // 8
-          // }
-          t = -t/U(k, k);
-          cblas_Xaxpy(m - k, t, udata + ustride*k + k, ustride,
-                      udata + k*ustride + j, ustride);
-          /*for (i = k; i < m; i++) {
-            udata[i*ustride + j] += t*udata[i*ustride + k];  // U(i, j) += t*U(i, k); // 4
-            }*/
-        }
-        for (i = k; i < m; i++ ) {
-          U(i, k) = -U(i, k);
-        }
-        U(k, k) = 1.0 + U(k, k);
-        for (i = 0; i < k-1; i++) {
-          U(i, k) = 0.0;
-        }
-      } else {
-        for (i = 0; i < m; i++) {
-          U(i, k) = 0.0;
-        }
-        U(k, k) = 1.0;
-      }
-    }
-  }
-
-  // If required, generate V.
-
-  if (wantv) {
-    for (k = n-1; k >= 0; k--) {
-      if ((k < nrt) & (e(k) != 0.0)) {
-        for (j = k+1; j < nu; j++) {
-          Real t = cblas_Xdot(n - (k+1), vdata + (k+1)*vstride + k, vstride,
-                              vdata + (k+1)*vstride + j, vstride); 
-          /*Real t (0.0);
-          for (i = k+1; i < n; i++) {
-            t += vdata[i*vstride + k]*vdata[i*vstride + j];  // t += V(i, k)*V(i, j); // 7
-            }*/
-          t = -t/V(k+1, k);
-          cblas_Xaxpy(n - (k+1), t, vdata + (k+1)*vstride + k, vstride,
-                      vdata + (k+1)*vstride + j, vstride);
-          /*for (i = k+1; i < n; i++) {
-            vdata[i*vstride + j] += t*vdata[i*vstride + k];  // V(i, j) += t*V(i, k); // 7
-            }*/
-        }
-      }
-      for (i = 0; i < n; i++) {
-        V(i, k) = 0.0;
-      }
-      V(k, k) = 1.0;
-    }
-  }
-
-  // Main iteration loop for the singular values.
-
-  int pp = p-1;
-  int iter = 0;
-  // note: -52.0 is from Jama code; the -23 is the extension
-  // to float, because mantissa length in (double, float)
-  // is (52, 23) bits respectively.
-  Real eps(pow(2.0, sizeof(Real) == 4 ? -23.0 : -52.0));
-  // Note: the -966 was taken from Jama code, but the -120 is a guess
-  // of how to extend this to float... the exponent in double goes
-  // from -1022 .. 1023, and in float from -126..127.  I'm not sure
-  // what the significance of 966 is, so -120 just represents a number
-  // that's a bit less negative than -126.  If we get convergence
-  // failure in float only, this may mean that we have to make the
-  // -120 value less negative.
-  Real tiny(pow(2.0, sizeof(Real) == 4 ? -120.0: -966.0 ));
-  
-  while (p > 0) {
-    int k = 0;
-    int kase = 0;
-
-    if (iter == 500 || iter == 750) {
-      KALDI_WARN << "Svd taking a long time: making convergence criterion less exact.";
-      eps = pow(static_cast<Real>(0.8), eps);
-      tiny = pow(static_cast<Real>(0.8), tiny);
-    }
-    if (iter > 1000) {
-      KALDI_WARN << "Svd not converging on matrix of size " << m << " by " <<n;
-      return false;
-    }
-
-    // This section of the program inspects for
-    // negligible elements in the s and e arrays.  On
-    // completion the variables kase and k are set as follows.
-
-    // kase = 1     if s(p) and e(k-1) are negligible and k < p
-    // kase = 2     if s(k) is negligible and k < p
-    // kase = 3     if e(k-1) is negligible, k < p, and
-    //              s(k), ..., s(p) are not negligible (qr step).
-    // kase = 4     if e(p-1) is negligible (convergence).
-
-    for (k = p-2; k >= -1; k--) {
-      if (k == -1) {
-        break;
-      }
-      if (std::abs(e(k)) <=
-          tiny + eps*(std::abs(s(k)) + std::abs(s(k+1)))) {
-        e(k) = 0.0;
-        break;
-      }
-    }
-    if (k == p-2) {
-      kase = 4;
-    } else {
-      int ks;
-      for (ks = p-1; ks >= k; ks--) {
-        if (ks == k) {
-          break;
-        }
-        Real t( (ks != p ? std::abs(e(ks)) : 0.) +
-                (ks != k+1 ? std::abs(e(ks-1)) : 0.));
-        if (std::abs(s(ks)) <= tiny + eps*t)  {
-          s(ks) = 0.0;
-          break;
-        }
-      }
-      if (ks == k) {
-        kase = 3;
-      } else if (ks == p-1) {
-        kase = 1;
-      } else {
-        kase = 2;
-        k = ks;
-      }
-    }
-    k++;
-
-    // Perform the task indicated by kase.
-
-    switch (kase) {
-
-      // Deflate negligible s(p).
-
-      case 1: {
-        Real f(e(p-2));
-        e(p-2) = 0.0;
-        for (j = p-2; j >= k; j--) {
-          Real t( hypot(s(j), f));
-          Real cs(s(j)/t);
-          Real sn(f/t);
-          s(j) = t;
-          if (j != k) {
-            f = -sn*e(j-1);
-            e(j-1) = cs*e(j-1);
-          }
-          if (wantv) {
-            for (i = 0; i < n; i++) {
-              t = cs*V(i, j) + sn*V(i, p-1);
-              V(i, p-1) = -sn*V(i, j) + cs*V(i, p-1);
-              V(i, j) = t;
-            }
-          }
-        }
-      }
-        break;
-
-        // Split at negligible s(k).
-
-      case 2: {
-        Real f(e(k-1));
-        e(k-1) = 0.0;
-        for (j = k; j < p; j++) {
-          Real t(hypot(s(j), f));
-          Real cs( s(j)/t);
-          Real sn(f/t);
-          s(j) = t;
-          f = -sn*e(j);
-          e(j) = cs*e(j);
-          if (wantu) {
-            for (i = 0; i < m; i++) {
-              t = cs*U(i, j) + sn*U(i, k-1);
-              U(i, k-1) = -sn*U(i, j) + cs*U(i, k-1);
-              U(i, j) = t;
-            }
-          }
-        }
-      }
-        break;
-
-        // Perform one qr step.
-
-      case 3: {
-
-        // Calculate the shift.
-
-        Real scale = std::max(std::max(std::max(std::max(
-            std::abs(s(p-1)), std::abs(s(p-2))), std::abs(e(p-2))),
-                                       std::abs(s(k))), std::abs(e(k)));
-        Real sp = s(p-1)/scale;
-        Real spm1 = s(p-2)/scale;
-        Real epm1 = e(p-2)/scale;
-        Real sk = s(k)/scale;
-        Real ek = e(k)/scale;
-        Real b = ((spm1 + sp)*(spm1 - sp) + epm1*epm1)/2.0;
-        Real c = (sp*epm1)*(sp*epm1);
-        Real shift = 0.0;
-        if ((b != 0.0) || (c != 0.0)) {
-          shift = std::sqrt(b*b + c);
-          if (b < 0.0) {
-            shift = -shift;
-          }
-          shift = c/(b + shift);
-        }
-        Real f = (sk + sp)*(sk - sp) + shift;
-        Real g = sk*ek;
-
-        // Chase zeros.
-
-        for (j = k; j < p-1; j++) {
-          Real t = hypot(f, g);
-          Real cs = f/t;
-          Real sn = g/t;
-          if (j != k) {
-            e(j-1) = t;
-          }
-          f = cs*s(j) + sn*e(j);
-          e(j) = cs*e(j) - sn*s(j);
-          g = sn*s(j+1);
-          s(j+1) = cs*s(j+1);
-          if (wantv) {
-            cblas_Xrot(n, vdata + j, vstride, vdata + j+1, vstride, cs, sn);
-            /*for (i = 0; i < n; i++) {
-              t = cs*vdata[i*vstride + j] + sn*vdata[i*vstride + j+1];  // t = cs*V(i, j) + sn*V(i, j+1);         // 13
-              vdata[i*vstride + j+1] = -sn*vdata[i*vstride + j] + cs*vdata[i*vstride + j+1];  // V(i, j+1) = -sn*V(i, j) + cs*V(i, j+1); // 5
-              vdata[i*vstride + j] = t;  // V(i, j) = t; // 4
-              }*/
-          }
-          t = hypot(f, g);
-          cs = f/t;
-          sn = g/t;
-          s(j) = t;
-          f = cs*e(j) + sn*s(j+1);
-          s(j+1) = -sn*e(j) + cs*s(j+1);
-          g = sn*e(j+1);
-          e(j+1) = cs*e(j+1);
-          if (wantu && (j < m-1)) {
-            cblas_Xrot(m, udata + j, ustride, udata + j+1, ustride, cs, sn);
-            /*for (i = 0; i < m; i++) {
-              t = cs*udata[i*ustride + j] + sn*udata[i*ustride + j+1];  // t = cs*U(i, j) + sn*U(i, j+1); // 7
-              udata[i*ustride + j+1] = -sn*udata[i*ustride + j] +cs*udata[i*ustride + j+1];  // U(i, j+1) = -sn*U(i, j) + cs*U(i, j+1); // 8
-              udata[i*ustride + j] = t;  // U(i, j) = t; // 1
-              }*/
-          }
-        }
-        e(p-2) = f;
-        iter = iter + 1;
-      }
-        break;
-
-        // Convergence.
-
-      case 4: {
-
-        // Make the singular values positive.
-
-        if (s(k) <= 0.0) {
-          s(k) = (s(k) < 0.0 ? -s(k) : 0.0);
-          if (wantv) {
-            for (i = 0; i <= pp; i++) {
-              V(i, k) = -V(i, k);
-            }
-          }
-        }
-
-        // Order the singular values.
-
-        while (k < pp) {
-          if (s(k) >= s(k+1)) {
-            break;
-          }
-          Real t = s(k);
-          s(k) = s(k+1);
-          s(k+1) = t;
-          if (wantv && (k < n-1)) {
-            for (i = 0; i < n; i++) {
-              t = V(i, k+1); V(i, k+1) = V(i, k); V(i, k) = t;
-            }
-          }
-          if (wantu && (k < m-1)) {
-            for (i = 0; i < m; i++) {
-              t = U(i, k+1); U(i, k+1) = U(i, k); U(i, k) = t;
-            }
-          }
-          k++;
-        }
-        iter = 0;
-        p--;
-      }
-        break;
-    }
-  }
-  return true;
-}
-
-#endif // defined(HAVE_ATLAS) || defined(USE_KALDI_SVD)
-
-} // namespace kaldi
-
-#endif // KALDI_MATRIX_JAMA_SVD_H_
diff --git a/kaldi_io/src/kaldi/matrix/kaldi-blas.h b/kaldi_io/src/kaldi/matrix/kaldi-blas.h
deleted file mode 100644
index 5d25ab8..0000000
--- a/kaldi_io/src/kaldi/matrix/kaldi-blas.h
+++ /dev/null
@@ -1,132 +0,0 @@
-// matrix/kaldi-blas.h
-
-// Copyright 2009-2011  Ondrej Glembek;  Microsoft Corporation
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-
-//  http://www.apache.org/licenses/LICENSE-2.0
-
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-#ifndef KALDI_MATRIX_KALDI_BLAS_H_
-#define KALDI_MATRIX_KALDI_BLAS_H_
-
-// This file handles the #includes for BLAS, LAPACK and so on.
-// It manipulates the declarations into a common format that kaldi can handle.
-// However, the kaldi code will check whether HAVE_ATLAS is defined as that
-// code is called a bit differently from CLAPACK that comes from other sources.
-
-// There are three alternatives:
-//   (i) you have ATLAS, which includes the ATLAS implementation of CBLAS
-//   plus a subset of CLAPACK (but with clapack_ in the function declarations).
-//   In this case, define HAVE_ATLAS and make sure the relevant directories are
-//   in the include path.
-
-//   (ii) you have CBLAS (some implementation thereof) plus CLAPACK.
-//   In this case, define HAVE_CLAPACK.
-//   [Since CLAPACK depends on BLAS, the presence of BLAS is implicit].
-
-//  (iii) you have the MKL library, which includes CLAPACK and CBLAS.
-
-// Note that if we are using ATLAS, no Svd implementation is supplied,
-// so we define HAVE_Svd to be zero and this directs our implementation to
-// supply its own "by hand" implementation which is based on TNT code.
-
-
-
-
-#if (defined(HAVE_CLAPACK) && (defined(HAVE_ATLAS) || defined(HAVE_MKL))) \
-    || (defined(HAVE_ATLAS) && defined(HAVE_MKL))
-#error "Do not define more than one of HAVE_CLAPACK, HAVE_ATLAS and HAVE_MKL"
-#endif
-
-#ifdef HAVE_ATLAS
-  extern "C" {
-    #include <cblas.h>
-    #include <clapack.h>
-  }
-#elif defined(HAVE_CLAPACK)
-  #ifdef __APPLE__
-    #ifndef __has_extension
-    #define __has_extension(x) 0
-    #endif
-    #define vImage_Utilities_h
-    #define vImage_CVUtilities_h
-    #include <Accelerate/Accelerate.h>
-    typedef __CLPK_integer          integer;
-    typedef __CLPK_logical          logical;
-    typedef __CLPK_real             real;
-    typedef __CLPK_doublereal       doublereal;
-    typedef __CLPK_complex          complex;
-    typedef __CLPK_doublecomplex    doublecomplex;
-    typedef __CLPK_ftnlen           ftnlen;
-  #else
-    extern "C" {
-      // May be in /usr/[local]/include if installed; else this uses the one
-      // from the tools/CLAPACK_include directory.
-      #include <cblas.h>
-      #include <f2c.h>
-      #include <clapack.h>  
-
-      // get rid of macros from f2c.h -- these are dangerous.
-      #undef abs
-      #undef dabs
-      #undef min
-      #undef max
-      #undef dmin
-      #undef dmax
-      #undef bit_test
-      #undef bit_clear
-      #undef bit_set
-    }
-  #endif
-#elif defined(HAVE_MKL)
-  extern "C" {
-    #include <mkl.h>
-  }
-#elif defined(HAVE_OPENBLAS)
-  // getting cblas.h and lapacke.h from <openblas-install-dir>/.
-  // putting in "" not <> to search -I before system libraries.
-  #include "cblas.h"
-  #include "lapacke.h"
-  #undef I
-  #undef complex
-  // get rid of macros from f2c.h -- these are dangerous.
-  #undef abs
-  #undef dabs
-  #undef min
-  #undef max
-  #undef dmin
-  #undef dmax
-  #undef bit_test
-  #undef bit_clear
-  #undef bit_set
-#else
-  #error "You need to define (using the preprocessor) either HAVE_CLAPACK or HAVE_ATLAS or HAVE_MKL (but not more than one)"  
-#endif
-
-#ifdef HAVE_OPENBLAS
-typedef int KaldiBlasInt; // try int.
-#endif
-#ifdef HAVE_CLAPACK
-typedef integer KaldiBlasInt;
-#endif
-#ifdef HAVE_MKL
-typedef MKL_INT KaldiBlasInt;
-#endif
-
-#ifdef HAVE_ATLAS
-// in this case there is no need for KaldiBlasInt-- this typedef is only needed
-// for Svd code which is not included in ATLAS (we re-implement it).
-#endif
-
-
-#endif  // KALDI_MATRIX_KALDI_BLAS_H_
diff --git a/kaldi_io/src/kaldi/matrix/kaldi-gpsr.h b/kaldi_io/src/kaldi/matrix/kaldi-gpsr.h
deleted file mode 100644
index c294bdd..0000000
--- a/kaldi_io/src/kaldi/matrix/kaldi-gpsr.h
+++ /dev/null
@@ -1,166 +0,0 @@
-// matrix/kaldi-gpsr.h
-
-// Copyright 2012  Arnab Ghoshal
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_MATRIX_KALDI_GPSR_H_
-#define KALDI_MATRIX_KALDI_GPSR_H_
-
-#include <string>
-#include <vector>
-
-#include "base/kaldi-common.h"
-#include "matrix/matrix-lib.h"
-#include "itf/options-itf.h"
-
-namespace kaldi {
-
-/// This is an implementation of the GPSR algorithm. See, Figueiredo, Nowak and
-/// Wright, "Gradient Projection for Sparse Reconstruction: Application to
-/// Compressed Sensing and Other Inverse Problems," IEEE Journal of Selected
-/// Topics in Signal Processing, vol. 1, no. 4, pp. 586-597, 2007.
-/// http://dx.doi.org/10.1109/JSTSP.2007.910281
-
-/// The GPSR algorithm, described in Figueiredo, et al., 2007, solves:
-/// \f[ \min_x 0.5 * ||y - Ax||_2^2 + \tau ||x||_1, \f]
-/// where \f$ x \in R^n, y \in R^k \f$, and \f$ A \in R^{n \times k} \f$.
-/// In this implementation, we solve:
-/// \f[ \min_x 0.5 * x^T H x - g^T x + \tau ||x||_1, \f]
-/// which is the more natural form in which such problems arise in our case.
-/// Here, \f$ H = A^T A \in R^{n \times n} \f$ and \f$ g = A^T y \in R^n \f$.
-
-
-/** \struct GpsrConfig
- *  Configuration variables needed in the GPSR algorithm.
- */
-struct GpsrConfig {
-  bool use_gpsr_bb;  ///< Use the Barzilai-Borwein gradient projection method
-
-  /// The following options are common to both the basic & Barzilai-Borwein
-  /// versions of GPSR
-  double stop_thresh;  ///< Stopping threshold
-  int32 max_iters;  ///< Maximum number of iterations
-  double gpsr_tau;  ///< Regularization scale
-  double alpha_min;  ///< Minimum step size in the feasible direction
-  double alpha_max;  ///< Maximum step size in the feasible direction
-  double max_sparsity;  ///< Maximum percentage of dimensions set to 0
-  double tau_reduction;  ///< Multiply tau by this if max_sparsity reached
-
-  /// The following options are for the backtracking line search in basic GPSR.
-  /// Step size reduction factor in backtracking line search. 0 < beta < 1
-  double gpsr_beta;
-  /// Improvement factor in backtracking line search, i.e. the new objective
-  /// function must be less than the old one by mu times the gradient in the
-  /// direction of the change in x. 0 < mu < 1
-  double gpsr_mu;
-  int32 max_iters_backtrak;  ///< Max iterations for backtracking line search
-
-  bool debias;  ///< Do debiasing, i.e. unconstrained optimization at the end
-  double stop_thresh_debias;  ///< Stopping threshold for debiasing stage
-  int32 max_iters_debias;  ///< Maximum number of iterations for debiasing stage
-
-  GpsrConfig() {
-    use_gpsr_bb = true;
-
-    stop_thresh = 0.005;
-    max_iters = 100;
-    gpsr_tau = 10;
-    alpha_min = 1.0e-10;
-    alpha_max = 1.0e+20;
-    max_sparsity = 0.9;
-    tau_reduction = 0.8;
-
-    gpsr_beta = 0.5;
-    gpsr_mu = 0.1;
-    max_iters_backtrak = 50;
-
-    debias = false;
-    stop_thresh_debias = 0.001;
-    max_iters_debias = 50;
-  }
-
-  void Register(OptionsItf *po);
-};
-
-inline void GpsrConfig::Register(OptionsItf *po) {
-  std::string module = "GpsrConfig: ";
-  po->Register("use-gpsr-bb", &use_gpsr_bb, module+
-               "Use the Barzilai-Borwein gradient projection method.");
-
-  po->Register("stop-thresh", &stop_thresh, module+
-               "Stopping threshold for GPSR.");
-  po->Register("max-iters", &max_iters, module+
-               "Maximum number of iterations of GPSR.");
-  po->Register("gpsr-tau", &gpsr_tau, module+
-               "Regularization scale for GPSR.");
-  po->Register("alpha-min", &alpha_min, module+
-               "Minimum step size in feasible direction.");
-  po->Register("alpha-max", &alpha_max, module+
-               "Maximum step size in feasible direction.");
-  po->Register("max-sparsity", &max_sparsity, module+
-               "Maximum percentage of dimensions set to 0.");
-  po->Register("tau-reduction", &tau_reduction, module+
-               "Multiply tau by this if maximum sparsity is reached.");
-
-  po->Register("gpsr-beta", &gpsr_beta, module+
-               "Step size reduction factor in backtracking line search (0<beta<1).");
-  po->Register("gpsr-mu", &gpsr_mu, module+
-               "Improvement factor in backtracking line search (0<mu<1).");
-  po->Register("max-iters-backtrack", &max_iters_backtrak, module+
-               "Maximum number of iterations of backtracking line search.");
-
-  po->Register("debias", &debias, module+
-               "Do final debiasing step.");
-  po->Register("stop-thresh-debias", &stop_thresh_debias, module+
-               "Stopping threshold for debiaisng step.");
-  po->Register("max-iters-debias", &max_iters_debias, module+
-               "Maximum number of iterations of debiasing.");
-}
-
-/// Solves a quadratic program in \f$ x \f$, with L_1 regularization:
-/// \f[ \min_x 0.5 * x^T H x - g^T x + \tau ||x||_1. \f]
-/// This is similar to SolveQuadraticProblem() in sp-matrix.h with an added
-/// L_1 term.
-template<typename Real>
-Real Gpsr(const GpsrConfig &opts, const SpMatrix<Real> &H,
-          const Vector<Real> &g, Vector<Real> *x,
-          const char *debug_str = "[unknown]") {
-  if (opts.use_gpsr_bb)
-    return GpsrBB(opts, H, g, x, debug_str);
-  else
-    return GpsrBasic(opts, H, g, x, debug_str);
-}
-
-/// This is the basic GPSR algorithm, where the step size is determined by a
-/// backtracking line search. The line search is called "Armijo rule along the
-/// projection arc" in Bertsekas, Nonlinear Programming, 2nd ed. page 230.
-template<typename Real>
-Real GpsrBasic(const GpsrConfig &opts, const SpMatrix<Real> &H,
-               const Vector<Real> &g, Vector<Real> *x,
-               const char *debug_str = "[unknown]");
-
-/// This is the paper calls the Barzilai-Borwein variant. This is a constrained
-/// Netwon's method where the Hessian is approximated by scaled identity matrix
-template<typename Real>
-Real GpsrBB(const GpsrConfig &opts, const SpMatrix<Real> &H,
-            const Vector<Real> &g, Vector<Real> *x,
-            const char *debug_str = "[unknown]");
-
-
-}  // namespace kaldi
-
-#endif  // KALDI_MATRIX_KALDI_GPSR_H_
diff --git a/kaldi_io/src/kaldi/matrix/kaldi-matrix-inl.h b/kaldi_io/src/kaldi/matrix/kaldi-matrix-inl.h
deleted file mode 100644
index 8bc4749..0000000
--- a/kaldi_io/src/kaldi/matrix/kaldi-matrix-inl.h
+++ /dev/null
@@ -1,62 +0,0 @@
-// matrix/kaldi-matrix-inl.h
-
-// Copyright 2009-2011  Microsoft Corporation;  Haihua Xu
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_MATRIX_KALDI_MATRIX_INL_H_
-#define KALDI_MATRIX_KALDI_MATRIX_INL_H_ 1
-
-#include "matrix/kaldi-vector.h"
-
-namespace kaldi {
-
-/// Empty constructor
-template<typename Real>
-Matrix<Real>::Matrix(): MatrixBase<Real>(NULL, 0, 0, 0) { }
-
-
-template<>
-template<>
-void MatrixBase<float>::AddVecVec(const float alpha, const VectorBase<float> &ra, const VectorBase<float> &rb);
-
-template<>
-template<>
-void MatrixBase<double>::AddVecVec(const double alpha, const VectorBase<double> &ra, const VectorBase<double> &rb); 
-
-template<typename Real>
-inline std::ostream & operator << (std::ostream & os, const MatrixBase<Real> & M) {
-  M.Write(os, false);
-  return os;
-}
-
-template<typename Real>
-inline std::istream & operator >> (std::istream & is, Matrix<Real> & M) {
-  M.Read(is, false);
-  return is;
-}
-
-
-template<typename Real>
-inline std::istream & operator >> (std::istream & is, MatrixBase<Real> & M) {
-  M.Read(is, false);
-  return is;
-}
-
-}// namespace kaldi
-
-
-#endif  // KALDI_MATRIX_KALDI_MATRIX_INL_H_
diff --git a/kaldi_io/src/kaldi/matrix/kaldi-matrix.h b/kaldi_io/src/kaldi/matrix/kaldi-matrix.h
deleted file mode 100644
index e6829e0..0000000
--- a/kaldi_io/src/kaldi/matrix/kaldi-matrix.h
+++ /dev/null
@@ -1,983 +0,0 @@
-// matrix/kaldi-matrix.h
-
-// Copyright 2009-2011  Ondrej Glembek;  Microsoft Corporation;  Lukas Burget;
-//                      Saarland University;  Petr Schwarz;  Yanmin Qian;
-//                      Karel Vesely;  Go Vivace Inc.;  Haihua Xu
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_MATRIX_KALDI_MATRIX_H_
-#define KALDI_MATRIX_KALDI_MATRIX_H_ 1
-
-#include "matrix/matrix-common.h"
-
-namespace kaldi {
-
-/// @{ \addtogroup matrix_funcs_scalar
-
-/// We need to declare this here as it will be a friend function.
-/// tr(A B), or tr(A B^T).
-template<typename Real>
-Real TraceMatMat(const MatrixBase<Real> &A, const MatrixBase<Real> &B,
-                 MatrixTransposeType trans = kNoTrans);
-/// @}
-
-/// \addtogroup matrix_group
-/// @{
-
-/// Base class which provides matrix operations not involving resizing
-/// or allocation.   Classes Matrix and SubMatrix inherit from it and take care
-/// of allocation and resizing.
-template<typename Real>
-class MatrixBase {
- public:
-  // so this child can access protected members of other instances.
-  friend class Matrix<Real>;
-  // friend declarations for CUDA matrices (see ../cudamatrix/)
-  friend class CuMatrixBase<Real>;
-  friend class CuMatrix<Real>;
-  friend class CuSubMatrix<Real>;
-  friend class CuPackedMatrix<Real>;
-  
-  friend class PackedMatrix<Real>;
-
-  /// Returns number of rows (or zero for emtpy matrix).
-  inline MatrixIndexT  NumRows() const { return num_rows_; }
-
-  /// Returns number of columns (or zero for emtpy matrix).
-  inline MatrixIndexT NumCols() const { return num_cols_; }
-
-  /// Stride (distance in memory between each row).  Will be >= NumCols.
-  inline MatrixIndexT Stride() const {  return stride_; }
-
-  /// Returns size in bytes of the data held by the matrix.
-  size_t  SizeInBytes() const {
-    return static_cast<size_t>(num_rows_) * static_cast<size_t>(stride_) *
-        sizeof(Real);
-  }
-
-  /// Gives pointer to raw data (const).
-  inline const Real* Data() const {
-    return data_;
-  }
-
-  /// Gives pointer to raw data (non-const).
-  inline Real* Data() { return data_; }
-
-  /// Returns pointer to data for one row (non-const)
-  inline  Real* RowData(MatrixIndexT i) {
-    KALDI_ASSERT(static_cast<UnsignedMatrixIndexT>(i) <
-                 static_cast<UnsignedMatrixIndexT>(num_rows_));
-    return data_ + i * stride_;
-  }
-
-  /// Returns pointer to data for one row (const)
-  inline const Real* RowData(MatrixIndexT i) const {
-    KALDI_ASSERT(static_cast<UnsignedMatrixIndexT>(i) <
-                 static_cast<UnsignedMatrixIndexT>(num_rows_));
-    return data_ + i * stride_;
-  }
-
-  /// Indexing operator, non-const
-  /// (only checks sizes if compiled with -DKALDI_PARANOID)
-  inline Real&  operator() (MatrixIndexT r, MatrixIndexT c) {
-    KALDI_PARANOID_ASSERT(static_cast<UnsignedMatrixIndexT>(r) <
-                          static_cast<UnsignedMatrixIndexT>(num_rows_) &&
-                          static_cast<UnsignedMatrixIndexT>(c) <
-                          static_cast<UnsignedMatrixIndexT>(num_cols_));
-    return *(data_ + r * stride_ + c);
-  }
-  /// Indexing operator, provided for ease of debugging (gdb doesn't work
-  /// with parenthesis operator).
-  Real &Index (MatrixIndexT r, MatrixIndexT c) {  return (*this)(r, c); }
-  
-  /// Indexing operator, const
-  /// (only checks sizes if compiled with -DKALDI_PARANOID)
-  inline const Real operator() (MatrixIndexT r, MatrixIndexT c) const {
-    KALDI_PARANOID_ASSERT(static_cast<UnsignedMatrixIndexT>(r) <
-                          static_cast<UnsignedMatrixIndexT>(num_rows_) &&
-                          static_cast<UnsignedMatrixIndexT>(c) <
-                          static_cast<UnsignedMatrixIndexT>(num_cols_));
-    return *(data_ + r * stride_ + c);
-  }
-
-  /*   Basic setting-to-special values functions. */
-
-  /// Sets matrix to zero.
-  void SetZero();
-  /// Sets all elements to a specific value.
-  void Set(Real);
-  /// Sets to zero, except ones along diagonal [for non-square matrices too]
-  void SetUnit();
-  /// Sets to random values of a normal distribution
-  void SetRandn();
-  /// Sets to numbers uniformly distributed on (0, 1)
-  void SetRandUniform();
-
-  /*  Copying functions.  These do not resize the matrix! */
-
-
-  /// Copy given matrix. (no resize is done).
-  template<typename OtherReal>
-  void CopyFromMat(const MatrixBase<OtherReal> & M,
-                   MatrixTransposeType trans = kNoTrans);
-
-  /// Copy from compressed matrix.
-  void CopyFromMat(const CompressedMatrix &M);
-  
-  /// Copy given spmatrix. (no resize is done).
-  template<typename OtherReal>
-  void CopyFromSp(const SpMatrix<OtherReal> &M);
-
-  /// Copy given tpmatrix. (no resize is done).
-  template<typename OtherReal>
-  void CopyFromTp(const TpMatrix<OtherReal> &M,
-                  MatrixTransposeType trans = kNoTrans);
-  
-  /// Copy from CUDA matrix.  Implemented in ../cudamatrix/cu-matrix.h
-  template<typename OtherReal>  
-  void CopyFromMat(const CuMatrixBase<OtherReal> &M,
-                   MatrixTransposeType trans = kNoTrans);
-
-  /// Inverse of vec() operator. Copies vector into matrix, row-by-row.
-  /// Note that rv.Dim() must either equal NumRows()*NumCols() or
-  /// NumCols()-- this has two modes of operation.
-  void CopyRowsFromVec(const VectorBase<Real> &v);
-
-  /// This version of CopyRowsFromVec is implemented in ../cudamatrix/cu-vector.cc
-  void CopyRowsFromVec(const CuVectorBase<Real> &v);
-  
-  template<typename OtherReal>
-  void CopyRowsFromVec(const VectorBase<OtherReal> &v);
-
-  /// Copies vector into matrix, column-by-column.
-  /// Note that rv.Dim() must either equal NumRows()*NumCols() or NumRows();
-  /// this has two modes of operation.
-  void CopyColsFromVec(const VectorBase<Real> &v);
-  
-  /// Copy vector into specific column of matrix.
-  void CopyColFromVec(const VectorBase<Real> &v, const MatrixIndexT col);
-  /// Copy vector into specific row of matrix.
-  void CopyRowFromVec(const VectorBase<Real> &v, const MatrixIndexT row);
-  /// Copy vector into diagonal of matrix.
-  void CopyDiagFromVec(const VectorBase<Real> &v);
-
-  /* Accessing of sub-parts of the matrix. */
-
-  /// Return specific row of matrix [const].
-  inline const SubVector<Real> Row(MatrixIndexT i) const {
-    KALDI_ASSERT(static_cast<UnsignedMatrixIndexT>(i) <
-                 static_cast<UnsignedMatrixIndexT>(num_rows_));
-    return SubVector<Real>(data_ + (i * stride_), NumCols());
-  }
-
-  /// Return specific row of matrix.
-  inline SubVector<Real> Row(MatrixIndexT i) {
-    KALDI_ASSERT(static_cast<UnsignedMatrixIndexT>(i) <
-                 static_cast<UnsignedMatrixIndexT>(num_rows_));
-    return SubVector<Real>(data_ + (i * stride_), NumCols());
-  }
-
-  /// Return a sub-part of matrix.
-  inline SubMatrix<Real> Range(const MatrixIndexT row_offset,
-                               const MatrixIndexT num_rows,
-                               const MatrixIndexT col_offset,
-                               const MatrixIndexT num_cols) const {
-    return SubMatrix<Real>(*this, row_offset, num_rows,
-                           col_offset, num_cols);
-  }
-  inline SubMatrix<Real> RowRange(const MatrixIndexT row_offset,
-                                  const MatrixIndexT num_rows) const {
-    return SubMatrix<Real>(*this, row_offset, num_rows, 0, num_cols_);
-  }  
-  inline SubMatrix<Real> ColRange(const MatrixIndexT col_offset,
-                                  const MatrixIndexT num_cols) const {
-    return SubMatrix<Real>(*this, 0, num_rows_, col_offset, num_cols);
-  }  
-
-  /* Various special functions. */
-  /// Returns sum of all elements in matrix.
-  Real Sum() const;
-  /// Returns trace of matrix.
-  Real Trace(bool check_square = true) const;
-  // If check_square = true, will crash if matrix is not square.
-
-  /// Returns maximum element of matrix.
-  Real Max() const;
-  /// Returns minimum element of matrix.
-  Real Min() const;
-
-  /// Element by element multiplication with a given matrix.
-  void MulElements(const MatrixBase<Real> &A);
-
-  /// Divide each element by the corresponding element of a given matrix.
-  void DivElements(const MatrixBase<Real> &A);
-
-  /// Multiply each element with a scalar value.
-  void Scale(Real alpha);
-
-  /// Set, element-by-element, *this = max(*this, A)
-  void Max(const MatrixBase<Real> &A);
-
-  /// Equivalent to (*this) = (*this) * diag(scale).  Scaling
-  /// each column by a scalar taken from that dimension of the vector.
-  void MulColsVec(const VectorBase<Real> &scale);
-
-  /// Equivalent to (*this) = diag(scale) * (*this).  Scaling
-  /// each row by a scalar taken from that dimension of the vector.
-  void MulRowsVec(const VectorBase<Real> &scale);
-
-  /// Divide each row into src.NumCols() equal groups, and then scale i'th row's
-  /// j'th group of elements by src(i, j).  Requires src.NumRows() ==
-  /// this->NumRows() and this->NumCols() % src.NumCols() == 0.
-  void MulRowsGroupMat(const MatrixBase<Real> &src);
-    
-  /// Returns logdet of matrix.
-  Real LogDet(Real *det_sign = NULL) const;
-  
-  /// matrix inverse.
-  /// if inverse_needed = false, will fill matrix with garbage.
-  /// (only useful if logdet wanted).
-  void Invert(Real *log_det = NULL, Real *det_sign = NULL,
-              bool inverse_needed = true);
-  /// matrix inverse [double].
-  /// if inverse_needed = false, will fill matrix with garbage
-  /// (only useful if logdet wanted).
-  /// Does inversion in double precision even if matrix was not double.
-  void InvertDouble(Real *LogDet = NULL, Real *det_sign = NULL,
-                      bool inverse_needed = true);
-
-  /// Inverts all the elements of the matrix
-  void InvertElements();
-
-  /// Transpose the matrix.  This one is only
-  /// applicable to square matrices (the one in the
-  /// Matrix child class works also for non-square.
-  void Transpose();
-
-  /// Copies column r from column indices[r] of src.
-  /// As a special case, if indexes[i] == -1, sets column i to zero
-  /// indices.size() must equal this->NumCols(),
-  /// all elements of "reorder" must be in [-1, src.NumCols()-1],
-  /// and src.NumRows() must equal this.NumRows()
-  void CopyCols(const MatrixBase<Real> &src,
-                const std::vector<MatrixIndexT> &indices);
-
-  /// Copies row r from row indices[r] of src.
-  /// As a special case, if indexes[i] == -1, sets row i to zero
-  /// "reorder".size() must equal this->NumRows(),
-  /// all elements of "reorder" must be in [-1, src.NumRows()-1],
-  /// and src.NumCols() must equal this.NumCols()
-  void CopyRows(const MatrixBase<Real> &src,
-                const std::vector<MatrixIndexT> &indices);
-  
-  /// Applies floor to all matrix elements
-  void ApplyFloor(Real floor_val);
-
-  /// Applies floor to all matrix elements
-  void ApplyCeiling(Real ceiling_val);
-
-  /// Calculates log of all the matrix elemnts
-  void ApplyLog();
-
-  /// Exponentiate each of the elements.
-  void ApplyExp();
-
-  /// Applies power to all matrix elements
-  void ApplyPow(Real power);
-
-  /// Apply power to the absolute value of each element. 
-  /// Include the sign of the input element if include_sign == true.
-  /// If the power is negative and the input to the power is zero,
-  /// The output will be set zero.
-  void ApplyPowAbs(Real power, bool include_sign=false);
-  
-  /// Applies the Heaviside step function (x > 0 ? 1 : 0) to all matrix elements
-  /// Note: in general you can make different choices for x = 0, but for now
-  /// please leave it as it (i.e. returning zero) because it affects the
-  /// RectifiedLinearComponent in the neural net code.
-  void ApplyHeaviside();
-  
-  /// Eigenvalue Decomposition of a square NxN matrix into the form (*this) = P D
-  /// P^{-1}.  Be careful: the relationship of D to the eigenvalues we output is
-  /// slightly complicated, due to the need for P to be real.  In the symmetric
-  /// case D is diagonal and real, but in
-  /// the non-symmetric case there may be complex-conjugate pairs of eigenvalues.
-  /// In this case, for the equation (*this) = P D P^{-1} to hold, D must actually
-  /// be block diagonal, with 2x2 blocks corresponding to any such pairs.  If a
-  /// pair is lambda +- i*mu, D will have a corresponding 2x2 block
-  /// [lambda, mu; -mu, lambda].
-  /// Note that if the input matrix (*this) is non-invertible, P may not be invertible
-  /// so in this case instead of the equation (*this) = P D P^{-1} holding, we have
-  /// instead (*this) P = P D.
-  ///
-  /// The non-member function CreateEigenvalueMatrix creates D from eigs_real and eigs_imag.
-  void Eig(MatrixBase<Real> *P,
-           VectorBase<Real> *eigs_real,
-           VectorBase<Real> *eigs_imag) const;
-
-  /// The Power method attempts to take the matrix to a power using a method that
-  /// works in general for fractional and negative powers.  The input matrix must
-  /// be invertible and have reasonable condition (or we don't guarantee the
-  /// results.  The method is based on the eigenvalue decomposition.  It will
-  /// return false and leave the matrix unchanged, if at entry the matrix had
-  /// real negative eigenvalues (or if it had zero eigenvalues and the power was
-  /// negative).
-  bool Power(Real pow);
-
-  /** Singular value decomposition
-     Major limitations:
-     For nonsquare matrices, we assume m>=n (NumRows >= NumCols), and we return
-     the "skinny" Svd, i.e. the matrix in the middle is diagonal, and the
-     one on the left is rectangular.
-
-     In Svd, *this = U*diag(S)*Vt.
-     Null pointers for U and/or Vt at input mean we do not want that output.  We
-     expect that S.Dim() == m, U is either NULL or m by n,
-     and v is either NULL or n by n.
-     The singular values are not sorted (use SortSvd for that).  */
-  void DestructiveSvd(VectorBase<Real> *s, MatrixBase<Real> *U,
-                      MatrixBase<Real> *Vt);  // Destroys calling matrix.
-
-  /// Compute SVD (*this) = U diag(s) Vt.   Note that the V in the call is already
-  /// transposed; the normal formulation is U diag(s) V^T.
-  /// Null pointers for U or V mean we don't want that output (this saves
-  /// compute).  The singular values are not sorted (use SortSvd for that).
-  void Svd(VectorBase<Real> *s, MatrixBase<Real> *U,
-           MatrixBase<Real> *Vt) const;
-  /// Compute SVD but only retain the singular values.
-  void Svd(VectorBase<Real> *s) const { Svd(s, NULL, NULL); }
-
-
-  /// Returns smallest singular value.
-  Real MinSingularValue() const {
-    Vector<Real> tmp(std::min(NumRows(), NumCols()));
-    Svd(&tmp);
-    return tmp.Min();
-  }
-
-  void TestUninitialized() const; // This function is designed so that if any element
-  // if the matrix is uninitialized memory, valgrind will complain.
-  
-  /// Returns condition number by computing Svd.  Works even if cols > rows.
-  /// Returns infinity if all singular values are zero.
-  Real Cond() const;
-
-  /// Returns true if matrix is Symmetric.
-  bool IsSymmetric(Real cutoff = 1.0e-05) const;  // replace magic number
-
-  /// Returns true if matrix is Diagonal.
-  bool IsDiagonal(Real cutoff = 1.0e-05) const;  // replace magic number
-
-  /// Returns true if the matrix is all zeros, except for ones on diagonal.  (it
-  /// does not have to be square).  More specifically, this function returns
-  /// false if for any i, j, (*this)(i, j) differs by more than cutoff from the
-  /// expression (i == j ? 1 : 0).
-  bool IsUnit(Real cutoff = 1.0e-05) const;     // replace magic number
-
-  /// Returns true if matrix is all zeros.
-  bool IsZero(Real cutoff = 1.0e-05) const;     // replace magic number
-
-  /// Frobenius norm, which is the sqrt of sum of square elements.  Same as Schatten 2-norm,
-  /// or just "2-norm".
-  Real FrobeniusNorm() const;
-
-  /// Returns true if ((*this)-other).FrobeniusNorm()
-  /// <= tol * (*this).FrobeniusNorm().
-  bool ApproxEqual(const MatrixBase<Real> &other, float tol = 0.01) const;
-
-  /// Tests for exact equality.  It's usually preferable to use ApproxEqual.
-  bool Equal(const MatrixBase<Real> &other) const;
-
-  /// largest absolute value.
-  Real LargestAbsElem() const;  // largest absolute value.
-
-  /// Returns log(sum(exp())) without exp overflow
-  /// If prune > 0.0, it uses a pruning beam, discarding
-  /// terms less than (max - prune).  Note: in future
-  /// we may change this so that if prune = 0.0, it takes
-  /// the max, so use -1 if you don't want to prune.
-  Real LogSumExp(Real prune = -1.0) const;
-
-  /// Apply soft-max to the collection of all elements of the
-  /// matrix and return normalizer (log sum of exponentials).
-  Real ApplySoftMax();
-  
-  /// Set each element to the sigmoid of the corresponding element of "src".
-  void Sigmoid(const MatrixBase<Real> &src);
-
-  /// Set each element to y = log(1 + exp(x))
-  void SoftHinge(const MatrixBase<Real> &src);
-  
-  /// Apply the function y(i) = (sum_{j = i*G}^{(i+1)*G-1} x_j^(power))^(1 / p).
-  /// Requires src.NumRows() == this->NumRows() and  src.NumCols() % this->NumCols() == 0.
-  void GroupPnorm(const MatrixBase<Real> &src, Real power);
-
-
-  /// Calculate derivatives for the GroupPnorm function above...
-  /// if "input" is the input to the GroupPnorm function above (i.e. the "src" variable),
-  /// and "output" is the result of the computation (i.e. the "this" of that function
-  /// call), and *this has the same dimension as "input", then it sets each element
-  /// of *this to the derivative d(output-elem)/d(input-elem) for each element of "input", where
-  /// "output-elem" is whichever element of output depends on that input element.
-  void GroupPnormDeriv(const MatrixBase<Real> &input, const MatrixBase<Real> &output,
-                       Real power);
-
-
-  /// Set each element to the tanh of the corresponding element of "src".
-  void Tanh(const MatrixBase<Real> &src);
-
-  // Function used in backpropagating derivatives of the sigmoid function:
-  // element-by-element, set *this = diff * value * (1.0 - value).
-  void DiffSigmoid(const MatrixBase<Real> &value,
-                   const MatrixBase<Real> &diff);
-
-  // Function used in backpropagating derivatives of the tanh function:
-  // element-by-element, set *this = diff * (1.0 - value^2).
-  void DiffTanh(const MatrixBase<Real> &value,
-                const MatrixBase<Real> &diff);
-  
-  /** Uses Svd to compute the eigenvalue decomposition of a symmetric positive
-   * semi-definite matrix: (*this) = rP * diag(rS) * rP^T, with rP an
-   * orthogonal matrix so rP^{-1} = rP^T.   Throws exception if input was not
-   * positive semi-definite (check_thresh controls how stringent the check is;
-   * set it to 2 to ensure it won't ever complain, but it will zero out negative
-   * dimensions in your matrix.
-  */
-  void SymPosSemiDefEig(VectorBase<Real> *s, MatrixBase<Real> *P,
-                        Real check_thresh = 0.001);
-
-  friend Real kaldi::TraceMatMat<Real>(const MatrixBase<Real> &A,
-      const MatrixBase<Real> &B, MatrixTransposeType trans);  // tr (A B)
-
-  // so it can get around const restrictions on the pointer to data_.
-  friend class SubMatrix<Real>;
-
-  /// Add a scalar to each element
-  void Add(const Real alpha);
-
-  /// Add a scalar to each diagonal element.
-  void AddToDiag(const Real alpha);
-
-  /// *this += alpha * a * b^T
-  template<typename OtherReal>
-  void AddVecVec(const Real alpha, const VectorBase<OtherReal> &a,
-                 const VectorBase<OtherReal> &b);
-
-  /// [each row of *this] += alpha * v
-  template<typename OtherReal>
-  void AddVecToRows(const Real alpha, const VectorBase<OtherReal> &v);
-  
-  /// [each col of *this] += alpha * v
-  template<typename OtherReal>
-  void AddVecToCols(const Real alpha, const VectorBase<OtherReal> &v);      
-  
-  /// *this += alpha * M [or M^T]
-  void AddMat(const Real alpha, const MatrixBase<Real> &M,
-              MatrixTransposeType transA = kNoTrans);
-
-  /// *this = beta * *this + alpha * M M^T, for symmetric matrices.  It only
-  /// updates the lower triangle of *this.  It will leave the matrix asymmetric;
-  /// if you need it symmetric as a regular matrix, do CopyLowerToUpper().
-  void SymAddMat2(const Real alpha, const MatrixBase<Real> &M,
-                  MatrixTransposeType transA, Real beta);
-
-  /// *this = beta * *this + alpha * diag(v) * M [or M^T].
-  /// The same as adding M but scaling each row M_i by v(i).
-  void AddDiagVecMat(const Real alpha, VectorBase<Real> &v,
-                     const MatrixBase<Real> &M, MatrixTransposeType transM, 
-                     Real beta = 1.0);
- 
-  /// *this = beta * *this + alpha * M [or M^T] * diag(v) 
-  /// The same as adding M but scaling each column M_j by v(j).
-  void AddMatDiagVec(const Real alpha, 
-                     const MatrixBase<Real> &M, MatrixTransposeType transM, 
-                     VectorBase<Real> &v,
-                     Real beta = 1.0);
-
-  /// *this = beta * *this + alpha * A .* B (.* element by element multiplication)
-  void AddMatMatElements(const Real alpha,
-                         const MatrixBase<Real>& A,
-                         const MatrixBase<Real>& B,
-                         const Real beta);
-  
-  /// *this += alpha * S
-  template<typename OtherReal>
-  void AddSp(const Real alpha, const SpMatrix<OtherReal> &S);
-
-  void AddMatMat(const Real alpha,
-                 const MatrixBase<Real>& A, MatrixTransposeType transA,
-                 const MatrixBase<Real>& B, MatrixTransposeType transB,
-                 const Real beta);
- 
-  /// *this = a * b / c (by element; when c = 0, *this = a)
-  void AddMatMatDivMat(const MatrixBase<Real>& A,
-                        const MatrixBase<Real>& B,
-                       const MatrixBase<Real>& C);
-
-  /// A version of AddMatMat specialized for when the second argument
-  /// contains a lot of zeroes.
-  void AddMatSmat(const Real alpha,
-                  const MatrixBase<Real>& A, MatrixTransposeType transA,
-                  const MatrixBase<Real>& B, MatrixTransposeType transB,
-                  const Real beta);
-
-  /// A version of AddMatMat specialized for when the first argument
-  /// contains a lot of zeroes.  
-  void AddSmatMat(const Real alpha,
-                  const MatrixBase<Real>& A, MatrixTransposeType transA,
-                  const MatrixBase<Real>& B, MatrixTransposeType transB,
-                  const Real beta);
-
-  /// this <-- beta*this + alpha*A*B*C.
-  void AddMatMatMat(const Real alpha,
-                    const MatrixBase<Real>& A, MatrixTransposeType transA,
-                    const MatrixBase<Real>& B, MatrixTransposeType transB,
-                    const MatrixBase<Real>& C, MatrixTransposeType transC,
-                    const Real beta);
-
-  /// this <-- beta*this + alpha*SpA*B.
-  // This and the routines below are really
-  // stubs that need to be made more efficient.
-  void AddSpMat(const Real alpha,
-                const SpMatrix<Real>& A,
-                const MatrixBase<Real>& B, MatrixTransposeType transB,
-                const Real beta) {
-    Matrix<Real> M(A);
-    return AddMatMat(alpha, M, kNoTrans, B, transB, beta);
-  }
-  /// this <-- beta*this + alpha*A*B.
-  void AddTpMat(const Real alpha,
-                const TpMatrix<Real>& A, MatrixTransposeType transA,
-                const MatrixBase<Real>& B, MatrixTransposeType transB,
-                const Real beta) {
-    Matrix<Real> M(A);
-    return AddMatMat(alpha, M, transA, B, transB, beta);
-  }
-  /// this <-- beta*this + alpha*A*B.
-  void AddMatSp(const Real alpha,
-                const MatrixBase<Real>& A, MatrixTransposeType transA,
-                const SpMatrix<Real>& B,
-                const Real beta) {
-    Matrix<Real> M(B);
-    return AddMatMat(alpha, A, transA, M, kNoTrans, beta);
-  }
-  /// this <-- beta*this + alpha*A*B*C.
-  void AddSpMatSp(const Real alpha,
-                  const SpMatrix<Real> &A,
-                  const MatrixBase<Real>& B, MatrixTransposeType transB,
-                  const SpMatrix<Real>& C,
-                const Real beta) {
-    Matrix<Real> M(A), N(C);
-    return AddMatMatMat(alpha, M, kNoTrans, B, transB, N, kNoTrans, beta);
-  }
-  /// this <-- beta*this + alpha*A*B.
-  void AddMatTp(const Real alpha,
-                const MatrixBase<Real>& A, MatrixTransposeType transA,
-                const TpMatrix<Real>& B, MatrixTransposeType transB,
-                const Real beta) {
-    Matrix<Real> M(B);
-    return AddMatMat(alpha, A, transA, M, transB, beta);
-  }
-
-  /// this <-- beta*this + alpha*A*B.
-  void AddTpTp(const Real alpha,
-               const TpMatrix<Real>& A, MatrixTransposeType transA,
-               const TpMatrix<Real>& B, MatrixTransposeType transB,
-               const Real beta) {
-    Matrix<Real> M(A), N(B);
-    return AddMatMat(alpha, M, transA, N, transB, beta);
-  }
-
-  /// this <-- beta*this + alpha*A*B.
-  // This one is more efficient, not like the others above.
-  void AddSpSp(const Real alpha,
-               const SpMatrix<Real>& A, const SpMatrix<Real>& B,
-               const Real beta);
-
-  /// Copy lower triangle to upper triangle (symmetrize)
-  void CopyLowerToUpper();
-
-  /// Copy upper triangle to lower triangle (symmetrize)
-  void CopyUpperToLower();
-  
-  /// This function orthogonalizes the rows of a matrix using the Gram-Schmidt
-  /// process.  It is only applicable if NumRows() <= NumCols().  It will use
-  /// random number generation to fill in rows with something nonzero, in cases
-  /// where the original matrix was of deficient row rank.
-  void OrthogonalizeRows();
-
-  /// stream read.
-  /// Use instead of stream<<*this, if you want to add to existing contents.
-  // Will throw exception on failure.
-  void Read(std::istream & in, bool binary, bool add = false);
-  /// write to stream.
-  void Write(std::ostream & out, bool binary) const;
-
-  // Below is internal methods for Svd, user does not have to know about this.
-#if !defined(HAVE_ATLAS) && !defined(USE_KALDI_SVD)
-  // protected:
-  // Should be protected but used directly in testing routine.
-  // destroys *this!
-  void LapackGesvd(VectorBase<Real> *s, MatrixBase<Real> *U,
-                     MatrixBase<Real> *Vt);
-#else
- protected:
-  // destroys *this!
-  bool JamaSvd(VectorBase<Real> *s, MatrixBase<Real> *U,
-               MatrixBase<Real> *V);
-
-#endif
- protected:
-
-  ///  Initializer, callable only from child.
-  explicit MatrixBase(Real *data, MatrixIndexT cols, MatrixIndexT rows, MatrixIndexT stride) :
-    data_(data), num_cols_(cols), num_rows_(rows), stride_(stride) {
-    KALDI_ASSERT_IS_FLOATING_TYPE(Real);
-  }
-
-  ///  Initializer, callable only from child.
-  /// Empty initializer, for un-initialized matrix.
-  explicit MatrixBase(): data_(NULL) {
-    KALDI_ASSERT_IS_FLOATING_TYPE(Real);
-  }
-
-  // Make sure pointers to MatrixBase cannot be deleted.
-  ~MatrixBase() { }
-
-  /// A workaround that allows SubMatrix to get a pointer to non-const data
-  /// for const Matrix. Unfortunately C++ does not allow us to declare a
-  /// "public const" inheritance or anything like that, so it would require
-  /// a lot of work to make the SubMatrix class totally const-correct--
-  /// we would have to override many of the Matrix functions.
-  inline Real*  Data_workaround() const {
-    return data_;
-  }
-
-  /// data memory area
-  Real*   data_;
-
-  /// these atributes store the real matrix size as it is stored in memory
-  /// including memalignment
-  MatrixIndexT    num_cols_;   /// < Number of columns
-  MatrixIndexT    num_rows_;   /// < Number of rows
-  /** True number of columns for the internal matrix. This number may differ
-   * from num_cols_ as memory alignment might be used. */
-  MatrixIndexT    stride_;
- private:
-  KALDI_DISALLOW_COPY_AND_ASSIGN(MatrixBase);
-};
-
-/// A class for storing matrices.
-template<typename Real>
-class Matrix : public MatrixBase<Real> {
- public:
-
-  /// Empty constructor.
-  Matrix();
-
-  /// Basic constructor.  Sets to zero by default.
-  /// if set_zero == false, memory contents are undefined.
-  Matrix(const MatrixIndexT r, const MatrixIndexT c,
-         MatrixResizeType resize_type = kSetZero):
-      MatrixBase<Real>() { Resize(r, c, resize_type); }
-  
-  /// Copy constructor from CUDA matrix
-  /// This is defined in ../cudamatrix/cu-matrix.h
-  template<typename OtherReal>
-  explicit Matrix(const CuMatrixBase<OtherReal> &cu,
-                  MatrixTransposeType trans = kNoTrans);
-
-
-  /// Swaps the contents of *this and *other.  Shallow swap.
-  void Swap(Matrix<Real> *other);
-
-  /// Defined in ../cudamatrix/cu-matrix.cc
-  void Swap(CuMatrix<Real> *mat);
-
-  /// Constructor from any MatrixBase. Can also copy with transpose.
-  /// Allocates new memory.
-  explicit Matrix(const MatrixBase<Real> & M,
-                  MatrixTransposeType trans = kNoTrans);
-  
-  /// Same as above, but need to avoid default copy constructor.
-  Matrix(const Matrix<Real> & M);  //  (cannot make explicit)
-
-  /// Copy constructor: as above, but from another type.
-  template<typename OtherReal>
-  explicit Matrix(const MatrixBase<OtherReal> & M,
-                    MatrixTransposeType trans = kNoTrans);
-
-  /// Copy constructor taking SpMatrix...
-  /// It is symmetric, so no option for transpose, and NumRows == Cols
-  template<typename OtherReal>
-  explicit Matrix(const SpMatrix<OtherReal> & M) : MatrixBase<Real>() {
-    Resize(M.NumRows(), M.NumRows(), kUndefined);
-    this->CopyFromSp(M);
-  }
-
-  /// Constructor from CompressedMatrix
-  explicit Matrix(const CompressedMatrix &C);
-  
-  /// Copy constructor taking TpMatrix...
-  template <typename OtherReal>
-  explicit Matrix(const TpMatrix<OtherReal> & M,
-                  MatrixTransposeType trans = kNoTrans) : MatrixBase<Real>() {
-    if (trans == kNoTrans) {
-      Resize(M.NumRows(), M.NumCols(), kUndefined);
-      this->CopyFromTp(M);
-    } else {
-      Resize(M.NumCols(), M.NumRows(), kUndefined);
-      this->CopyFromTp(M, kTrans);
-    }
-  }
-
-  /// read from stream.
-  // Unlike one in base, allows resizing.
-  void Read(std::istream & in, bool binary, bool add = false);
-
-  /// Remove a specified row.
-  void RemoveRow(MatrixIndexT i);
-  
-  /// Transpose the matrix.  Works for non-square
-  /// matrices as well as square ones.
-  void Transpose();
-
-  /// Distructor to free matrices.
-  ~Matrix() { Destroy(); }
-
-  /// Sets matrix to a specified size (zero is OK as long as both r and c are
-  /// zero).  The value of the new data depends on resize_type:
-  ///   -if kSetZero, the new data will be zero
-  ///   -if kUndefined, the new data will be undefined
-  ///   -if kCopyData, the new data will be the same as the old data in any
-  ///      shared positions, and zero elsewhere.
-  /// This function takes time proportional to the number of data elements.
-  void Resize(const MatrixIndexT r,
-              const MatrixIndexT c,
-              MatrixResizeType resize_type = kSetZero);
-
-  /// Assignment operator that takes MatrixBase.
-  Matrix<Real> &operator = (const MatrixBase<Real> &other) {
-    if (MatrixBase<Real>::NumRows() != other.NumRows() ||
-        MatrixBase<Real>::NumCols() != other.NumCols())
-      Resize(other.NumRows(), other.NumCols(), kUndefined);
-    MatrixBase<Real>::CopyFromMat(other);
-    return *this;
-  }
-
-  /// Assignment operator. Needed for inclusion in std::vector.
-  Matrix<Real> &operator = (const Matrix<Real> &other) {
-    if (MatrixBase<Real>::NumRows() != other.NumRows() ||
-        MatrixBase<Real>::NumCols() != other.NumCols())
-      Resize(other.NumRows(), other.NumCols(), kUndefined);
-    MatrixBase<Real>::CopyFromMat(other);
-    return *this;
-  }
-  
-
- private:
-  /// Deallocates memory and sets to empty matrix (dimension 0, 0).
-  void Destroy();
-  
-  /// Init assumes the current class contents are invalid (i.e. junk or have
-  /// already been freed), and it sets the matrix to newly allocated memory with
-  /// the specified number of rows and columns.  r == c == 0 is acceptable.  The data
-  /// memory contents will be undefined.
-  void Init(const MatrixIndexT r,
-            const MatrixIndexT c);
-
-};
-/// @} end "addtogroup matrix_group"
-
-/// \addtogroup matrix_funcs_io
-/// @{
-
-/// A structure containing the HTK header.
-/// [TODO: change the style of the variables to Kaldi-compliant]
-struct HtkHeader {
-  /// Number of samples.
-  int32    mNSamples;
-  /// Sample period.
-  int32    mSamplePeriod;
-  /// Sample size
-  int16    mSampleSize;
-  /// Sample kind.
-  uint16   mSampleKind;
-};
-
-// Read HTK formatted features from file into matrix.
-template<typename Real>
-bool ReadHtk(std::istream &is, Matrix<Real> *M, HtkHeader *header_ptr);
-
-// Write (HTK format) features to file from matrix.
-template<typename Real>
-bool WriteHtk(std::ostream &os, const MatrixBase<Real> &M, HtkHeader htk_hdr);
-
-// Write (CMUSphinx format) features to file from matrix.
-template<typename Real>
-bool WriteSphinx(std::ostream &os, const MatrixBase<Real> &M);
-
-/// @} end of "addtogroup matrix_funcs_io"
-
-/**
-  Sub-matrix representation.
-  Can work with sub-parts of a matrix using this class.
-  Note that SubMatrix is not very const-correct-- it allows you to
-  change the contents of a const Matrix.  Be careful!
-*/
-
-template<typename Real>
-class SubMatrix : public MatrixBase<Real> {
- public:
-  // Initialize a SubMatrix from part of a matrix; this is
-  // a bit like A(b:c, d:e) in Matlab.
-  // This initializer is against the proper semantics of "const", since
-  // SubMatrix can change its contents.  It would be hard to implement
-  // a "const-safe" version of this class.
-  SubMatrix(const MatrixBase<Real>& T,
-            const MatrixIndexT ro,  // row offset, 0 < ro < NumRows()
-            const MatrixIndexT r,   // number of rows, r > 0
-            const MatrixIndexT co,  // column offset, 0 < co < NumCols()
-            const MatrixIndexT c);   // number of columns, c > 0
-  
-  // This initializer is mostly intended for use in CuMatrix and related
-  // classes.  Be careful!
-  SubMatrix(Real *data,
-            MatrixIndexT num_rows,
-            MatrixIndexT num_cols,
-            MatrixIndexT stride);
-  
-  ~SubMatrix<Real>() {}
-  
-  /// This type of constructor is needed for Range() to work [in Matrix base
-  /// class]. Cannot make it explicit.
-  SubMatrix<Real> (const SubMatrix &other):
-  MatrixBase<Real> (other.data_, other.num_cols_, other.num_rows_,
-                    other.stride_) {}
-
- private:
-  /// Disallow assignment.
-  SubMatrix<Real> &operator = (const SubMatrix<Real> &other);
-};
-/// @} End of "addtogroup matrix_funcs_io".
-
-/// \addtogroup matrix_funcs_scalar
-/// @{
-
-// Some declarations.  These are traces of products.
-
-
-template<typename Real>
-bool ApproxEqual(const MatrixBase<Real> &A,
-                 const MatrixBase<Real> &B, Real tol = 0.01) {
-  return A.ApproxEqual(B, tol);
-}
-
-template<typename Real>
-inline void AssertEqual(const MatrixBase<Real> &A, const MatrixBase<Real> &B,
-                        float tol = 0.01) {
-  KALDI_ASSERT(A.ApproxEqual(B, tol));
-}
-
-/// Returns trace of matrix.
-template <typename Real>
-double TraceMat(const MatrixBase<Real> &A) { return A.Trace(); }
-
-
-/// Returns tr(A B C)
-template <typename Real>
-Real TraceMatMatMat(const MatrixBase<Real> &A, MatrixTransposeType transA,
-                      const MatrixBase<Real> &B, MatrixTransposeType transB,
-                      const MatrixBase<Real> &C, MatrixTransposeType transC);
-
-/// Returns tr(A B C D)
-template <typename Real>
-Real TraceMatMatMatMat(const MatrixBase<Real> &A, MatrixTransposeType transA,
-                         const MatrixBase<Real> &B, MatrixTransposeType transB,
-                         const MatrixBase<Real> &C, MatrixTransposeType transC,
-                         const MatrixBase<Real> &D, MatrixTransposeType transD);
-
-/// @} end "addtogroup matrix_funcs_scalar"
-
-
-/// \addtogroup matrix_funcs_misc
-/// @{
-
-
-/// Function to ensure that SVD is sorted.  This function is made as generic as
-/// possible, to be applicable to other types of problems.  s->Dim() should be
-/// the same as U->NumCols(), and we sort s from greatest to least absolute
-/// value (if sort_on_absolute_value == true) or greatest to least value
-/// otherwise, moving the columns of U, if it exists, and the rows of Vt, if it
-/// exists, around in the same way.  Note: the "absolute value" part won't matter
-/// if this is an actual SVD, since singular values are non-negative.
-template<typename Real> void SortSvd(VectorBase<Real> *s, MatrixBase<Real> *U,
-                                     MatrixBase<Real>* Vt = NULL,
-                                     bool sort_on_absolute_value = true);
-
-/// Creates the eigenvalue matrix D that is part of the decomposition used Matrix::Eig.
-/// D will be block-diagonal with blocks of size 1 (for real eigenvalues) or 2x2
-/// for complex pairs.  If a complex pair is lambda +- i*mu, D will have a corresponding
-/// 2x2 block [lambda, mu; -mu, lambda].
-/// This function will throw if any complex eigenvalues are not in complex conjugate
-/// pairs (or the members of such pairs are not consecutively numbered).
-template<typename Real>
-void CreateEigenvalueMatrix(const VectorBase<Real> &real, const VectorBase<Real> &imag,
-                            MatrixBase<Real> *D);
-
-/// The following function is used in Matrix::Power, and separately tested, so we
-/// declare it here mainly for the testing code to see.  It takes a complex value to
-/// a power using a method that will work for noninteger powers (but will fail if the
-/// complex value is real and negative).
-template<typename Real>
-bool AttemptComplexPower(Real *x_re, Real *x_im, Real power);
-
-
-
-/// @} end of addtogroup matrix_funcs_misc
-
-/// \addtogroup matrix_funcs_io
-/// @{
-template<typename Real>
-std::ostream & operator << (std::ostream & Out, const MatrixBase<Real> & M);
-
-template<typename Real>
-std::istream & operator >> (std::istream & In, MatrixBase<Real> & M);
-
-// The Matrix read allows resizing, so we override the MatrixBase one.
-template<typename Real>
-std::istream & operator >> (std::istream & In, Matrix<Real> & M);
-
-
-template<typename Real>
-bool SameDim(const MatrixBase<Real> &M, const MatrixBase<Real> &N) {
-  return (M.NumRows() == N.NumRows() && M.NumCols() == N.NumCols());
-}
-
-/// @} end of \addtogroup matrix_funcs_io
-
-
-}  // namespace kaldi
-
-
-
-// we need to include the implementation and some
-// template specializations.
-#include "matrix/kaldi-matrix-inl.h"
-
-
-#endif  // KALDI_MATRIX_KALDI_MATRIX_H_
diff --git a/kaldi_io/src/kaldi/matrix/kaldi-vector-inl.h b/kaldi_io/src/kaldi/matrix/kaldi-vector-inl.h
deleted file mode 100644
index c3a4f52..0000000
--- a/kaldi_io/src/kaldi/matrix/kaldi-vector-inl.h
+++ /dev/null
@@ -1,58 +0,0 @@
-// matrix/kaldi-vector-inl.h
-
-// Copyright 2009-2011   Ondrej Glembek;  Microsoft Corporation;
-//                       Haihua Xu
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-// This is an internal header file, included by other library headers.
-// You should not attempt to use it directly.
-
-#ifndef KALDI_MATRIX_KALDI_VECTOR_INL_H_
-#define KALDI_MATRIX_KALDI_VECTOR_INL_H_ 1
-
-namespace kaldi {
-
-template<typename Real>
-std::ostream & operator << (std::ostream &os, const VectorBase<Real> &rv) {
-  rv.Write(os, false);
-  return os;
-}
-
-template<typename Real>
-std::istream &operator >> (std::istream &is, VectorBase<Real> &rv) {
-  rv.Read(is, false);
-  return is;
-}
-
-template<typename Real>
-std::istream &operator >> (std::istream &is, Vector<Real> &rv) {
-  rv.Read(is, false);
-  return is;
-}
-
-template<>
-template<>
-void VectorBase<float>::AddVec(const float alpha, const VectorBase<float> &rv);
-
-template<>
-template<>
-void VectorBase<double>::AddVec<double>(const double alpha,
-                                        const VectorBase<double> &rv);
-
-}  // namespace kaldi
-
-#endif  // KALDI_MATRIX_KALDI_VECTOR_INL_H_
diff --git a/kaldi_io/src/kaldi/matrix/kaldi-vector.h b/kaldi_io/src/kaldi/matrix/kaldi-vector.h
deleted file mode 100644
index 2b3395b..0000000
--- a/kaldi_io/src/kaldi/matrix/kaldi-vector.h
+++ /dev/null
@@ -1,585 +0,0 @@
-// matrix/kaldi-vector.h
-
-// Copyright 2009-2012   Ondrej Glembek;  Microsoft Corporation;  Lukas Burget;
-//                       Saarland University (Author: Arnab Ghoshal);
-//                       Ariya Rastrow;  Petr Schwarz;  Yanmin Qian;
-//                       Karel Vesely;  Go Vivace Inc.;  Arnab Ghoshal
-//                       Wei Shi;
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_MATRIX_KALDI_VECTOR_H_
-#define KALDI_MATRIX_KALDI_VECTOR_H_ 1
-
-#include "matrix/matrix-common.h"
-
-namespace kaldi {
-
-/// \addtogroup matrix_group
-/// @{
-
-///  Provides a vector abstraction class.
-///  This class provides a way to work with vectors in kaldi.
-///  It encapsulates basic operations and memory optimizations.
-template<typename Real>
-class VectorBase {
- public:
-  /// Set vector to all zeros.
-  void SetZero();
-
-  /// Returns true if matrix is all zeros.
-  bool IsZero(Real cutoff = 1.0e-06) const;     // replace magic number
-
-  /// Set all members of a vector to a specified value.
-  void Set(Real f);
-
-  /// Set vector to random normally-distributed noise.
-  void SetRandn();
-
-  /// This function returns a random index into this vector,
-  /// chosen with probability proportional to the corresponding
-  /// element.  Requires that this->Min() >= 0 and this->Sum() > 0.
-  MatrixIndexT RandCategorical() const;
-  
-  /// Returns the  dimension of the vector.
-  inline MatrixIndexT Dim() const { return dim_; }
-
-  /// Returns the size in memory of the vector, in bytes.
-  inline MatrixIndexT SizeInBytes() const { return (dim_*sizeof(Real)); }
-
-  /// Returns a pointer to the start of the vector's data.
-  inline Real* Data() { return data_; }
-
-  /// Returns a pointer to the start of the vector's data (const).
-  inline const Real* Data() const { return data_; }
-
-  /// Indexing  operator (const).
-  inline Real operator() (MatrixIndexT i) const {
-    KALDI_PARANOID_ASSERT(static_cast<UnsignedMatrixIndexT>(i) <
-                 static_cast<UnsignedMatrixIndexT>(dim_));
-    return *(data_ + i);
-  }
-
-  /// Indexing operator (non-const).
-  inline Real & operator() (MatrixIndexT i) {
-    KALDI_PARANOID_ASSERT(static_cast<UnsignedMatrixIndexT>(i) <
-                 static_cast<UnsignedMatrixIndexT>(dim_));
-    return *(data_ + i);
-  }
-
-  /** @brief Returns a sub-vector of a vector (a range of elements).
-   *  @param o [in] Origin, 0 < o < Dim()
-   *  @param l [in] Length 0 < l < Dim()-o
-   *  @return A SubVector object that aliases the data of the Vector object.
-   *  See @c SubVector class for details   */
-  SubVector<Real> Range(const MatrixIndexT o, const MatrixIndexT l) {
-    return SubVector<Real>(*this, o, l);
-  }
-
-  /** @brief Returns a const sub-vector of a vector (a range of elements).
-   *  @param o [in] Origin, 0 < o < Dim()
-   *  @param l [in] Length 0 < l < Dim()-o
-   *  @return A SubVector object that aliases the data of the Vector object.
-   *  See @c SubVector class for details   */
-  const SubVector<Real> Range(const MatrixIndexT o,
-                              const MatrixIndexT l) const {
-    return SubVector<Real>(*this, o, l);
-  }
-
-  /// Copy data from another vector (must match own size).
-  void CopyFromVec(const VectorBase<Real> &v);
-
-  /// Copy data from a SpMatrix or TpMatrix (must match own size).
-  template<typename OtherReal>
-  void CopyFromPacked(const PackedMatrix<OtherReal> &M);
-  
-  /// Copy data from another vector of different type (double vs. float)
-  template<typename OtherReal>
-  void CopyFromVec(const VectorBase<OtherReal> &v);
-
-  /// Copy from CuVector.  This is defined in ../cudamatrix/cu-vector.h
-  template<typename OtherReal>
-  void CopyFromVec(const CuVectorBase<OtherReal> &v);
-
-  
-  /// Apply natural log to all elements.  Throw if any element of
-  /// the vector is negative (but doesn't complain about zero; the
-  /// log will be -infinity
-  void ApplyLog();
-
-  /// Apply natural log to another vector and put result in *this.
-  void ApplyLogAndCopy(const VectorBase<Real> &v);
-
-  /// Apply exponential to each value in vector.
-  void ApplyExp();
-
-  /// Take absolute value of each of the elements
-  void ApplyAbs();
-
-  /// Applies floor to all elements. Returns number of elements floored.
-  MatrixIndexT ApplyFloor(Real floor_val);
-
-  /// Applies ceiling to all elements. Returns number of elements changed.
-  MatrixIndexT ApplyCeiling(Real ceil_val);
-  
-  /// Applies floor to all elements. Returns number of elements floored.
-  MatrixIndexT ApplyFloor(const VectorBase<Real> &floor_vec);
-
-  /// Apply soft-max to vector and return normalizer (log sum of exponentials).
-  /// This is the same as: \f$ x(i) = exp(x(i)) / \sum_i exp(x(i)) \f$
-  Real ApplySoftMax();
-
-  /// Sets each element of *this to the tanh of the corresponding element of "src".
-  void Tanh(const VectorBase<Real> &src);
-
-  /// Sets each element of *this to the sigmoid function of the corresponding
-  /// element of "src".
-  void Sigmoid(const VectorBase<Real> &src);
-  
-  /// Take all  elements of vector to a power.
-  void ApplyPow(Real power);
-
-  /// Take the absolute value of all elements of a vector to a power.
-  /// Include the sign of the input element if include_sign == true.
-  /// If power is negative and the input value is zero, the output is set zero.
-  void ApplyPowAbs(Real power, bool include_sign=false);
-  
-  /// Compute the p-th norm of the vector.
-  Real Norm(Real p) const;
-  
-  /// Returns true if ((*this)-other).Norm(2.0) <= tol * (*this).Norm(2.0).
-  bool ApproxEqual(const VectorBase<Real> &other, float tol = 0.01) const;
-  
-  /// Invert all elements.
-  void InvertElements();
-
-  /// Add vector : *this = *this + alpha * rv (with casting between floats and
-  /// doubles)
-  template<typename OtherReal>
-  void AddVec(const Real alpha, const VectorBase<OtherReal> &v);
-
-  /// Add vector : *this = *this + alpha * rv^2  [element-wise squaring].
-  void AddVec2(const Real alpha, const VectorBase<Real> &v);
-
-  /// Add vector : *this = *this + alpha * rv^2  [element-wise squaring],
-  /// with casting between floats and doubles.
-  template<typename OtherReal>
-  void AddVec2(const Real alpha, const VectorBase<OtherReal> &v);
-
-  /// Add matrix times vector : this <-- beta*this + alpha*M*v.
-  /// Calls BLAS GEMV.
-  void AddMatVec(const Real alpha, const MatrixBase<Real> &M,
-                 const MatrixTransposeType trans,  const VectorBase<Real> &v,
-                 const Real beta); // **beta previously defaulted to 0.0**
-
-  /// This is as AddMatVec, except optimized for where v contains a lot
-  /// of zeros.
-  void AddMatSvec(const Real alpha, const MatrixBase<Real> &M,
-                  const MatrixTransposeType trans,  const VectorBase<Real> &v,
-                  const Real beta); // **beta previously defaulted to 0.0**
-
-  
-  /// Add symmetric positive definite matrix times vector:
-  ///  this <-- beta*this + alpha*M*v.   Calls BLAS SPMV.
-  void AddSpVec(const Real alpha, const SpMatrix<Real> &M,
-                const VectorBase<Real> &v, const Real beta);  // **beta previously defaulted to 0.0**
-
-  /// Add triangular matrix times vector: this <-- beta*this + alpha*M*v.
-  /// Works even if rv == *this.
-  void AddTpVec(const Real alpha, const TpMatrix<Real> &M,
-                const MatrixTransposeType trans, const VectorBase<Real> &v,
-                const Real beta);  // **beta previously defaulted to 0.0**
-
-  /// Set each element to y = (x == orig ? changed : x).
-  void ReplaceValue(Real orig, Real changed);
-
-  /// Multipy element-by-element by another vector.
-  void MulElements(const VectorBase<Real> &v);
-  /// Multipy element-by-element by another vector of different type.
-  template<typename OtherReal>
-  void MulElements(const VectorBase<OtherReal> &v);
-
-  /// Divide element-by-element by a vector.
-  void DivElements(const VectorBase<Real> &v);
-  /// Divide element-by-element by a vector of different type.
-  template<typename OtherReal>
-  void DivElements(const VectorBase<OtherReal> &v);
-
-  /// Add a constant to each element of a vector.
-  void Add(Real c);
-
-  /// Add element-by-element product of vectlrs:
-  //  this <-- alpha * v .* r + beta*this .
-  void AddVecVec(Real alpha, const VectorBase<Real> &v,
-                 const VectorBase<Real> &r, Real beta);
-
-  /// Add element-by-element quotient of two vectors.
-  ///  this <---- alpha*v/r + beta*this
-  void AddVecDivVec(Real alpha, const VectorBase<Real> &v,
-                    const VectorBase<Real> &r, Real beta);
-
-  /// Multiplies all elements by this constant.
-  void Scale(Real alpha);
-
-  /// Multiplies this vector by lower-triangular marix:  *this <-- *this *M
-  void MulTp(const TpMatrix<Real> &M, const MatrixTransposeType trans);
-
-  /// If trans == kNoTrans, solves M x = b, where b is the value of *this at input
-  /// and x is the value of *this at output.
-  /// If trans == kTrans, solves M' x = b.
-  /// Does not test for M being singular or near-singular, so test it before
-  /// calling this routine.
-  void Solve(const TpMatrix<Real> &M, const MatrixTransposeType trans);
-
-  /// Performs a row stack of the matrix M
-  void CopyRowsFromMat(const MatrixBase<Real> &M);
-  template<typename OtherReal>
-  void CopyRowsFromMat(const MatrixBase<OtherReal> &M);
-
-  /// The following is implemented in ../cudamatrix/cu-matrix.cc
-  void CopyRowsFromMat(const CuMatrixBase<Real> &M);
-
-  /// Performs a column stack of the matrix M
-  void CopyColsFromMat(const MatrixBase<Real> &M);
-
-  /// Extracts a row of the matrix M.  Could also do this with
-  /// this->Copy(M[row]).
-  void CopyRowFromMat(const MatrixBase<Real> &M, MatrixIndexT row);
-  /// Extracts a row of the matrix M with type conversion.
-  template<typename OtherReal>
-  void CopyRowFromMat(const MatrixBase<OtherReal> &M, MatrixIndexT row);
-
-  /// Extracts a row of the symmetric matrix S.
-  template<typename OtherReal>
-  void CopyRowFromSp(const SpMatrix<OtherReal> &S, MatrixIndexT row);
-  
-  /// Extracts a column of the matrix M.
-  template<typename OtherReal>
-  void CopyColFromMat(const MatrixBase<OtherReal> &M , MatrixIndexT col);
-
-  /// Extracts the diagonal of the matrix M.
-  void CopyDiagFromMat(const MatrixBase<Real> &M);
-
-  /// Extracts the diagonal of a packed matrix M; works for Sp or Tp.
-  void CopyDiagFromPacked(const PackedMatrix<Real> &M);
-
-
-  /// Extracts the diagonal of a symmetric matrix.
-  inline void CopyDiagFromSp(const SpMatrix<Real> &M) { CopyDiagFromPacked(M); }
-
-  /// Extracts the diagonal of a triangular matrix.
-  inline void CopyDiagFromTp(const TpMatrix<Real> &M) { CopyDiagFromPacked(M); }
-
-  /// Returns the maximum value of any element, or -infinity for the empty vector.
-  Real Max() const;
-
-  /// Returns the maximum value of any element, and the associated index.
-  /// Error if vector is empty.
-  Real Max(MatrixIndexT *index) const;
-  
-  /// Returns the minimum value of any element, or +infinity for the empty vector.
-  Real Min() const;
-
-  /// Returns the minimum value of any element, and the associated index.
-  /// Error if vector is empty.
-  Real Min(MatrixIndexT *index) const;
-  
-  /// Returns sum of the elements
-  Real Sum() const;
-
-  /// Returns sum of the logs of the elements.  More efficient than
-  /// just taking log of each.  Will return NaN if any elements are
-  /// negative.
-  Real SumLog() const;
-
-  /// Does *this = alpha * (sum of rows of M) + beta * *this.
-  void AddRowSumMat(Real alpha, const MatrixBase<Real> &M, Real beta = 1.0);
-  
-  /// Does *this = alpha * (sum of columns of M) + beta * *this.
-  void AddColSumMat(Real alpha, const MatrixBase<Real> &M, Real beta = 1.0);
-
-  /// Add the diagonal of a matrix times itself:
-  /// *this = diag(M M^T) +  beta * *this (if trans == kNoTrans), or
-  /// *this = diag(M^T M) +  beta * *this (if trans == kTrans).
-  void AddDiagMat2(Real alpha, const MatrixBase<Real> &M,
-                   MatrixTransposeType trans = kNoTrans, Real beta = 1.0);
-
-  /// Add the diagonal of a matrix product: *this = diag(M N), assuming the
-  /// "trans" arguments are both kNoTrans; for transpose arguments, it behaves
-  /// as you would expect.
-  void AddDiagMatMat(Real alpha, const MatrixBase<Real> &M, MatrixTransposeType transM,
-                     const MatrixBase<Real> &N, MatrixTransposeType transN,
-                     Real beta = 1.0);  
-
-  /// Returns log(sum(exp())) without exp overflow
-  /// If prune > 0.0, ignores terms less than the max - prune.
-  /// [Note: in future, if prune = 0.0, it will take the max.
-  /// For now, use -1 if you don't want it to prune.]
-  Real LogSumExp(Real prune = -1.0) const;
-
-  /// Reads from C++ stream (option to add to existing contents).
-  /// Throws exception on failure
-  void Read(std::istream & in, bool binary, bool add = false);
-
-  /// Writes to C++ stream (option to write in binary).
-  void Write(std::ostream &Out, bool binary) const;
-
-  friend class VectorBase<double>;
-  friend class VectorBase<float>;
-  friend class CuVectorBase<Real>;
-  friend class CuVector<Real>;
- protected:
-  /// Destructor;  does not deallocate memory, this is handled by child classes.
-  /// This destructor is protected so this object so this object can only be
-  /// deleted via a child.
-  ~VectorBase() {}
-
-  /// Empty initializer, corresponds to vector of zero size.
-  explicit VectorBase(): data_(NULL), dim_(0) {
-    KALDI_ASSERT_IS_FLOATING_TYPE(Real);
-  }
-
-// Took this out since it is not currently used, and it is possible to create
-// objects where the allocated memory is not the same size as dim_ : Arnab
-//  /// Initializer from a pointer and a size; keeps the pointer internally
-//  /// (ownership or non-ownership depends on the child class).
-//  explicit VectorBase(Real* data, MatrixIndexT dim)
-//      : data_(data), dim_(dim) {}
-
-  // Arnab : made this protected since it is unsafe too.
-  /// Load data into the vector: sz must match own size.
-  void CopyFromPtr(const Real* Data, MatrixIndexT sz);
-
-  /// data memory area
-  Real* data_;
-  /// dimension of vector
-  MatrixIndexT dim_;
-  KALDI_DISALLOW_COPY_AND_ASSIGN(VectorBase);
-}; // class VectorBase
-
-/** @brief A class representing a vector.
- *
- *  This class provides a way to work with vectors in kaldi.
- *  It encapsulates basic operations and memory optimizations.  */
-template<typename Real>
-class Vector: public VectorBase<Real> {
- public:
-  /// Constructor that takes no arguments.  Initializes to empty.
-  Vector(): VectorBase<Real>() {}
-
-  /// Constructor with specific size.  Sets to all-zero by default
-  /// if set_zero == false, memory contents are undefined.
-  explicit Vector(const MatrixIndexT s,
-                  MatrixResizeType resize_type = kSetZero)
-      : VectorBase<Real>() {  Resize(s, resize_type);  }
-
-  /// Copy constructor from CUDA vector
-  /// This is defined in ../cudamatrix/cu-vector.h
-  template<typename OtherReal>
-  explicit Vector(const CuVectorBase<OtherReal> &cu);
-
-  /// Copy constructor.  The need for this is controversial.
-  Vector(const Vector<Real> &v) : VectorBase<Real>()  { //  (cannot be explicit)
-    Resize(v.Dim(), kUndefined);
-    this->CopyFromVec(v);
-  }
-
-  /// Copy-constructor from base-class, needed to copy from SubVector.
-  explicit Vector(const VectorBase<Real> &v) : VectorBase<Real>() {
-    Resize(v.Dim(), kUndefined);
-    this->CopyFromVec(v);
-  }
-
-  /// Type conversion constructor.
-  template<typename OtherReal>
-  explicit Vector(const VectorBase<OtherReal> &v): VectorBase<Real>() {
-    Resize(v.Dim(), kUndefined);
-    this->CopyFromVec(v);
-  }
-
-// Took this out since it is unsafe : Arnab
-//  /// Constructor from a pointer and a size; copies the data to a location
-//  /// it owns.
-//  Vector(const Real* Data, const MatrixIndexT s): VectorBase<Real>() {
-//    Resize(s);
-  //    CopyFromPtr(Data, s);
-//  }
-
-
-  /// Swaps the contents of *this and *other.  Shallow swap.
-  void Swap(Vector<Real> *other);
-
-  /// Destructor.  Deallocates memory.
-  ~Vector() { Destroy(); }
-
-  /// Read function using C++ streams.  Can also add to existing contents
-  /// of matrix.
-  void Read(std::istream & in, bool binary, bool add = false);
-
-  /// Set vector to a specified size (can be zero).
-  /// The value of the new data depends on resize_type:
-  ///   -if kSetZero, the new data will be zero
-  ///   -if kUndefined, the new data will be undefined
-  ///   -if kCopyData, the new data will be the same as the old data in any
-  ///      shared positions, and zero elsewhere.
-  /// This function takes time proportional to the number of data elements.
-  void Resize(MatrixIndexT length, MatrixResizeType resize_type = kSetZero);
-
-  /// Remove one element and shifts later elements down.
-  void RemoveElement(MatrixIndexT i);
-
-  /// Assignment operator, protected so it can only be used by std::vector
-  Vector<Real> &operator = (const Vector<Real> &other) {
-    Resize(other.Dim(), kUndefined);
-    this->CopyFromVec(other);
-    return *this;
-  }
-
-  /// Assignment operator that takes VectorBase.
-  Vector<Real> &operator = (const VectorBase<Real> &other) {
-    Resize(other.Dim(), kUndefined);
-    this->CopyFromVec(other);
-    return *this;
-  }
- private:
-  /// Init assumes the current contents of the class are invalid (i.e. junk or
-  /// has already been freed), and it sets the vector to newly allocated memory
-  /// with the specified dimension.  dim == 0 is acceptable.  The memory contents
-  /// pointed to by data_ will be undefined.
-  void Init(const MatrixIndexT dim);
-
-  /// Destroy function, called internally.
-  void Destroy();
-
-};
-
-
-/// Represents a non-allocating general vector which can be defined
-/// as a sub-vector of higher-level vector [or as the row of a matrix].
-template<typename Real>
-class SubVector : public VectorBase<Real> {
- public:
-  /// Constructor from a Vector or SubVector.
-  /// SubVectors are not const-safe and it's very hard to make them
-  /// so for now we just give up.  This function contains const_cast.
-  SubVector(const VectorBase<Real> &t, const MatrixIndexT origin,
-            const MatrixIndexT length) : VectorBase<Real>() {
-    // following assert equiv to origin>=0 && length>=0 &&
-    // origin+length <= rt.dim_
-    KALDI_ASSERT(static_cast<UnsignedMatrixIndexT>(origin)+
-                 static_cast<UnsignedMatrixIndexT>(length) <=
-                 static_cast<UnsignedMatrixIndexT>(t.Dim()));
-    VectorBase<Real>::data_ = const_cast<Real*> (t.Data()+origin);
-    VectorBase<Real>::dim_   = length;
-  }
-
-  /// This constructor initializes the vector to point at the contents
-  /// of this packed matrix (SpMatrix or TpMatrix).
-  SubVector(const PackedMatrix<Real> &M) {
-    VectorBase<Real>::data_ = const_cast<Real*> (M.Data());
-    VectorBase<Real>::dim_   = (M.NumRows()*(M.NumRows()+1))/2;
-  }
-  
-  /// Copy constructor
-  SubVector(const SubVector &other) : VectorBase<Real> () {
-    // this copy constructor needed for Range() to work in base class.
-    VectorBase<Real>::data_ = other.data_;
-    VectorBase<Real>::dim_ = other.dim_;
-  }
-
-  /// Constructor from a pointer to memory and a length.  Keeps a pointer
-  /// to the data but does not take ownership (will never delete).
-  SubVector(Real *data, MatrixIndexT length) : VectorBase<Real> () {
-    VectorBase<Real>::data_ = data;
-    VectorBase<Real>::dim_   = length;
-  }
-
-
-  /// This operation does not preserve const-ness, so be careful.
-  SubVector(const MatrixBase<Real> &matrix, MatrixIndexT row) {
-    VectorBase<Real>::data_ = const_cast<Real*>(matrix.RowData(row));
-    VectorBase<Real>::dim_   = matrix.NumCols();
-  }
-
-  ~SubVector() {}  ///< Destructor (does nothing; no pointers are owned here).
-
- private:
-  /// Disallow assignment operator.
-  SubVector & operator = (const SubVector &other) {}
-};
-
-/// @} end of "addtogroup matrix_group"
-/// \addtogroup matrix_funcs_io
-/// @{
-/// Output to a C++ stream.  Non-binary by default (use Write for
-/// binary output).
-template<typename Real>
-std::ostream & operator << (std::ostream & out, const VectorBase<Real> & v);
-
-/// Input from a C++ stream.  Will automatically read text or
-/// binary data from the stream.
-template<typename Real>
-std::istream & operator >> (std::istream & in, VectorBase<Real> & v);
-
-/// Input from a C++ stream. Will automatically read text or
-/// binary data from the stream.
-template<typename Real>
-std::istream & operator >> (std::istream & in, Vector<Real> & v);
-/// @} end of \addtogroup matrix_funcs_io
-
-/// \addtogroup matrix_funcs_scalar
-/// @{
-
-
-template<typename Real>
-bool ApproxEqual(const VectorBase<Real> &a,
-                 const VectorBase<Real> &b, Real tol = 0.01) {
-  return a.ApproxEqual(b, tol);
-}
-
-template<typename Real>
-inline void AssertEqual(VectorBase<Real> &a, VectorBase<Real> &b,
-                        float tol = 0.01) {
-  KALDI_ASSERT(a.ApproxEqual(b, tol));
-}
-
-
-/// Returns dot product between v1 and v2.
-template<typename Real>
-Real VecVec(const VectorBase<Real> &v1, const VectorBase<Real> &v2);
-
-template<typename Real, typename OtherReal>
-Real VecVec(const VectorBase<Real> &v1, const VectorBase<OtherReal> &v2);
-
-
-/// Returns \f$ v_1^T M v_2  \f$ .
-/// Not as efficient as it could be where v1 == v2.
-template<typename Real>
-Real VecMatVec(const VectorBase<Real> &v1, const MatrixBase<Real> &M,
-               const VectorBase<Real> &v2);
-
-/// @} End of "addtogroup matrix_funcs_scalar"
-
-
-}  // namespace kaldi
-
-// we need to include the implementation
-#include "matrix/kaldi-vector-inl.h"
-
-
-
-#endif  // KALDI_MATRIX_KALDI_VECTOR_H_
-
diff --git a/kaldi_io/src/kaldi/matrix/matrix-common.h b/kaldi_io/src/kaldi/matrix/matrix-common.h
deleted file mode 100644
index d202b2e..0000000
--- a/kaldi_io/src/kaldi/matrix/matrix-common.h
+++ /dev/null
@@ -1,100 +0,0 @@
-// matrix/matrix-common.h
-
-// Copyright 2009-2011  Microsoft Corporation
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-
-//  http://www.apache.org/licenses/LICENSE-2.0
-
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-#ifndef KALDI_MATRIX_MATRIX_COMMON_H_
-#define KALDI_MATRIX_MATRIX_COMMON_H_
-
-// This file contains some #includes, forward declarations
-// and typedefs that are needed by all the main header
-// files in this directory.
-
-#include "base/kaldi-common.h"
-#include "matrix/kaldi-blas.h"
-
-namespace kaldi {
-typedef enum {
-  kTrans    = CblasTrans,
-  kNoTrans = CblasNoTrans
-} MatrixTransposeType;
-
-typedef enum {
-  kSetZero,
-  kUndefined,
-  kCopyData
-} MatrixResizeType;
-
-typedef enum {
-  kTakeLower,
-  kTakeUpper,
-  kTakeMean,
-  kTakeMeanAndCheck
-} SpCopyType;
-
-template<typename Real> class VectorBase;
-template<typename Real> class Vector;
-template<typename Real> class SubVector;
-template<typename Real> class MatrixBase;
-template<typename Real> class SubMatrix;
-template<typename Real> class Matrix;
-template<typename Real> class SpMatrix;
-template<typename Real> class TpMatrix;
-template<typename Real> class PackedMatrix;
-
-// these are classes that won't be defined in this
-// directory; they're mostly needed for friend declarations.
-template<typename Real> class CuMatrixBase;
-template<typename Real> class CuSubMatrix;
-template<typename Real> class CuMatrix;
-template<typename Real> class CuVectorBase;
-template<typename Real> class CuSubVector;
-template<typename Real> class CuVector;
-template<typename Real> class CuPackedMatrix;
-template<typename Real> class CuSpMatrix;
-template<typename Real> class CuTpMatrix;
-
-class CompressedMatrix;
-
-/// This class provides a way for switching between double and float types.
-template<typename T> class OtherReal { };  // useful in reading+writing routines
-                                           // to switch double and float.
-/// A specialized class for switching from float to double.
-template<> class OtherReal<float> {
- public:
-  typedef double Real;
-};
-/// A specialized class for switching from double to float.
-template<> class OtherReal<double> {
- public:
-  typedef float Real;
-};
-
-
-typedef int32 MatrixIndexT;
-typedef int32 SignedMatrixIndexT;
-typedef uint32 UnsignedMatrixIndexT;
-
-// If you want to use size_t for the index type, do as follows instead:
-//typedef size_t MatrixIndexT;
-//typedef ssize_t SignedMatrixIndexT;
-//typedef size_t UnsignedMatrixIndexT;
-
-}
-
-
-
-#endif  // KALDI_MATRIX_MATRIX_COMMON_H_
diff --git a/kaldi_io/src/kaldi/matrix/matrix-functions-inl.h b/kaldi_io/src/kaldi/matrix/matrix-functions-inl.h
deleted file mode 100644
index 9fac851..0000000
--- a/kaldi_io/src/kaldi/matrix/matrix-functions-inl.h
+++ /dev/null
@@ -1,56 +0,0 @@
-// matrix/matrix-functions-inl.h
-
-// Copyright 2009-2011 Microsoft Corporation
-//
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-//
-// (*) incorporates, with permission, FFT code from his book
-// "Signal Processing with Lapped Transforms", Artech, 1992.
-
-
-
-#ifndef KALDI_MATRIX_MATRIX_FUNCTIONS_INL_H_
-#define KALDI_MATRIX_MATRIX_FUNCTIONS_INL_H_
-
-namespace kaldi {
-
-//! ComplexMul implements, inline, the complex multiplication b *= a.
-template<typename Real> inline void ComplexMul(const Real &a_re, const Real &a_im,
-                                            Real *b_re, Real *b_im) {
-  Real tmp_re = (*b_re * a_re) - (*b_im * a_im);
-  *b_im = *b_re * a_im + *b_im * a_re;
-  *b_re = tmp_re;
-}
-
-template<typename Real> inline void ComplexAddProduct(const Real &a_re, const Real &a_im,
-                                                   const Real &b_re, const Real &b_im,
-                                                   Real *c_re, Real *c_im) {
-  *c_re += b_re*a_re - b_im*a_im;
-  *c_im += b_re*a_im + b_im*a_re;
-}
-
-
-template<typename Real> inline void ComplexImExp(Real x, Real *a_re, Real *a_im) {
-  *a_re = std::cos(x);
-  *a_im = std::sin(x);
-}
-
-
-} // end namespace kaldi
-
-
-#endif // KALDI_MATRIX_MATRIX_FUNCTIONS_INL_H_
-
diff --git a/kaldi_io/src/kaldi/matrix/matrix-functions.h b/kaldi_io/src/kaldi/matrix/matrix-functions.h
deleted file mode 100644
index b70ca56..0000000
--- a/kaldi_io/src/kaldi/matrix/matrix-functions.h
+++ /dev/null
@@ -1,235 +0,0 @@
-// matrix/matrix-functions.h
-
-// Copyright 2009-2011  Microsoft Corporation;  Go Vivace Inc.;  Jan Silovsky;
-//                      Yanmin Qian;   1991 Henrique (Rico) Malvar (*)
-//
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-//
-// (*) incorporates, with permission, FFT code from his book
-// "Signal Processing with Lapped Transforms", Artech, 1992.
-
-
-
-#ifndef KALDI_MATRIX_MATRIX_FUNCTIONS_H_
-#define KALDI_MATRIX_MATRIX_FUNCTIONS_H_
-
-#include "matrix/kaldi-vector.h"
-#include "matrix/kaldi-matrix.h"
-
-namespace kaldi {
-
-/// @addtogroup matrix_funcs_misc
-/// @{
-
-/** The function ComplexFft does an Fft on the vector argument v.
-   v is a vector of even dimension, interpreted for both input
-   and output as a vector of complex numbers i.e.
-   \f[ v = ( re_0, im_0, re_1, im_1, ... )    \f]
-   The dimension of v must be a power of 2.
-
-   If "forward == true" this routine does the Discrete Fourier Transform
-   (DFT), i.e.:
-   \f[   vout[m] \leftarrow \sum_{n = 0}^{N-1} vin[i] exp( -2pi m n / N )  \f]
-
-   If "backward" it does the Inverse Discrete Fourier Transform (IDFT)
-   *WITHOUT THE FACTOR 1/N*,
-   i.e.:
-   \f[   vout[m] <-- \sum_{n = 0}^{N-1} vin[i] exp(  2pi m n / N )   \f]
-   [note the sign difference on the 2 pi for the backward one.]
-
-   Note that this is the definition of the FT given in most texts, but
-   it differs from the Numerical Recipes version in which the forward
-   and backward algorithms are flipped.
-
-   Note that you would have to multiply by 1/N after the IDFT to get
-   back to where you started from.  We don't do this because
-   in some contexts, the transform is made symmetric by multiplying
-   by sqrt(N) in both passes.   The user can do this by themselves.
-
-   See also SplitRadixComplexFft, declared in srfft.h, which is more efficient
-   but only works if the length of the input is a power of 2.
- */
-template<typename Real> void ComplexFft (VectorBase<Real> *v, bool forward, Vector<Real> *tmp_work = NULL);
-
-/// ComplexFt is the same as ComplexFft but it implements the Fourier
-/// transform in an inefficient way.  It is mainly included for testing purposes.
-/// See comment for ComplexFft to describe the input and outputs and what it does.
-template<typename Real> void ComplexFt (const VectorBase<Real> &in,
-                                     VectorBase<Real> *out, bool forward);
-
-/// RealFft is a fourier transform of real inputs.  Internally it uses
-/// ComplexFft.  The input dimension N must be even.  If forward == true,
-/// it transforms from a sequence of N real points to its complex fourier
-/// transform; otherwise it goes in the reverse direction.  If you call it
-/// in the forward and then reverse direction and multiply by 1.0/N, you
-/// will get back the original data.
-/// The interpretation of the complex-FFT data is as follows: the array
-/// is a sequence of complex numbers C_n of length N/2 with (real, im) format,
-/// i.e. [real0, real_{N/2}, real1, im1, real2, im2, real3, im3, ...].
-/// See also SplitRadixRealFft, declared in srfft.h, which is more efficient
-/// but only works if the length of the input is a power of 2.
-
-template<typename Real> void RealFft (VectorBase<Real> *v, bool forward);
-
-
-/// RealFt has the same input and output format as RealFft above, but it is
-/// an inefficient implementation included for testing purposes.
-template<typename Real> void RealFftInefficient (VectorBase<Real> *v, bool forward);
-
-/// ComputeDctMatrix computes a matrix corresponding to the DCT, such that
-/// M * v equals the DCT of vector v.  M must be square at input.
-/// This is the type = III DCT with normalization, corresponding to the
-/// following equations, where x is the signal and X is the DCT:
-/// X_0 = 1/sqrt(2*N) \sum_{n = 0}^{N-1} x_n
-/// X_k = 1/sqrt(N) \sum_{n = 0}^{N-1} x_n cos( \pi/N (n + 1/2) k )
-/// This matrix's transpose is its own inverse, so transposing this
-/// matrix will give the inverse DCT.
-/// Caution: the type III DCT is generally known as the "inverse DCT" (with the
-/// type II being the actual DCT), so this function is somewhatd mis-named.  It
-/// was probably done this way for HTK compatibility.  We don't change it
-/// because it was this way from the start and changing it would affect the
-/// feature generation.
-
-template<typename Real> void ComputeDctMatrix(Matrix<Real> *M);
-
-
-/// ComplexMul implements, inline, the complex multiplication b *= a.
-template<typename Real> inline void ComplexMul(const Real &a_re, const Real &a_im,
-                                            Real *b_re, Real *b_im);
-
-/// ComplexMul implements, inline, the complex operation c += (a * b).
-template<typename Real> inline void ComplexAddProduct(const Real &a_re, const Real &a_im,
-                                                   const Real &b_re, const Real &b_im,
-                                                   Real *c_re, Real *c_im);
-
-
-/// ComplexImExp implements a <-- exp(i x), inline.
-template<typename Real> inline void ComplexImExp(Real x, Real *a_re, Real *a_im);
-
-
-// This class allows you to compute the matrix exponential function
-// B = I + A + 1/2! A^2 + 1/3! A^3 + ...
-// This method is most accurate where the result is of the same order of
-// magnitude as the unit matrix (it will typically not work well when
-// the answer has almost-zero eigenvalues or is close to zero).
-// It also provides a function that allows you do back-propagate the
-// derivative of a scalar function through this calculation.
-// The
-template<typename Real>
-class MatrixExponential {
- public:
-  MatrixExponential() { }
-
-  void Compute(const MatrixBase<Real> &M, MatrixBase<Real> *X);  // does *X = exp(M)
-
-  // Version for symmetric matrices (it just copies to full matrix).
-  void Compute(const SpMatrix<Real> &M, SpMatrix<Real> *X);  // does *X = exp(M)
-
-  void Backprop(const MatrixBase<Real> &hX, MatrixBase<Real> *hM) const;  // Propagates
-  // the gradient of a scalar function f backwards through this operation, i.e.:
-  // if the parameter dX represents df/dX (with no transpose, so element i, j of dX
-  // is the derivative of f w.r.t. E(i, j)), it sets dM to df/dM, again with no
-  // transpose (of course, only the part thereof that comes through the effect of
-  // A on B).  This applies to the values of A and E that were called most recently
-  // with Compute().
-
-  // Version for symmetric matrices (it just copies to full matrix).
-  void Backprop(const SpMatrix<Real> &hX, SpMatrix<Real> *hM) const;
-  
- private:
-  void Clear();
-
-  static MatrixIndexT ComputeN(const MatrixBase<Real> &M);
-
-  // This is intended for matrices P with small norms: compute B_0 = exp(P) - I.
-  // Keeps adding terms in the Taylor series till there is no further
-  // change in the result.  Stores some of the powers of A in powers_,
-  // and the number of terms K as K_.
-  void ComputeTaylor(const MatrixBase<Real> &P, MatrixBase<Real> *B0);
-
-  // Backprop through the Taylor-series computation above.
-  // note: hX is \hat{X} in the math; hM is \hat{M} in the math.
-  void BackpropTaylor(const MatrixBase<Real> &hX,
-                      MatrixBase<Real> *hM) const;
-
-  Matrix<Real> P_;  // Equals M * 2^(-N_)
-  std::vector<Matrix<Real> > B_;  // B_[0] = exp(P_) - I,
-                                 //  B_[k] = 2 B_[k-1] + B_[k-1]^2   [k > 0],
-                                 //  ( = exp(P_)^k - I )
-                                 // goes from 0..N_ [size N_+1].
-
-  std::vector<Matrix<Real> > powers_;  // powers (>1) of P_ stored here,
-  // up to all but the last one used in the Taylor expansion (this is the
-  // last one we need in the backprop).  The index is the power minus 2.
-
-  MatrixIndexT N_;  // Power N_ >=0 such that P_ = A * 2^(-N_),
-  // we choose it so that P_ has a sufficiently small norm
-  // that the Taylor series will converge fast.
-};
-
-
-/**
-    ComputePCA does a PCA computation, using either outer products
-    or inner products, whichever is more efficient.  Let D be
-    the dimension of the data points, N be the number of data
-    points, and G be the PCA dimension we want to retain.  We assume
-    G <= N and G <= D.
-
-    @param X [in]  An N x D matrix.  Each row of X is a point x_i.
-    @param U [out] A G x D matrix.  Each row of U is a basis element u_i.
-    @param A [out] An N x D matrix, or NULL.  Each row of A is a set of coefficients
-         in the basis for a point x_i, so A(i, g) is the coefficient of u_i
-         in x_i.
-    @param print_eigs [in] If true, prints out diagnostic information about the
-         eigenvalues.
-    @param exact [in] If true, does the exact computation; if false, does
-         a much faster (but almost exact) computation based on the Lanczos
-         method.
-*/
-
-template<typename Real>
-void ComputePca(const MatrixBase<Real> &X,
-                MatrixBase<Real> *U,
-                MatrixBase<Real> *A,
-                bool print_eigs = false,
-                bool exact = true);
-
-
-
-// This function does: *plus += max(0, a b^T),
-// *minus += max(0, -(a b^T)).
-template<typename Real>
-void AddOuterProductPlusMinus(Real alpha,
-                              const VectorBase<Real> &a,
-                              const VectorBase<Real> &b,
-                              MatrixBase<Real> *plus, 
-                              MatrixBase<Real> *minus);
-
-template<typename Real1, typename Real2>
-inline void AssertSameDim(const MatrixBase<Real1> &mat1, const MatrixBase<Real2> &mat2) {
-  KALDI_ASSERT(mat1.NumRows() == mat2.NumRows()
-               && mat1.NumCols() == mat2.NumCols());
-}
-
-
-/// @} end of "addtogroup matrix_funcs_misc"
-
-} // end namespace kaldi
-
-#include "matrix/matrix-functions-inl.h"
-
-
-#endif
diff --git a/kaldi_io/src/kaldi/matrix/matrix-lib.h b/kaldi_io/src/kaldi/matrix/matrix-lib.h
deleted file mode 100644
index 39acec5..0000000
--- a/kaldi_io/src/kaldi/matrix/matrix-lib.h
+++ /dev/null
@@ -1,37 +0,0 @@
-// matrix/matrix-lib.h
-
-// Copyright 2009-2011  Ondrej Glembek;  Microsoft Corporation;  Haihua Xu
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-
-//  http://www.apache.org/licenses/LICENSE-2.0
-
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-// Include everything from this directory.
-// These files include other stuff that we need.
-#ifndef KALDI_MATRIX_MATRIX_LIB_H_
-#define KALDI_MATRIX_MATRIX_LIB_H_
-
-#include "matrix/cblas-wrappers.h"
-#include "base/kaldi-common.h"
-#include "matrix/kaldi-vector.h"
-#include "matrix/kaldi-matrix.h"
-#include "matrix/sp-matrix.h"
-#include "matrix/tp-matrix.h"
-#include "matrix/matrix-functions.h"
-#include "matrix/srfft.h"
-#include "matrix/compressed-matrix.h"
-#include "matrix/optimization.h"
-
-#endif
-
diff --git a/kaldi_io/src/kaldi/matrix/optimization.h b/kaldi_io/src/kaldi/matrix/optimization.h
deleted file mode 100644
index 66309ac..0000000
--- a/kaldi_io/src/kaldi/matrix/optimization.h
+++ /dev/null
@@ -1,248 +0,0 @@
-// matrix/optimization.h
-
-// Copyright 2012  Johns Hopkins University (author: Daniel Povey)
-//
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-//
-// (*) incorporates, with permission, FFT code from his book
-// "Signal Processing with Lapped Transforms", Artech, 1992.
-
-
-
-#ifndef KALDI_MATRIX_OPTIMIZATION_H_
-#define KALDI_MATRIX_OPTIMIZATION_H_
-
-#include "matrix/kaldi-vector.h"
-#include "matrix/kaldi-matrix.h"
-
-namespace kaldi {
-
-
-/// @addtogroup matrix_optimization
-/// @{
-
-struct LinearCgdOptions {
-  int32 max_iters;  //  Maximum number of iters (if >= 0).
-  BaseFloat max_error;  // Maximum 2-norm of the residual A x - b (convergence
-                        // test)
-  // Every time the residual 2-norm decreases by this recompute_residual_factor
-  // since the last time it was computed from scratch, recompute it from
-  // scratch.  This helps to keep the computed residual accurate even in the
-  // presence of roundoff.
-  BaseFloat recompute_residual_factor;
-  
-  LinearCgdOptions(): max_iters(-1),
-                      max_error(0.0),
-                      recompute_residual_factor(0.01) { }
-};
-  
-/*
-  This function uses linear conjugate gradient descent to approximately solve
-  the system A x = b.  The value of x at entry corresponds to the initial guess
-  of x.  The algorithm continues until the number of iterations equals b.Dim(),
-  or until the 2-norm of (A x - b) is <= max_error, or until the number of
-  iterations equals max_iter, whichever happens sooner.  It is a requirement
-  that A be positive definite.
-  It returns the number of iterations that were actually executed (this is
-  useful for testing purposes).
-*/
-template<typename Real>
-int32 LinearCgd(const LinearCgdOptions &opts,
-                const SpMatrix<Real> &A, const VectorBase<Real> &b,
-                VectorBase<Real> *x);
-
-
-
-
-
-
-/**
-   This is an implementation of L-BFGS.  It pushes responsibility for
-   determining when to stop, onto the user.  There is no call-back here:
-   everything is done via calls to the class itself (see the example in
-   matrix-lib-test.cc).  This does not implement constrained L-BFGS, but it will
-   handle constrained problems correctly as long as the function approaches
-   +infinity (or -infinity for maximization problems) when it gets close to the
-   bound of the constraint.  In these types of problems, you just let the
-   function value be +infinity for minimization problems, or -infinity for
-   maximization problems, outside these bounds).
-*/
-
-struct LbfgsOptions {
-  bool minimize; // if true, we're minimizing, else maximizing.
-  int m; // m is the number of stored vectors L-BFGS keeps.
-  float first_step_learning_rate; // The very first step of L-BFGS is
-  // like gradient descent.  If you want to configure the size of that step,
-  // you can do it using this variable.
-  float first_step_length; // If this variable is >0.0, it overrides
-  // first_step_learning_rate; on the first step we choose an approximate
-  // Hessian that is the multiple of the identity that would generate this
-  // step-length, or 1.0 if the gradient is zero.
-  float first_step_impr; // If this variable is >0.0, it overrides
-  // first_step_learning_rate; on the first step we choose an approximate
-  // Hessian that is the multiple of the identity that would generate this
-  // amount of objective function improvement (assuming the "real" objf
-  // was linear).
-  float c1; // A constant in Armijo rule = Wolfe condition i)
-  float c2; // A constant in Wolfe condition ii)
-  float d; // An amount > 1.0 (default 2.0) that we initially multiply or
-  // divide the step length by, in the line search.
-  int max_line_search_iters; // after this many iters we restart L-BFGS.
-  int avg_step_length; // number of iters to avg step length over, in
-  // RecentStepLength().
-  
-  LbfgsOptions (bool minimize = true):
-      minimize(minimize),
-      m(10),
-      first_step_learning_rate(1.0),
-      first_step_length(0.0),
-      first_step_impr(0.0),
-      c1(1.0e-04),
-      c2(0.9),
-      d(2.0),
-      max_line_search_iters(50),
-      avg_step_length(4) { }
-};
-
-template<typename Real>
-class OptimizeLbfgs {
- public:
-  /// Initializer takes the starting value of x.
-  OptimizeLbfgs(const VectorBase<Real> &x,
-                const LbfgsOptions &opts);
-  
-  /// This returns the value of the variable x that has the best objective
-  /// function so far, and the corresponding objective function value if
-  /// requested.  This would typically be called only at the end.
-  const VectorBase<Real>& GetValue(Real *objf_value = NULL) const;
-  
-  /// This returns the value at which the function wants us
-  /// to compute the objective function and gradient.
-  const VectorBase<Real>& GetProposedValue() const { return new_x_; }
-  
-  /// Returns the average magnitude of the last n steps (but not
-  /// more than the number we have stored).  Before we have taken
-  /// any steps, returns +infinity.  Note: if the most recent
-  /// step length was 0, it returns 0, regardless of the other
-  /// step lengths.  This makes it suitable as a convergence test
-  /// (else we'd generate NaN's).
-  Real RecentStepLength() const;
-  
-  /// The user calls this function to provide the class with the
-  /// function and gradient info at the point GetProposedValue().
-  /// If this point is outside the constraints you can set function_value
-  /// to {+infinity,-infinity} for {minimization,maximization} problems.
-  /// In this case the gradient, and also the second derivative (if you call
-  /// the second overloaded version of this function) will be ignored.
-  void DoStep(Real function_value,
-              const VectorBase<Real> &gradient);
-  
-  /// The user can call this version of DoStep() if it is desired to set some
-  /// kind of approximate Hessian on this iteration.  Note: it is a prerequisite
-  /// that diag_approx_2nd_deriv must be strictly positive (minimizing), or
-  /// negative (maximizing).
-  void DoStep(Real function_value,
-              const VectorBase<Real> &gradient,
-              const VectorBase<Real> &diag_approx_2nd_deriv);
-  
- private:
-  KALDI_DISALLOW_COPY_AND_ASSIGN(OptimizeLbfgs);
-
-
-  // The following variable says what stage of the computation we're at.
-  // Refer to Algorithm 7.5 (L-BFGS) of Nodecdal & Wright, "Numerical
-  // Optimization", 2nd edition.
-  // kBeforeStep means we're about to do
-  /// "compute p_k <-- - H_k \delta f_k" (i.e. Algorithm 7.4).
-  // kWithinStep means we're at some point within line search; note
-  // that line search is iterative so we can stay in this state more
-  // than one time on each iteration.
-  enum ComputationState {
-    kBeforeStep,
-    kWithinStep, // This means we're within the step-size computation, and
-    // have not yet done the 1st function evaluation.
-  };
-  
-  inline MatrixIndexT Dim() { return x_.Dim(); }
-  inline MatrixIndexT M() { return opts_.m; }
-  SubVector<Real> Y(MatrixIndexT i) {
-    return SubVector<Real>(data_, (i % M()) * 2); // vector y_i
-  }
-  SubVector<Real> S(MatrixIndexT i) {
-    return SubVector<Real>(data_, (i % M()) * 2 + 1); // vector s_i
-  }
-  // The following are subroutines within DoStep():
-  bool AcceptStep(Real function_value,
-                  const VectorBase<Real> &gradient);
-  void Restart(const VectorBase<Real> &x,
-               Real function_value,
-               const VectorBase<Real> &gradient);
-  void ComputeNewDirection(Real function_value,
-                           const VectorBase<Real> &gradient);
-  void ComputeHifNeeded(const VectorBase<Real> &gradient);
-  void StepSizeIteration(Real function_value,
-                         const VectorBase<Real> &gradient);
-  void RecordStepLength(Real s);
-  
-  
-  LbfgsOptions opts_;
-  SignedMatrixIndexT k_; // Iteration number, starts from zero.  Gets set back to zero
-  // when we restart.
-  
-  ComputationState computation_state_;
-  bool H_was_set_; // True if the user specified H_; if false,
-  // we'll use a heuristic to estimate it.
-
-
-  Vector<Real> x_; // current x.
-  Vector<Real> new_x_; // the x proposed in the line search.
-  Vector<Real> best_x_; // the x with the best objective function so far
-                        // (either the same as x_ or something in the current line search.)
-  Vector<Real> deriv_; // The most recently evaluated derivative-- at x_k.
-  Vector<Real> temp_;
-  Real f_; // The function evaluated at x_k.
-  Real best_f_; // the best objective function so far.
-  Real d_; // a number d > 1.0, but during an iteration we may decrease this, when
-  // we switch between armijo and wolfe failures.
-
-  int num_wolfe_i_failures_; // the num times we decreased step size.
-  int num_wolfe_ii_failures_; // the num times we increased step size.
-  enum { kWolfeI, kWolfeII, kNone } last_failure_type_; // last type of step-search
-  // failure on this iter.
-  
-  Vector<Real> H_; // Current inverse-Hessian estimate.  May be computed by this class itself,
-  // or provided by user using 2nd form of SetGradientInfo().
-  Matrix<Real> data_; // dimension (m*2) x dim.  Even rows store
-  // gradients y_i, odd rows store steps s_i.
-  Vector<Real> rho_; // dimension m; rho_(m) = 1/(y_m^T s_m), Eq. 7.17.
-
-  std::vector<Real> step_lengths_; // The step sizes we took on the last
-  // (up to m) iterations; these are not stored in a rotating buffer but
-  // are shifted by one each time (this is more convenient when we
-  // restart, as we keep this info past restarting).
-  
-
-};
-  
-/// @} 
-
-
-} // end namespace kaldi
-
-
-
-#endif
-
diff --git a/kaldi_io/src/kaldi/matrix/packed-matrix.h b/kaldi_io/src/kaldi/matrix/packed-matrix.h
deleted file mode 100644
index 722d932..0000000
--- a/kaldi_io/src/kaldi/matrix/packed-matrix.h
+++ /dev/null
@@ -1,197 +0,0 @@
-// matrix/packed-matrix.h
-
-// Copyright 2009-2013  Ondrej Glembek;  Lukas Burget;  Microsoft Corporation;
-//                      Saarland University;  Yanmin Qian;
-//                      Johns Hopkins University (Author: Daniel Povey)
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-
-//  http://www.apache.org/licenses/LICENSE-2.0
-
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_MATRIX_PACKED_MATRIX_H_
-#define KALDI_MATRIX_PACKED_MATRIX_H_
-
-#include "matrix/matrix-common.h"
-#include <algorithm>
-
-namespace kaldi {
-
-/// \addtogroup matrix_funcs_io
-// we need to declare the friend << operator here
-template<typename Real>
-std::ostream & operator <<(std::ostream & out, const PackedMatrix<Real>& M);
-
-
-/// \addtogroup matrix_group
-/// @{
-
-/// @brief Packed matrix: base class for triangular and symmetric matrices.
-template<typename Real> class PackedMatrix {
-  friend class CuPackedMatrix<Real>;
- public:
-  //friend class CuPackedMatrix<Real>;
-
-  PackedMatrix() : data_(NULL), num_rows_(0) {}
-
-  explicit PackedMatrix(MatrixIndexT r, MatrixResizeType resize_type = kSetZero):
-      data_(NULL) {  Resize(r, resize_type);  }
-
-  explicit PackedMatrix(const PackedMatrix<Real> &orig) : data_(NULL) {
-    Resize(orig.num_rows_, kUndefined);
-    CopyFromPacked(orig);
-  }
-
-  template<typename OtherReal>
-  explicit PackedMatrix(const PackedMatrix<OtherReal> &orig) : data_(NULL) {
-    Resize(orig.NumRows(), kUndefined);
-    CopyFromPacked(orig);
-  }
-  
-  void SetZero();  /// < Set to zero
-  void SetUnit();  /// < Set to unit matrix.
-  void SetRandn(); /// < Set to random values of a normal distribution
-
-  Real Trace() const;
-
-  // Needed for inclusion in std::vector
-  PackedMatrix<Real> & operator =(const PackedMatrix<Real> &other) {
-    Resize(other.NumRows());
-    CopyFromPacked(other);
-    return *this;
-  }
-
-  ~PackedMatrix() {
-    Destroy();
-  }
-
-  /// Set packed matrix to a specified size (can be zero).
-  /// The value of the new data depends on resize_type:
-  ///   -if kSetZero, the new data will be zero
-  ///   -if kUndefined, the new data will be undefined
-  ///   -if kCopyData, the new data will be the same as the old data in any
-  ///      shared positions, and zero elsewhere.
-  /// This function takes time proportional to the number of data elements.
-  void Resize(MatrixIndexT nRows, MatrixResizeType resize_type = kSetZero);
-
-  void AddToDiag(const Real r); // Adds r to diaginal
-
-  void ScaleDiag(const Real alpha);  // Scales diagonal by alpha.
-
-  void SetDiag(const Real alpha);  // Sets diagonal to this value.
-
-  template<typename OtherReal>
-  void CopyFromPacked(const PackedMatrix<OtherReal> &orig);
-  
-  /// CopyFromVec just interprets the vector as having the same layout
-  /// as the packed matrix.  Must have the same dimension, i.e.
-  /// orig.Dim() == (NumRows()*(NumRows()+1)) / 2;
-  template<typename OtherReal>
-  void CopyFromVec(const SubVector<OtherReal> &orig);
-  
-  Real* Data() { return data_; }
-  const Real* Data() const { return data_; }
-  inline MatrixIndexT NumRows() const { return num_rows_; }
-  inline MatrixIndexT NumCols() const { return num_rows_; }
-  size_t SizeInBytes() const {
-    size_t nr = static_cast<size_t>(num_rows_);
-    return ((nr * (nr+1)) / 2) * sizeof(Real);
-  }
-
-  //MatrixIndexT Stride() const { return stride_; }
-
-  // This code is duplicated in child classes to avoid extra levels of calls.
-  Real operator() (MatrixIndexT r, MatrixIndexT c) const {
-    KALDI_ASSERT(static_cast<UnsignedMatrixIndexT>(r) <
-                 static_cast<UnsignedMatrixIndexT>(num_rows_) &&
-                 static_cast<UnsignedMatrixIndexT>(c) <
-                 static_cast<UnsignedMatrixIndexT>(num_rows_)
-                 && c <= r);
-    return *(data_ + (r * (r + 1)) / 2 + c);
-  }
-
-  // This code is duplicated in child classes to avoid extra levels of calls.
-  Real &operator() (MatrixIndexT r, MatrixIndexT c) {
-    KALDI_ASSERT(static_cast<UnsignedMatrixIndexT>(r) <
-                 static_cast<UnsignedMatrixIndexT>(num_rows_) &&
-                 static_cast<UnsignedMatrixIndexT>(c) <
-                 static_cast<UnsignedMatrixIndexT>(num_rows_)
-                 && c <= r);
-    return *(data_ + (r * (r + 1)) / 2 + c);
-  }
-
-  Real Max() const {
-    KALDI_ASSERT(num_rows_ > 0);
-    return * (std::max_element(data_, data_ + ((num_rows_*(num_rows_+1))/2) ));
-  }
-
-  Real Min() const {
-    KALDI_ASSERT(num_rows_ > 0);
-    return * (std::min_element(data_, data_ + ((num_rows_*(num_rows_+1))/2) ));
-  }
-
-  void Scale(Real c);
-
-  friend std::ostream & operator << <> (std::ostream & out,
-                                     const PackedMatrix<Real> &m);
-  // Use instead of stream<<*this, if you want to add to existing contents.
-  // Will throw exception on failure.
-  void Read(std::istream &in, bool binary, bool add = false);
-
-  void Write(std::ostream &out, bool binary) const;
-  
-  void Destroy();
-
-  /// Swaps the contents of *this and *other.  Shallow swap.
-  void Swap(PackedMatrix<Real> *other);
-  void Swap(Matrix<Real> *other);
-
-
- protected:
-  // Will only be called from this class or derived classes.
-  void AddPacked(const Real alpha, const PackedMatrix<Real>& M);
-  Real *data_;
-  MatrixIndexT num_rows_;
-  //MatrixIndexT stride_;
- private:
-  /// Init assumes the current contents of the class are is invalid (i.e. junk or
-  /// has already been freed), and it sets the matrixd to newly allocated memory
-  /// with the specified dimension.  dim == 0 is acceptable.  The memory contents
-  /// pointed to by data_ will be undefined.
-  void Init(MatrixIndexT dim);
-
-};
-/// @} end "addtogroup matrix_group"
-
-
-/// \addtogroup matrix_funcs_io
-/// @{
-
-template<typename Real>
-std::ostream & operator << (std::ostream & os, const PackedMatrix<Real>& M) {
-  M.Write(os, false);
-  return os;
-}
-
-template<typename Real>
-std::istream & operator >> (std::istream &is, PackedMatrix<Real> &M) {
-  M.Read(is, false);
-  return is;
-}
-
-/// @}
-
-}  // namespace kaldi
-
-#endif
-
diff --git a/kaldi_io/src/kaldi/matrix/sp-matrix-inl.h b/kaldi_io/src/kaldi/matrix/sp-matrix-inl.h
deleted file mode 100644
index 1579592..0000000
--- a/kaldi_io/src/kaldi/matrix/sp-matrix-inl.h
+++ /dev/null
@@ -1,42 +0,0 @@
-// matrix/sp-matrix-inl.h
-
-// Copyright 2009-2011  Ondrej Glembek;  Microsoft Corporation;  Haihua Xu
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-
-//  http://www.apache.org/licenses/LICENSE-2.0
-
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_MATRIX_SP_MATRIX_INL_H_
-#define KALDI_MATRIX_SP_MATRIX_INL_H_
-
-#include "matrix/tp-matrix.h"
-
-namespace kaldi {
-
-// All the lines in this file seem to be declaring template specializations.
-// These tell the compiler that we'll implement the templated function
-// separately for the different template arguments (float, double).
-
-template<>
-double SolveQuadraticProblem(const SpMatrix<double> &H, const VectorBase<double> &g,
-                             const SolverOptions &opts, VectorBase<double> *x);
-
-template<>
-float SolveQuadraticProblem(const SpMatrix<float> &H, const VectorBase<float> &g,
-                            const SolverOptions &opts, VectorBase<float> *x);
-
-}  // namespace kaldi
-
-
-#endif  // KALDI_MATRIX_SP_MATRIX_INL_H_
diff --git a/kaldi_io/src/kaldi/matrix/sp-matrix.h b/kaldi_io/src/kaldi/matrix/sp-matrix.h
deleted file mode 100644
index 209d24a..0000000
--- a/kaldi_io/src/kaldi/matrix/sp-matrix.h
+++ /dev/null
@@ -1,524 +0,0 @@
-// matrix/sp-matrix.h
-
-// Copyright 2009-2011   Ondrej Glembek;  Microsoft Corporation;  Lukas Burget;
-//                       Saarland University;  Ariya Rastrow;  Yanmin Qian;
-//                       Jan Silovsky
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-
-//  http://www.apache.org/licenses/LICENSE-2.0
-
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-#ifndef KALDI_MATRIX_SP_MATRIX_H_
-#define KALDI_MATRIX_SP_MATRIX_H_
-
-#include <algorithm>
-#include <vector>
-
-#include "matrix/packed-matrix.h"
-
-namespace kaldi {
-
-
-/// \addtogroup matrix_group
-/// @{
-template<typename Real> class SpMatrix;
-
-
-/**
- * @brief Packed symetric matrix class
-*/
-template<typename Real>
-class SpMatrix : public PackedMatrix<Real> {
-  friend class CuSpMatrix<Real>;
- public:
-  // so it can use our assignment operator.
-  friend class std::vector<Matrix<Real> >;
-
-  SpMatrix(): PackedMatrix<Real>() {}
-
-  /// Copy constructor from CUDA version of SpMatrix
-  /// This is defined in ../cudamatrix/cu-sp-matrix.h
-  
-  explicit SpMatrix(const CuSpMatrix<Real> &cu);
- 
-  explicit SpMatrix(MatrixIndexT r, MatrixResizeType resize_type = kSetZero)
-      : PackedMatrix<Real>(r, resize_type) {}
-
-  SpMatrix(const SpMatrix<Real> &orig)
-      : PackedMatrix<Real>(orig) {}
-
-  template<typename OtherReal>
-  explicit SpMatrix(const SpMatrix<OtherReal> &orig)
-      : PackedMatrix<Real>(orig) {}
-
-#ifdef KALDI_PARANOID
-  explicit SpMatrix(const MatrixBase<Real> & orig,
-                    SpCopyType copy_type = kTakeMeanAndCheck)
-      : PackedMatrix<Real>(orig.NumRows(), kUndefined) {
-    CopyFromMat(orig, copy_type);
-  }
-#else
-  explicit SpMatrix(const MatrixBase<Real> & orig,
-                    SpCopyType copy_type = kTakeMean)
-      : PackedMatrix<Real>(orig.NumRows(), kUndefined) {
-    CopyFromMat(orig, copy_type);
-  }
-#endif
-
-  /// Shallow swap.
-  void Swap(SpMatrix *other);
-
-  inline void Resize(MatrixIndexT nRows, MatrixResizeType resize_type = kSetZero) {
-    PackedMatrix<Real>::Resize(nRows, resize_type);
-  }
-
-  void CopyFromSp(const SpMatrix<Real> &other) {
-    PackedMatrix<Real>::CopyFromPacked(other);
-  }
-
-  template<typename OtherReal>
-  void CopyFromSp(const SpMatrix<OtherReal> &other) {
-    PackedMatrix<Real>::CopyFromPacked(other);
-  }
-
-#ifdef KALDI_PARANOID
-  void CopyFromMat(const MatrixBase<Real> &orig,
-                   SpCopyType copy_type = kTakeMeanAndCheck);
-#else  // different default arg if non-paranoid mode.
-  void CopyFromMat(const MatrixBase<Real> &orig,
-                   SpCopyType copy_type = kTakeMean);
-#endif
-
-  inline Real operator() (MatrixIndexT r, MatrixIndexT c) const {
-    // if column is less than row, then swap these as matrix is stored
-    // as upper-triangular...  only allowed for const matrix object.
-    if (static_cast<UnsignedMatrixIndexT>(c) >
-        static_cast<UnsignedMatrixIndexT>(r))
-      std::swap(c, r);
-    // c<=r now so don't have to check c.
-    KALDI_ASSERT(static_cast<UnsignedMatrixIndexT>(r) <
-                 static_cast<UnsignedMatrixIndexT>(this->num_rows_));
-    return *(this->data_ + (r*(r+1)) / 2 + c);
-    // Duplicating code from PackedMatrix.h
-  }
-
-  inline Real &operator() (MatrixIndexT r, MatrixIndexT c) {
-    if (static_cast<UnsignedMatrixIndexT>(c) >
-        static_cast<UnsignedMatrixIndexT>(r))
-      std::swap(c, r);
-    // c<=r now so don't have to check c.
-    KALDI_ASSERT(static_cast<UnsignedMatrixIndexT>(r) <
-                 static_cast<UnsignedMatrixIndexT>(this->num_rows_));
-    return *(this->data_ + (r * (r + 1)) / 2 + c);
-    // Duplicating code from PackedMatrix.h
-  }
-
-  using PackedMatrix<Real>::operator =;
-  using PackedMatrix<Real>::Scale;
-
-  /// matrix inverse.
-  /// if inverse_needed = false, will fill matrix with garbage.
-  /// (only useful if logdet wanted).
-  void Invert(Real *logdet = NULL, Real *det_sign= NULL,
-              bool inverse_needed = true);
-
-  // Below routine does inversion in double precision,
-  // even for single-precision object.
-  void InvertDouble(Real *logdet = NULL, Real *det_sign = NULL,
-                    bool inverse_needed = true);
-
-  /// Returns maximum ratio of singular values.
-  inline Real Cond() const {
-    Matrix<Real> tmp(*this);
-    return tmp.Cond();
-  }
-
-  /// Takes matrix to a fraction power via Svd.
-  /// Will throw exception if matrix is not positive semidefinite
-  /// (to within a tolerance)
-  void ApplyPow(Real exponent);
-
-  /// This is the version of SVD that we implement for symmetric positive
-  /// definite matrices.  This exists for historical reasons; right now its
-  /// internal implementation is the same as Eig().  It computes the eigenvalue
-  /// decomposition (*this) = P * diag(s) * P^T with P orthogonal.  Will throw
-  /// exception if input is not positive semidefinite to within a tolerance.
-  void SymPosSemiDefEig(VectorBase<Real> *s, MatrixBase<Real> *P,
-                        Real tolerance = 0.001) const;
-
-  /// Solves the symmetric eigenvalue problem: at end we should have (*this) = P
-  /// * diag(s) * P^T.  We solve the problem using the symmetric QR method.
-  /// P may be NULL.
-  /// Implemented in qr.cc.
-  /// If you need the eigenvalues sorted, the function SortSvd declared in
-  /// kaldi-matrix is suitable.
-  void Eig(VectorBase<Real> *s, MatrixBase<Real> *P = NULL) const;
-  
-  /// This function gives you, approximately, the largest eigenvalues of the
-  /// symmetric matrix and the corresponding eigenvectors.  (largest meaning,
-  /// further from zero).  It does this by doing a SVD within the Krylov
-  /// subspace generated by this matrix and a random vector.  This is
-  /// a form of the Lanczos method with complete reorthogonalization, followed
-  /// by SVD within a smaller dimension ("lanczos_dim").
-  ///
-  /// If *this is m by m, s should be of dimension n and P should be of
-  /// dimension m by n, with n <= m.  The *columns* of P are the approximate
-  /// eigenvectors; P * diag(s) * P^T would be a low-rank reconstruction of
-  /// *this.  The columns of P will be orthogonal, and the elements of s will be
-  /// the eigenvalues of *this projected into that subspace, but beyond that
-  /// there are no exact guarantees.  (This is because the convergence of this
-  /// method is statistical).  Note: it only makes sense to use this
-  /// method if you are in very high dimension and n is substantially smaller
-  /// than m: for example, if you want the 100 top eigenvalues of a 10k by 10k
-  /// matrix.  This function calls Rand() to initialize the lanczos
-  /// iterations and also for restarting.
-  /// If lanczos_dim is zero, it will default to the greater of:
-  /// s->Dim() + 50 or s->Dim() + s->Dim()/2, but not more than this->Dim().
-  /// If lanczos_dim == this->Dim(), you might as well just call the function
-  /// Eig() since the result will be the same, and Eig() would be faster; the
-  /// whole point of this function is to reduce the dimension of the SVD
-  /// computation.
-  void TopEigs(VectorBase<Real> *s, MatrixBase<Real> *P,
-               MatrixIndexT lanczos_dim = 0) const;
-
-
-  
-  /// Takes log of the matrix (does eigenvalue decomposition then takes
-  /// log of eigenvalues and reconstructs).  Will throw of not +ve definite.
-  void Log();
-
-
-  // Takes exponential of the matrix (equivalent to doing eigenvalue
-  // decomposition then taking exp of eigenvalues and reconstructing).
-  void Exp();
-
-  /// Returns the maximum of the absolute values of any of the
-  /// eigenvalues.
-  Real MaxAbsEig() const;
-
-  void PrintEigs(const char *name) {
-    Vector<Real> s((*this).NumRows());
-    Matrix<Real> P((*this).NumRows(), (*this).NumCols());
-    SymPosSemiDefEig(&s, &P);
-    KALDI_LOG << "PrintEigs: " << name << ": " << s;
-  }
-
-  bool IsPosDef() const;  // returns true if Cholesky succeeds.
-  void AddSp(const Real alpha, const SpMatrix<Real> &Ma) {
-    this->AddPacked(alpha, Ma);
-  }
-
-  /// Computes log determinant but only for +ve-def matrices
-  /// (it uses Cholesky).
-  /// If matrix is not +ve-def, it will throw an exception
-  /// was LogPDDeterminant()
-  Real LogPosDefDet() const;
-
-  Real LogDet(Real *det_sign = NULL) const;
-
-  /// rank-one update, this <-- this + alpha v v'
-  template<typename OtherReal>
-  void AddVec2(const Real alpha, const VectorBase<OtherReal> &v);
-
-  /// rank-two update, this <-- this + alpha (v w' + w v').
-  void AddVecVec(const Real alpha, const VectorBase<Real> &v,
-                 const VectorBase<Real> &w);
-
-  /// Does *this = beta * *thi + alpha * diag(v) * S * diag(v)
-  void AddVec2Sp(const Real alpha, const VectorBase<Real> &v,
-                 const SpMatrix<Real> &S, const Real beta);
-  
-  /// diagonal update, this <-- this + diag(v)
-  template<typename OtherReal>
-  void AddDiagVec(const Real alpha, const VectorBase<OtherReal> &v);
-
-  /// rank-N update:
-  /// if (transM == kNoTrans)
-  /// (*this) = beta*(*this) + alpha * M * M^T,
-  /// or  (if transM == kTrans)
-  ///  (*this) = beta*(*this) + alpha * M^T * M
-  /// Note: beta used to default to 0.0.
-  void AddMat2(const Real alpha, const MatrixBase<Real> &M,
-               MatrixTransposeType transM, const Real beta);
-
-  /// Extension of rank-N update:
-  /// this <-- beta*this  +  alpha * M * A * M^T.
-  /// (*this) and A are allowed to be the same.
-  /// If transM == kTrans, then we do it as M^T * A * M.
-  void AddMat2Sp(const Real alpha, const MatrixBase<Real> &M,
-                 MatrixTransposeType transM, const SpMatrix<Real> &A,
-                 const Real beta = 0.0);
-
-  /// This is a version of AddMat2Sp specialized for when M is fairly sparse.
-  /// This was required for making the raw-fMLLR code efficient.
-  void AddSmat2Sp(const Real alpha, const MatrixBase<Real> &M,
-                  MatrixTransposeType transM, const SpMatrix<Real> &A,
-                  const Real beta = 0.0);
-
-  /// The following function does:
-  /// this <-- beta*this  +  alpha * T * A * T^T.
-  /// (*this) and A are allowed to be the same.
-  /// If transM == kTrans, then we do it as alpha * T^T * A * T.
-  /// Currently it just calls AddMat2Sp, but if needed we
-  /// can implement it more efficiently.
-  void AddTp2Sp(const Real alpha, const TpMatrix<Real> &T,
-                MatrixTransposeType transM, const SpMatrix<Real> &A,
-                const Real beta = 0.0);
-
-  /// The following function does:
-  /// this <-- beta*this  +  alpha * T * T^T.
-  /// (*this) and A are allowed to be the same.
-  /// If transM == kTrans, then we do it as alpha * T^T *  T
-  /// Currently it just calls AddMat2, but if needed we
-  /// can implement it more efficiently.
-  void AddTp2(const Real alpha, const TpMatrix<Real> &T,
-              MatrixTransposeType transM, const Real beta = 0.0);
-
-  /// Extension of rank-N update:
-  /// this <-- beta*this + alpha * M * diag(v) * M^T.
-  /// if transM == kTrans, then
-  /// this <-- beta*this + alpha * M^T * diag(v) * M.
-  void AddMat2Vec(const Real alpha, const MatrixBase<Real> &M,
-                  MatrixTransposeType transM, const VectorBase<Real> &v,
-                  const Real beta = 0.0);
-
-
-  ///  Floors this symmetric matrix to the matrix
-  /// alpha * Floor, where the matrix Floor is positive
-  /// definite.
-  /// It is floored in the sense that after flooring,
-  ///  x^T (*this) x  >= x^T (alpha*Floor) x.
-  /// This is accomplished using an Svd.  It will crash
-  /// if Floor is not positive definite. Returns the number of
-  /// elements that were floored.
-  int ApplyFloor(const SpMatrix<Real> &Floor, Real alpha = 1.0,
-                 bool verbose = false);
-
-  /// Floor: Given a positive semidefinite matrix, floors the eigenvalues
-  /// to the specified quantity.  A previous version of this function had
-  /// a tolerance which is now no longer needed since we have code to
-  /// do the symmetric eigenvalue decomposition and no longer use the SVD
-  /// code for that purose.
-  int ApplyFloor(Real floor);
-  
-  bool IsDiagonal(Real cutoff = 1.0e-05) const;
-  bool IsUnit(Real cutoff = 1.0e-05) const;
-  bool IsZero(Real cutoff = 1.0e-05) const;
-  bool IsTridiagonal(Real cutoff = 1.0e-05) const;
-
-  /// sqrt of sum of square elements.
-  Real FrobeniusNorm() const;
-
-  /// Returns true if ((*this)-other).FrobeniusNorm() <=
-  ///   tol*(*this).FrobeniusNorma()
-  bool ApproxEqual(const SpMatrix<Real> &other, float tol = 0.01) const;
-
-  // LimitCond:
-  // Limits the condition of symmetric positive semidefinite matrix to
-  // a specified value
-  // by flooring all eigenvalues to a positive number which is some multiple
-  // of the largest one (or zero if there are no positive eigenvalues).
-  // Takes the condition number we are willing to accept, and floors
-  // eigenvalues to the largest eigenvalue divided by this.
-  //  Returns #eigs floored or already equal to the floor. 
-  // Throws exception if input is not positive definite.
-  // returns #floored.
-  MatrixIndexT LimitCond(Real maxCond = 1.0e+5, bool invert = false);
-
-  // as LimitCond but all done in double precision. // returns #floored.
-  MatrixIndexT LimitCondDouble(Real maxCond = 1.0e+5, bool invert = false) {
-    SpMatrix<double> dmat(*this);
-    MatrixIndexT ans = dmat.LimitCond(maxCond, invert);
-    (*this).CopyFromSp(dmat);
-    return ans;
-  }
-  Real Trace() const;
-
-  /// Tridiagonalize the matrix with an orthogonal transformation.  If
-  /// *this starts as S, produce T (and Q, if non-NULL) such that
-  /// T = Q A Q^T, i.e. S = Q^T T Q.  Caution: this is the other way
-  /// round from most authors (it's more efficient in row-major indexing).
-  void Tridiagonalize(MatrixBase<Real> *Q);
-
-  /// The symmetric QR algorithm.  This will mostly be useful in internal code.
-  /// Typically, you will call this after Tridiagonalize(), on the same object.
-  /// When called, *this (call it A at this point) must be tridiagonal; at exit,
-  /// *this will be a diagonal matrix D that is similar to A via orthogonal
-  /// transformations.  This algorithm right-multiplies Q by orthogonal
-  /// transformations.  It turns *this from a tridiagonal into a diagonal matrix
-  /// while maintaining that (Q *this Q^T) has the same value at entry and exit.
-  /// At entry Q should probably be either NULL or orthogonal, but we don't check
-  /// this.
-  void Qr(MatrixBase<Real> *Q);
-  
- private:
- void EigInternal(VectorBase<Real> *s, MatrixBase<Real> *P,
-                   Real tolerance, int recurse) const;
-};
-
-/// @} end of "addtogroup matrix_group"
-
-/// \addtogroup matrix_funcs_scalar
-/// @{
-
-
-/// Returns tr(A B).
-float TraceSpSp(const SpMatrix<float> &A, const SpMatrix<float> &B);
-double TraceSpSp(const SpMatrix<double> &A, const SpMatrix<double> &B);
-
-
-template<typename Real>
-inline bool ApproxEqual(const SpMatrix<Real> &A,
-                        const SpMatrix<Real> &B, Real tol = 0.01) {
-  return  A.ApproxEqual(B, tol);
-}
-
-template<typename Real>
-inline void AssertEqual(const SpMatrix<Real> &A,
-                        const SpMatrix<Real> &B, Real tol = 0.01) {
-  KALDI_ASSERT(ApproxEqual(A, B, tol));
-}
-
-
-
-/// Returns tr(A B).
-template<typename Real, typename OtherReal>
-Real TraceSpSp(const SpMatrix<Real> &A, const SpMatrix<OtherReal> &B);
-
-
-
-// TraceSpSpLower is the same as Trace(A B) except the lower-diagonal elements
-// are counted only once not twice as they should be.  It is useful in certain
-// optimizations.
-template<typename Real>
-Real TraceSpSpLower(const SpMatrix<Real> &A, const SpMatrix<Real> &B);
-
-
-/// Returns tr(A B).
-/// No option to transpose B because would make no difference.
-template<typename Real>
-Real TraceSpMat(const SpMatrix<Real> &A, const MatrixBase<Real> &B);
-
-/// Returns tr(A B C)
-/// (A and C may be transposed as specified by transA and transC).
-template<typename Real>
-Real TraceMatSpMat(const MatrixBase<Real> &A, MatrixTransposeType transA,
-                   const SpMatrix<Real> &B, const MatrixBase<Real> &C,
-                   MatrixTransposeType transC);
-
-/// Returns tr (A B C D)
-/// (A and C may be transposed as specified by transA and transB).
-template<typename Real>
-Real TraceMatSpMatSp(const MatrixBase<Real> &A, MatrixTransposeType transA,
-                     const SpMatrix<Real> &B, const MatrixBase<Real> &C,
-                     MatrixTransposeType transC, const SpMatrix<Real> &D);
-
-/** Computes v1^T * M * v2.  Not as efficient as it could be where v1 == v2
- * (but no suitable blas routines available).
- */
-
-/// Returns \f$ v_1^T M v_2 \f$
-/// Not as efficient as it could be where v1 == v2.
-template<typename Real>
-Real VecSpVec(const VectorBase<Real> &v1, const SpMatrix<Real> &M,
-               const VectorBase<Real> &v2);
-
-
-/// @} \addtogroup matrix_funcs_scalar
-
-/// \addtogroup matrix_funcs_misc
-/// @{
-
-
-/// This class describes the options for maximizing various quadratic objective
-/// functions.  It's mostly as described in the SGMM paper "the subspace
-/// Gaussian mixture model -- a structured model for speech recognition", but
-/// the diagonal_precondition option is newly added, to handle problems where
-/// different dimensions have very different scaling (we recommend to use the
-/// option but it's set false for back compatibility).
-struct SolverOptions {
-  BaseFloat K; // maximum condition number
-  BaseFloat eps; 
-  std::string name;
-  bool optimize_delta;
-  bool diagonal_precondition;
-  bool print_debug_output;
-  explicit SolverOptions(const std::string &name):
-      K(1.0e+4), eps(1.0e-40), name(name),
-      optimize_delta(true), diagonal_precondition(false),
-      print_debug_output(true) { }
-  SolverOptions(): K(1.0e+4), eps(1.0e-40), name("[unknown]"),
-                   optimize_delta(true), diagonal_precondition(false),
-                   print_debug_output(true) { }
-  void Check() const;
-};
-
-
-/// Maximizes the auxiliary function
-/// \f[    Q(x) = x.g - 0.5 x^T H x     \f]
-/// using a numerically stable method. Like a numerically stable version of
-/// \f$  x := Q^{-1} g.    \f$
-/// Assumes H positive semidefinite.
-/// Returns the objective-function change.
-
-template<typename Real>
-Real SolveQuadraticProblem(const SpMatrix<Real> &H,
-                           const VectorBase<Real> &g,
-                           const SolverOptions &opts,
-                           VectorBase<Real> *x);
-                           
-
-
-/// Maximizes the auxiliary function :
-/// \f[   Q(x) = tr(M^T P Y) - 0.5 tr(P M Q M^T)        \f]
-/// Like a numerically stable version of  \f$  M := Y Q^{-1}   \f$.
-/// Assumes Q and P positive semidefinite, and matrix dimensions match
-/// enough to make expressions meaningful.
-/// This is mostly as described in the SGMM paper "the subspace Gaussian mixture
-/// model -- a structured model for speech recognition", but the
-/// diagonal_precondition option is newly added, to handle problems
-/// where different dimensions have very different scaling (we recommend to use
-/// the option but it's set false for back compatibility).
-template<typename Real>
-Real SolveQuadraticMatrixProblem(const SpMatrix<Real> &Q,
-                                 const MatrixBase<Real> &Y,
-                                 const SpMatrix<Real> &P,
-                                 const SolverOptions &opts,
-                                 MatrixBase<Real> *M);
-
-/// Maximizes the auxiliary function :
-/// \f[   Q(M) =  tr(M^T G) -0.5 tr(P_1 M Q_1 M^T) -0.5 tr(P_2 M Q_2 M^T).   \f]
-/// Encountered in matrix update with a prior. We also apply a limit on the
-/// condition but it should be less frequently necessary, and can be set larger.
-template<typename Real>
-Real SolveDoubleQuadraticMatrixProblem(const MatrixBase<Real> &G,
-                                       const SpMatrix<Real> &P1,
-                                       const SpMatrix<Real> &P2,
-                                       const SpMatrix<Real> &Q1,
-                                       const SpMatrix<Real> &Q2,
-                                       const SolverOptions &opts,
-                                       MatrixBase<Real> *M);
-
-
-/// @} End of "addtogroup matrix_funcs_misc"
-
-}  // namespace kaldi
-
-
-// Including the implementation (now actually just includes some
-// template specializations).
-#include "matrix/sp-matrix-inl.h"
-
-
-#endif  // KALDI_MATRIX_SP_MATRIX_H_
-
diff --git a/kaldi_io/src/kaldi/matrix/srfft.h b/kaldi_io/src/kaldi/matrix/srfft.h
deleted file mode 100644
index c0d36af..0000000
--- a/kaldi_io/src/kaldi/matrix/srfft.h
+++ /dev/null
@@ -1,132 +0,0 @@
-// matrix/srfft.h
-
-// Copyright 2009-2011  Microsoft Corporation;  Go Vivace Inc.
-//                2014  Daniel Povey
-//
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-//
-// This file includes a modified version of code originally published in Malvar,
-// H., "Signal processing with lapped transforms, " Artech House, Inc., 1992.  The
-// current copyright holder of the original code, Henrique S. Malvar, has given
-// his permission for the release of this modified version under the Apache
-// License v2.0.
-
-#ifndef KALDI_MATRIX_SRFFT_H_
-#define KALDI_MATRIX_SRFFT_H_
-
-#include "matrix/kaldi-vector.h"
-#include "matrix/kaldi-matrix.h"
-
-namespace kaldi {
-
-/// @addtogroup matrix_funcs_misc
-/// @{
-
-
-// This class is based on code by Henrique (Rico) Malvar, from his book
-// "Signal Processing with Lapped Transforms" (1992).  Copied with
-// permission, optimized by Go Vivace Inc., and converted into C++ by
-// Microsoft Corporation
-// This is a more efficient way of doing the complex FFT than ComplexFft
-// (declared in matrix-functios.h), but it only works for powers of 2.
-// Note: in multi-threaded code, you would need to have one of these objects per
-// thread, because multiple calls to Compute in parallel would not work.
-template<typename Real>
-class SplitRadixComplexFft {
- public:
-  typedef MatrixIndexT Integer;
-
-  // N is the number of complex points (must be a power of two, or this
-  // will crash).  Note that the constructor does some work so it's best to
-  // initialize the object once and do the computation many times.
-  SplitRadixComplexFft(Integer N);
-
-  // Does the FFT computation, given pointers to the real and
-  // imaginary parts.  If "forward", do the forward FFT; else
-  // do the inverse FFT (without the 1/N factor).
-  // xr and xi are pointers to zero-based arrays of size N,
-  // containing the real and imaginary parts
-  // respectively.
-  void Compute(Real *xr, Real *xi, bool forward) const;
-
-  // This version of Compute takes a single array of size N*2,
-  // containing [ r0 im0 r1 im1 ... ].  Otherwise its behavior is  the
-  // same as the version above.
-  void Compute(Real *x, bool forward);
-
-
-  // This version of Compute is const; it operates on an array of size N*2
-  // containing [ r0 im0 r1 im1 ... ], but it uses the argument "temp_buffer" as
-  // temporary storage instead of a class-member variable.  It will allocate it if
-  // needed.
-  void Compute(Real *x, bool forward, std::vector<Real> *temp_buffer) const;
-
-  ~SplitRadixComplexFft();
-
- protected:
-  // temp_buffer_ is allocated only if someone calls Compute with only one Real*
-  // argument and we need a temporary buffer while creating interleaved data.
-  std::vector<Real> temp_buffer_;
- private:
-  void ComputeTables();
-  void ComputeRecursive(Real *xr, Real *xi, Integer logn) const;
-  void BitReversePermute(Real *x, Integer logn) const;
-
-  Integer N_;
-  Integer logn_;  // log(N)
-
-  Integer *brseed_;
-  // brseed is Evans' seed table, ref:  (Ref: D. M. W.
-  // Evans, "An improved digit-reversal permutation algorithm ...",
-  // IEEE Trans. ASSP, Aug. 1987, pp. 1120-1125).
-  Real **tab_;       // Tables of butterfly coefficients.
-
-  KALDI_DISALLOW_COPY_AND_ASSIGN(SplitRadixComplexFft);
-};
-
-template<typename Real>
-class SplitRadixRealFft: private SplitRadixComplexFft<Real> {
- public:
-  SplitRadixRealFft(MatrixIndexT N):  // will fail unless N>=4 and N is a power of 2.
-      SplitRadixComplexFft<Real> (N/2), N_(N) { }
-  
-  /// If forward == true, this function transforms from a sequence of N real points to its complex fourier
-  /// transform; otherwise it goes in the reverse direction.  If you call it
-  /// in the forward and then reverse direction and multiply by 1.0/N, you
-  /// will get back the original data.
-  /// The interpretation of the complex-FFT data is as follows: the array
-  /// is a sequence of complex numbers C_n of length N/2 with (real, im) format,
-  /// i.e. [real0, real_{N/2}, real1, im1, real2, im2, real3, im3, ...].
-  void Compute(Real *x, bool forward);
-
-
-  /// This is as the other Compute() function, but it is a const version that
-  /// uses a user-supplied buffer.
-  void Compute(Real *x, bool forward, std::vector<Real> *temp_buffer) const;
-
- private:
-  KALDI_DISALLOW_COPY_AND_ASSIGN(SplitRadixRealFft);  
-  int N_;
-};
-
-
-/// @} end of "addtogroup matrix_funcs_misc"
-
-} // end namespace kaldi
-
-
-#endif
-
diff --git a/kaldi_io/src/kaldi/matrix/tp-matrix.h b/kaldi_io/src/kaldi/matrix/tp-matrix.h
deleted file mode 100644
index f43e86c..0000000
--- a/kaldi_io/src/kaldi/matrix/tp-matrix.h
+++ /dev/null
@@ -1,131 +0,0 @@
-// matrix/tp-matrix.h
-
-// Copyright 2009-2011  Ondrej Glembek;  Lukas Burget;  Microsoft Corporation;
-//                      Saarland University;  Yanmin Qian;   Haihua Xu
-//                2013  Johns Hopkins Universith (author: Daniel Povey)
-
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-
-//  http://www.apache.org/licenses/LICENSE-2.0
-
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-#ifndef KALDI_MATRIX_TP_MATRIX_H_
-#define KALDI_MATRIX_TP_MATRIX_H_
-
-
-#include "matrix/packed-matrix.h"
-
-namespace kaldi {
-/// \addtogroup matrix_group
-/// @{
-
-template<typename Real> class TpMatrix;
-
-/// @brief Packed symetric matrix class
-template<typename Real>
-class TpMatrix : public PackedMatrix<Real> {
-  friend class CuTpMatrix<float>;
-  friend class CuTpMatrix<double>;
- public:
-  TpMatrix() : PackedMatrix<Real>() {}
-  explicit TpMatrix(MatrixIndexT r, MatrixResizeType resize_type = kSetZero)
-      : PackedMatrix<Real>(r, resize_type) {}
-  TpMatrix(const TpMatrix<Real>& orig) : PackedMatrix<Real>(orig) {}
-
-  /// Copy constructor from CUDA TpMatrix
-  /// This is defined in ../cudamatrix/cu-tp-matrix.cc
-  explicit TpMatrix(const CuTpMatrix<Real> &cu);
-  
-  
-  template<typename OtherReal> explicit TpMatrix(const TpMatrix<OtherReal>& orig)
-      : PackedMatrix<Real>(orig) {}
-  
-  Real operator() (MatrixIndexT r, MatrixIndexT c) const {
-    if (static_cast<UnsignedMatrixIndexT>(c) >
-        static_cast<UnsignedMatrixIndexT>(r)) {
-      KALDI_ASSERT(static_cast<UnsignedMatrixIndexT>(c) <
-                   static_cast<UnsignedMatrixIndexT>(this->num_rows_));
-      return 0;
-    }
-    KALDI_ASSERT(static_cast<UnsignedMatrixIndexT>(r) <
-                 static_cast<UnsignedMatrixIndexT>(this->num_rows_));
-    // c<=r now so don't have to check c.
-    return *(this->data_ + (r*(r+1)) / 2 + c);
-    // Duplicating code from PackedMatrix.h
-  }
-
-  Real &operator() (MatrixIndexT r, MatrixIndexT c) {
-    KALDI_ASSERT(static_cast<UnsignedMatrixIndexT>(r) <
-                 static_cast<UnsignedMatrixIndexT>(this->num_rows_));
-    KALDI_ASSERT(static_cast<UnsignedMatrixIndexT>(c) <=
-                 static_cast<UnsignedMatrixIndexT>(r) &&
-                 "you cannot access the upper triangle of TpMatrix using "
-                 "a non-const matrix object.");
-    return *(this->data_ + (r*(r+1)) / 2 + c);
-    // Duplicating code from PackedMatrix.h
-  }
-  // Note: Cholesky may throw std::runtime_error
-  void Cholesky(const SpMatrix<Real>& orig);
-  
-  void Invert();
-
-  // Inverts in double precision.
-  void InvertDouble() {
-    TpMatrix<double> dmat(*this);
-    dmat.Invert();
-    (*this).CopyFromTp(dmat);
-  }
-
-  /// Shallow swap
-  void Swap(TpMatrix<Real> *other);
-
-  /// Returns the determinant of the matrix (product of diagonals)
-  Real Determinant();
-
-  /// CopyFromMat copies the lower triangle of M into *this
-  /// (or the upper triangle, if Trans == kTrans).
-  void CopyFromMat(const MatrixBase<Real> &M,
-                   MatrixTransposeType Trans = kNoTrans);
-
-  /// This is implemented in ../cudamatrix/cu-tp-matrix.cc
-  void CopyFromMat(const CuTpMatrix<Real> &other);
-  
-  /// CopyFromTp copies another triangular matrix into this one.
-  void CopyFromTp(const TpMatrix<Real> &other) {
-    PackedMatrix<Real>::CopyFromPacked(other);
-  }
-
-  template<typename OtherReal> void CopyFromTp(const TpMatrix<OtherReal> &other) {
-    PackedMatrix<Real>::CopyFromPacked(other);
-  }
-
-  /// AddTp does *this += alpha * M.
-  void AddTp(const Real alpha, const TpMatrix<Real> &M) {
-    this->AddPacked(alpha, M);
-  }
-
-  using PackedMatrix<Real>::operator =;
-  using PackedMatrix<Real>::Scale;
-
-  void Resize(MatrixIndexT nRows, MatrixResizeType resize_type = kSetZero) {
-    PackedMatrix<Real>::Resize(nRows, resize_type);
-  }
-};
-
-/// @} end of "addtogroup matrix_group".
-
-}  // namespace kaldi
-
-
-#endif
-
diff --git a/kaldi_io/src/kaldi/tree/build-tree-questions.h b/kaldi_io/src/kaldi/tree/build-tree-questions.h
deleted file mode 100644
index a6bcfdd..0000000
--- a/kaldi_io/src/kaldi/tree/build-tree-questions.h
+++ /dev/null
@@ -1,133 +0,0 @@
-// tree/build-tree-questions.h
-
-// Copyright 2009-2011  Microsoft Corporation
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_TREE_BUILD_TREE_QUESTIONS_H_
-#define KALDI_TREE_BUILD_TREE_QUESTIONS_H_
-
-#include "util/stl-utils.h"
-#include "tree/context-dep.h"
-
-namespace kaldi {
-
-
-/// \addtogroup tree_group
-/// @{
-/// Typedef for statistics to build trees.
-typedef std::vector<std::pair<EventType, Clusterable*> > BuildTreeStatsType;
-
-/// Typedef used when we get "all keys" from a set of stats-- used in specifying
-/// which kinds of questions to ask.
-typedef enum { kAllKeysInsistIdentical, kAllKeysIntersection, kAllKeysUnion } AllKeysType;
-
-/// @}
-
-/// \defgroup tree_group_questions Question sets for decision-tree clustering
-///  See \ref tree_internals (and specifically \ref treei_func_questions) for context.
-/// \ingroup tree_group
-/// @{
-
-/// QuestionsForKey is a class used to define the questions for a key,
-/// and also options that allow us to refine the question during tree-building
-/// (i.e. make a question specific to the location in the tree).
-/// The Questions class handles aggregating these options for a set
-/// of different keys.
-struct QuestionsForKey {  // Configuration class associated with a particular key
-  // (of type EventKeyType).  It also contains the questions themselves.
-  std::vector<std::vector<EventValueType> > initial_questions;
-  RefineClustersOptions refine_opts;  // if refine_opts.max_iter == 0,
-  // we just pick from the initial questions.
-  
-  QuestionsForKey(int32 num_iters = 5): refine_opts(num_iters, 2) {
-    // refine_cfg with 5 iters and top-n = 2 (this is no restriction because
-    // RefineClusters called with 2 clusters; would get set to that anyway as
-    // it's the only possible value for 2 clusters).  User has to add questions.
-    // This config won't work as-is, as it has no questions.
-  }
-
-  void Check() const {
-    for (size_t i = 0;i < initial_questions.size();i++) KALDI_ASSERT(IsSorted(initial_questions[i]));
-  }
-
-  void Write(std::ostream &os, bool binary) const;
-  void Read(std::istream &is, bool binary);
-
-  // copy and assign allowed.
-};
-
-/// This class defines, for each EventKeyType, a set of initial questions that
-/// it tries and also a number of iterations for which to refine the questions to increase
-/// likelihood. It is perhaps a bit more than an options class, as it contains the
-/// actual questions.
-class Questions {  // careful, this is a class.
- public:
-  const QuestionsForKey &GetQuestionsOf(EventKeyType key) const {
-    std::map<EventKeyType, size_t>::const_iterator iter;
-    if ( (iter = key_idx_.find(key)) == key_idx_.end()) {
-      KALDI_ERR << "Questions: no options for key "<< key;
-    }
-    size_t idx = iter->second;
-    KALDI_ASSERT(idx < key_options_.size());
-    key_options_[idx]->Check();
-    return *(key_options_[idx]);
-  }
-  void SetQuestionsOf(EventKeyType key, const QuestionsForKey &options_of_key) {
-    options_of_key.Check();
-    if (key_idx_.count(key) == 0) {
-      key_idx_[key] = key_options_.size();
-      key_options_.push_back(new QuestionsForKey());
-      *(key_options_.back()) = options_of_key;
-    } else {
-      size_t idx = key_idx_[key];
-      KALDI_ASSERT(idx < key_options_.size());
-      *(key_options_[idx]) = options_of_key;
-    }
-  }
-  void GetKeysWithQuestions(std::vector<EventKeyType> *keys_out) const {
-    KALDI_ASSERT(keys_out != NULL);
-    CopyMapKeysToVector(key_idx_, keys_out);
-  }
-  const bool HasQuestionsForKey(EventKeyType key) const { return (key_idx_.count(key) != 0); }
-  ~Questions() { kaldi::DeletePointers(&key_options_); }
-
-
-  /// Initializer with arguments.  After using this you would have to set up the config for each key you
-  /// are going to use, or use InitRand().
-  Questions() { }
-
-
-  /// InitRand attempts to generate "reasonable" random questions.  Only
-  /// of use for debugging.  This initializer creates a config that is
-  /// ready to use.
-  /// e.g. num_iters_refine = 0 means just use stated questions (if >1, will use
-  /// different questions at each split of the tree).
-  void InitRand(const BuildTreeStatsType &stats, int32 num_quest, int32 num_iters_refine, AllKeysType all_keys_type);
-
-  void Write(std::ostream &os, bool binary) const;
-  void Read(std::istream &is, bool binary);
- private:
-  std::vector<QuestionsForKey*> key_options_;
-  std::map<EventKeyType, size_t> key_idx_;
-  KALDI_DISALLOW_COPY_AND_ASSIGN(Questions);
-};
-
-/// @}
-
-}// end namespace kaldi
-
-#endif // KALDI_TREE_BUILD_TREE_QUESTIONS_H_
diff --git a/kaldi_io/src/kaldi/tree/build-tree-utils.h b/kaldi_io/src/kaldi/tree/build-tree-utils.h
deleted file mode 100644
index 464fc6b..0000000
--- a/kaldi_io/src/kaldi/tree/build-tree-utils.h
+++ /dev/null
@@ -1,324 +0,0 @@
-// tree/build-tree-utils.h
-
-// Copyright 2009-2011  Microsoft Corporation
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_TREE_BUILD_TREE_UTILS_H_
-#define KALDI_TREE_BUILD_TREE_UTILS_H_
-
-#include "tree/build-tree-questions.h"
-
-// build-tree-questions.h needed for this typedef:
-// typedef std::vector<std::pair<EventType, Clusterable*> > BuildTreeStatsType;
-// and for other #includes.
-
-namespace kaldi {
-
-
-///   \defgroup tree_group_lower Low-level functions for manipulating statistics and event-maps
-///    See \ref tree_internals and specifically \ref treei_func for context.
-///   \ingroup tree_group
-///
-///   @{
-
-
-
-/// This frees the Clusterable* pointers in "stats", where non-NULL, and sets them to NULL.
-/// Does not delete the pointer "stats" itself.
-void DeleteBuildTreeStats(BuildTreeStatsType *stats);
-
-/// Writes BuildTreeStats object.  This works even if pointers are NULL.
-void WriteBuildTreeStats(std::ostream &os, bool binary,
-                         const BuildTreeStatsType &stats);
-
-/// Reads BuildTreeStats object.  The "example" argument must be of the same
-/// type as the stats on disk, and is needed for access to the correct "Read"
-/// function.  It was organized this way for easier extensibility (so adding new
-/// Clusterable derived classes isn't painful)
-void ReadBuildTreeStats(std::istream &is, bool binary,
-                        const Clusterable &example, BuildTreeStatsType *stats);
-
-/// Convenience function e.g. to work out possible values of the phones from just the stats.
-/// Returns true if key was always defined inside the stats.
-/// May be used with and == NULL to find out of key was always defined.
-bool PossibleValues(EventKeyType key, const BuildTreeStatsType &stats,
-                    std::vector<EventValueType> *ans);
-
-
-/// Splits stats according to the EventMap, indexing them at output by the
-/// leaf type.   A utility function.  NOTE-- pointers in stats_out point to
-/// the same memory location as those in stats.  No copying of Clusterable*
-/// objects happens.  Will add to stats in stats_out if non-empty at input.
-/// This function may increase the size of vector stats_out as necessary
-/// to accommodate stats, but will never decrease the size.
-void SplitStatsByMap(const BuildTreeStatsType &stats_in, const EventMap &e,
-                     std::vector<BuildTreeStatsType> *stats_out);
-
-/// SplitStatsByKey splits stats up according to the value of a particular key,
-/// which must be always defined and nonnegative.  Like MapStats.  Pointers to
-/// Clusterable* in stats_out are not newly allocated-- they are the same as the
-/// ones in stats_in.  Generally they will still be owned at stats_in (user can
-/// decide where to allocate ownership).
-void SplitStatsByKey(const BuildTreeStatsType &stats_in, EventKeyType key,
-                     std::vector<BuildTreeStatsType> *stats_out);
-
-
-/// Converts stats from a given context-window (N) and central-position (P) to a
-/// different N and P, by possibly reducing context.  This function does a job
-/// that's quite specific to the "normal" stats format we use.  See \ref
-/// tree_window for background.  This function may delete some keys and change
-/// others, depending on the N and P values.  It expects that at input, all keys
-/// will either be -1 or lie between 0 and oldN-1.  At output, keys will be
-/// either -1 or between 0 and newN-1.
-/// Returns false if we could not convert the stats (e.g. because newN is larger
-/// than oldN).
-bool ConvertStats(int32 oldN, int32 oldP, int32 newN, int32 newP,
-                  BuildTreeStatsType *stats);
-
-
-/// FilterStatsByKey filters the stats according the value of a specified key.
-/// If include_if_present == true, it only outputs the stats whose key is in
-/// "values"; otherwise it only outputs the stats whose key is not in "values".
-/// At input, "values" must be sorted and unique, and all stats in "stats_in"
-/// must have "key" defined.  At output, pointers to Clusterable* in stats_out
-/// are not newly allocated-- they are the same as the ones in stats_in.
-void FilterStatsByKey(const BuildTreeStatsType &stats_in,
-                      EventKeyType key,
-                      std::vector<EventValueType> &values,
-                      bool include_if_present,  // true-> retain only if in "values",
-                      // false-> retain only if not in "values".
-                      BuildTreeStatsType *stats_out);
-
-
-/// Sums stats, or returns NULL stats_in has no non-NULL stats.
-/// Stats are newly allocated, owned by caller.
-Clusterable *SumStats(const BuildTreeStatsType &stats_in);
-
-/// Sums the normalizer [typically, data-count] over the stats.
-BaseFloat SumNormalizer(const BuildTreeStatsType &stats_in);
-
-/// Sums the objective function over the stats.
-BaseFloat SumObjf(const BuildTreeStatsType &stats_in);
-
-
-/// Sum a vector of stats.  Leaves NULL as pointer if no stats available.
-/// The pointers in stats_out are owned by caller.  At output, there may be
-/// NULLs in the vector stats_out.
-void SumStatsVec(const std::vector<BuildTreeStatsType> &stats_in, std::vector<Clusterable*> *stats_out);
-
-/// Cluster the stats given the event map return the total objf given those clusters.
-BaseFloat ObjfGivenMap(const BuildTreeStatsType &stats_in, const EventMap &e);
-
-
-/// FindAllKeys puts in *keys the (sorted, unique) list of all key identities in the stats.
-/// If type == kAllKeysInsistIdentical, it will insist that this set of keys is the same for all the
-///   stats (else exception is thrown).
-/// if type == kAllKeysIntersection, it will return the smallest common set of keys present in
-///   the set of stats
-/// if type== kAllKeysUnion (currently probably not so useful since maps will return "undefined"
-///   if key is not present), it will return the union of all the keys present in the stats.
-void FindAllKeys(const BuildTreeStatsType &stats, AllKeysType keys_type,
-                 std::vector<EventKeyType> *keys);
-
-
-/// @}
-
-
-/**
- \defgroup tree_group_intermediate Intermediate-level functions used in building the tree
-    These functions are are used in top-level tree-building code (\ref tree_group_top); see
-     \ref tree_internals for documentation.
- \ingroup tree_group
- @{
-*/
-
-
-/// Returns a tree with just one node.  Used @ start of tree-building process.
-/// Not really used in current recipes.
-inline EventMap *TrivialTree(int32 *num_leaves) {
-  KALDI_ASSERT(*num_leaves == 0);  // in envisaged usage.
-  return new ConstantEventMap( (*num_leaves)++ );
-}
-
-/// DoTableSplit does a complete split on this key (e.g. might correspond to central phone
-/// (key = P-1), or HMM-state position (key == kPdfClass == -1).  Stats used to work out possible
-/// values of the event. "num_leaves" is used to allocate new leaves.   All stats must have
-/// this key defined, or this function will crash.
-EventMap *DoTableSplit(const EventMap &orig, EventKeyType key,
-                       const BuildTreeStatsType &stats, int32 *num_leaves);
-
-
-/// DoTableSplitMultiple does a complete split on all the keys, in order from keys[0],
-/// keys[1]
-/// and so on.  The stats are used to work out possible values corresponding to the key.
-/// "num_leaves" is used to allocate new leaves.   All stats must have
-/// the keys defined, or this function will crash.
-/// Returns a newly allocated event map.
-EventMap *DoTableSplitMultiple(const EventMap &orig,
-                               const std::vector<EventKeyType> &keys,
-                               const BuildTreeStatsType &stats,
-                               int32 *num_leaves);
-
-
-/// "ClusterEventMapGetMapping" clusters the leaves of the EventMap, with "thresh" a delta-likelihood
-/// threshold to control how many leaves we combine (might be the same as the delta-like
-/// threshold used in splitting.
-// The function returns the #leaves we combined.  The same leaf-ids of the leaves being clustered
-// will be used for the clustered leaves (but other than that there is no special rule which
-// leaf-ids should be used at output).
-// It outputs the mapping for leaves, in "mapping", which may be empty at the start
-// but may also contain mappings for other parts of the tree, which must contain
-// disjoint leaves from this part.  This is so that Cluster can
-// be called multiple times for sub-parts of the tree (with disjoint sets of leaves),
-// e.g. if we want to avoid sharing across phones.  Afterwards you can use Copy function
-// of EventMap to apply the mapping, i.e. call e_in.Copy(mapping) to get the new map.
-// Note that the application of Cluster creates gaps in the leaves.  You should then
-// call RenumberEventMap(e_in.Copy(mapping), num_leaves).
-// *If you only want to cluster a subset of the leaves (e.g. just non-silence, or just
-// a particular phone, do this by providing a set of "stats" that correspond to just
-// this subset of leaves*.  Leaves with no stats will not be clustered.
-// See build-tree.cc for an example of usage.
-int ClusterEventMapGetMapping(const EventMap &e_in, const BuildTreeStatsType &stats,
-                              BaseFloat thresh, std::vector<EventMap*> *mapping);
-
-/// This is as ClusterEventMapGetMapping but a more convenient interface
-/// that exposes less of the internals.  It uses a bottom-up clustering to
-/// combine the leaves, until the log-likelihood decrease from combinging two
-/// leaves exceeds the threshold.
-EventMap *ClusterEventMap(const EventMap &e_in, const BuildTreeStatsType &stats,
-                          BaseFloat thresh, int32 *num_removed);
-
-/// This is as ClusterEventMap, but first splits the stats on the keys specified
-/// in "keys" (e.g. typically keys = [ -1, P ]), and only clusters within the
-/// classes defined by that splitting.
-/// Note-- leaves will be non-consecutive at output, use RenumberEventMap.
-EventMap *ClusterEventMapRestrictedByKeys(const EventMap &e_in,
-                                          const BuildTreeStatsType &stats,
-                                          BaseFloat thresh,
-                                          const std::vector<EventKeyType> &keys,
-                                          int32 *num_removed);
-
-
-/// This version of ClusterEventMapRestricted restricts the clustering to only
-/// allow things that "e_restrict" maps to the same value to be clustered
-/// together.
-EventMap *ClusterEventMapRestrictedByMap(const EventMap &e_in,
-                                         const BuildTreeStatsType &stats,
-                                         BaseFloat thresh,
-                                         const EventMap &e_restrict,
-                                         int32 *num_removed);
-
-
-/// RenumberEventMap [intended to be used after calling ClusterEventMap] renumbers
-/// an EventMap so its leaves are consecutive.
-/// It puts the number of leaves in *num_leaves.  If later you need the mapping of
-/// the leaves, modify the function and add a new argument.
-EventMap *RenumberEventMap(const EventMap &e_in, int32 *num_leaves);
-
-/// This function remaps the event-map leaves using this mapping,
-/// indexed by the number at leaf.
-EventMap *MapEventMapLeaves(const EventMap &e_in,
-                            const std::vector<int32> &mapping);
-
-
-
-/// ShareEventMapLeaves performs a quite specific function that allows us to
-/// generate trees where, for a certain list of phones, and for all states in
-/// the phone, all the pdf's are shared.
-/// Each element of "values" contains a list of phones (may be just one phone),
-/// all states of which we want shared together).  Typically at input, "key" will
-/// equal P, the central-phone position, and "values" will contain just one
-/// list containing the silence phone.
-/// This function renumbers the event map leaves after doing the sharing, to
-/// make the event-map leaves contiguous.
-EventMap *ShareEventMapLeaves(const EventMap &e_in, EventKeyType key,
-                              std::vector<std::vector<EventValueType> > &values,
-                              int32 *num_leaves);
-
-
-
-/// Does a decision-tree split at the leaves of an EventMap.
-/// @param orig [in] The EventMap whose leaves we want to split. [may be either a trivial or a
-///           non-trivial one].
-/// @param stats [in] The statistics for splitting the tree; if you do not want a particular
-///          subset of leaves to be split, make sure the stats corresponding to those leaves
-///          are not present in "stats".
-/// @param qcfg [in] Configuration class that contains initial questions (e.g. sets of phones)
-///          for each key and says whether to refine these questions during tree building.
-/// @param thresh [in] A log-likelihood threshold (e.g. 300) that can be used to
-///           limit the number of leaves; you can use zero and set max_leaves instead.
-/// @param max_leaves [in] Will stop leaves being split after they reach this number.
-/// @param num_leaves [in,out] A pointer used to allocate leaves; always corresponds to the
-///             current number of leaves (is incremented when this is increased).
-/// @param objf_impr_out [out] If non-NULL, will be set to the objective improvement due to splitting
-///           (not normalized by the number of frames).
-/// @param smallest_split_change_out If non-NULL, will be set to the smallest objective-function
-///         improvement that we got from splitting any leaf; useful to provide a threshold
-///         for ClusterEventMap.
-/// @return The EventMap after splitting is returned; pointer is owned by caller.
-EventMap *SplitDecisionTree(const EventMap &orig,
-                            const BuildTreeStatsType &stats,
-                            Questions &qcfg,
-                            BaseFloat thresh,
-                            int32 max_leaves,  // max_leaves<=0 -> no maximum.
-                            int32 *num_leaves,
-                            BaseFloat *objf_impr_out,
-                            BaseFloat *smallest_split_change_out);
-
-/// CreateRandomQuestions will initialize a Questions randomly, in a reasonable
-/// way [for testing purposes, or when hand-designed questions are not available].
-/// e.g. num_quest = 5 might be a reasonable value if num_iters > 0, or num_quest = 20 otherwise.
-void CreateRandomQuestions(const BuildTreeStatsType &stats, int32 num_quest, Questions *cfg_out);
-
-
-/// FindBestSplitForKey is a function used in DoDecisionTreeSplit.
-/// It finds the best split for this key, given these stats.
-/// It will return 0 if the key was not always defined for the stats.
-BaseFloat FindBestSplitForKey(const BuildTreeStatsType &stats,
-                              const Questions &qcfg,
-                              EventKeyType key,
-                              std::vector<EventValueType> *yes_set);
-
-
-/// GetStubMap is used in tree-building functions to get the initial
-/// to-states map, before the decision-tree-building process.  It creates
-/// a simple map that splits on groups of phones.  For the set of phones in
-/// phone_sets[i] it creates either: if share_roots[i] == true, a single
-/// leaf node, or if share_roots[i] == false, separate root nodes for
-/// each HMM-position (it goes up to the highest position for any
-/// phone in the set, although it will warn if you share roots between
-/// phones with different numbers of states, which is a weird thing to
-/// do but should still work.  If any phone is present
-/// in "phone_sets" but "phone2num_pdf_classes" does not map it to a length,
-/// it is an error.  Note that the behaviour of the resulting map is
-/// undefined for phones not present in "phone_sets".
-/// At entry, this function should be called with (*num_leaves == 0).
-/// It will number the leaves starting from (*num_leaves).
-
-EventMap *GetStubMap(int32 P,
-                     const std::vector<std::vector<int32> > &phone_sets,
-                     const std::vector<int32> &phone2num_pdf_classes,
-                     const std::vector<bool> &share_roots,  // indexed by index into phone_sets.
-                     int32 *num_leaves);
-/// Note: GetStubMap with P = 0 can be used to get a standard monophone system.
-
-/// @}
-
-
-}// end namespace kaldi
-
-#endif
diff --git a/kaldi_io/src/kaldi/tree/build-tree.h b/kaldi_io/src/kaldi/tree/build-tree.h
deleted file mode 100644
index 37bb108..0000000
--- a/kaldi_io/src/kaldi/tree/build-tree.h
+++ /dev/null
@@ -1,250 +0,0 @@
-// tree/build-tree.h
-
-// Copyright 2009-2011  Microsoft Corporation
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_TREE_BUILD_TREE_H_
-#define KALDI_TREE_BUILD_TREE_H_
-
-// The file build-tree.h contains outer-level routines used in tree-building
-// and related tasks, that are directly called by the command-line tools.
-
-#include "tree/build-tree-utils.h"
-#include "tree/context-dep.h"
-namespace kaldi {
-
-/// \defgroup tree_group_top Top-level tree-building functions
-/// See \ref tree_internals for context.
-/// \ingroup tree_group
-/// @{
-
-// Note, in tree_group_top we also include AccumulateTreeStats, in
-// ../hmm/tree-accu.h (it has some extra dependencies so we didn't
-// want to include it here).
-
-/**
- *  BuildTree is the normal way to build a set of decision trees.
- *  The sets "phone_sets" dictate how we set up the roots of the decision trees.
- *  each set of phones phone_sets[i] has shared decision-tree roots, and if
- *  the corresponding variable share_roots[i] is true, the root will be shared
- *  for the different HMM-positions in the phone.  All phones in "phone_sets"
- *  should be in the stats (use FixUnseenPhones to ensure this).
- *  if for any i, do_split[i] is false, we will not do any tree splitting for
- *  phones in that set.
- * @param qopts [in] Questions options class, contains questions for each key
- *                   (e.g. each phone position)
- * @param phone_sets [in] Each element of phone_sets is a set of phones whose
- *                 roots are shared together (prior to decision-tree splitting).
- * @param phone2num_pdf_classes [in] A map from phones to the number of
- *                 \ref pdf_class "pdf-classes"
- *                 in the phone (this info is derived from the HmmTopology object)
- * @param share_roots [in] A vector the same size as phone_sets; says for each
- *                phone set whether the root should be shared among all the
- *                pdf-classes or not.
- * @param do_split [in] A vector the same size as phone_sets; says for each
- *                phone set whether decision-tree splitting should be done
- *                 (generally true for non-silence phones).
- * @param stats [in] The statistics used in tree-building.
- * @param thresh [in] Threshold used in decision-tree splitting (e.g. 1000),
- *                   or you may use 0 in which case max_leaves becomes the
- *                    constraint.
- * @param max_leaves [in] Maximum number of leaves it will create; set this
- *                  to a large number if you want to just specify  "thresh".
- * @param cluster_thresh [in] Threshold for clustering leaves after decision-tree
- *                  splitting (only within each phone-set); leaves will be combined
- *                  if log-likelihood change is less than this.  A value about equal
- *                  to "thresh" is suitable
- *                  if thresh != 0; otherwise, zero will mean no clustering is done,
- *                  or a negative value (e.g. -1) sets it to the smallest likelihood
- *                  change seen during the splitting algorithm; this typically causes
- *                  about a 20% reduction in the number of leaves.
- 
- * @param P [in] The central position of the phone context window, e.g. 1 for a
- *                triphone system.
- * @return  Returns a pointer to an EventMap object that is the tree.
-
-*/
-
-EventMap *BuildTree(Questions &qopts,
-                    const std::vector<std::vector<int32> > &phone_sets,
-                    const std::vector<int32> &phone2num_pdf_classes,
-                    const std::vector<bool> &share_roots,
-                    const std::vector<bool> &do_split,
-                    const BuildTreeStatsType &stats,
-                    BaseFloat thresh,
-                    int32 max_leaves,
-                    BaseFloat cluster_thresh,  // typically == thresh.  If negative, use smallest split.
-                    int32 P);
-
-
-/**
- *
- *  BuildTreeTwoLevel builds a two-level tree, useful for example in building tied mixture
- *  systems with multiple codebooks.  It first builds a small tree by splitting to
- *  "max_leaves_first".  It then splits at the leaves of "max_leaves_first" (think of this
- *  as creating multiple little trees at the leaves of the first tree), until the total
- *  number of leaves reaches "max_leaves_second".  It then outputs the second tree, along
- *  with a mapping from the leaf-ids of the second tree to the leaf-ids of the first tree.
- *  Note that the interface is similar to BuildTree, and in fact it calls BuildTree
- *  internally.
- *
- *  The sets "phone_sets" dictate how we set up the roots of the decision trees.
- *  each set of phones phone_sets[i] has shared decision-tree roots, and if
- *  the corresponding variable share_roots[i] is true, the root will be shared
- *  for the different HMM-positions in the phone.  All phones in "phone_sets"
- *  should be in the stats (use FixUnseenPhones to ensure this).
- *  if for any i, do_split[i] is false, we will not do any tree splitting for
- *  phones in that set.
- *
- * @param qopts [in] Questions options class, contains questions for each key
- *                   (e.g. each phone position)
- * @param phone_sets [in] Each element of phone_sets is a set of phones whose
- *                 roots are shared together (prior to decision-tree splitting).
- * @param phone2num_pdf_classes [in] A map from phones to the number of
- *                 \ref pdf_class "pdf-classes"
- *                 in the phone (this info is derived from the HmmTopology object)
- * @param share_roots [in] A vector the same size as phone_sets; says for each
- *                phone set whether the root should be shared among all the
- *                pdf-classes or not.
- * @param do_split [in] A vector the same size as phone_sets; says for each
- *                phone set whether decision-tree splitting should be done
- *                 (generally true for non-silence phones).
- * @param stats [in] The statistics used in tree-building.
- * @param max_leaves_first [in] Maximum number of leaves it will create in first
- *                  level of decision tree. 
- * @param max_leaves_second [in] Maximum number of leaves it will create in second
- *                  level of decision tree.  Must be > max_leaves_first.
- * @param cluster_leaves [in] Boolean value; if true, we post-cluster the leaves produced
- *                  in the second level of decision-tree split; if false, we don't.
- *                  The threshold for post-clustering is the log-like change of the last
- *                  decision-tree split; this typically causes about a 20% reduction in
- *                  the number of leaves.
- * @param P [in]   The central position of the phone context window, e.g. 1 for a
- *                 triphone system.
- * @param leaf_map [out]  Will be set to be a mapping from the leaves of the
- *                 "big" tree to the leaves of the "little" tree, which you can
- *                 view as cluster centers.
- * @return  Returns a pointer to an EventMap object that is the (big) tree.
-
-*/
-
-EventMap *BuildTreeTwoLevel(Questions &qopts,
-                            const std::vector<std::vector<int32> > &phone_sets,
-                            const std::vector<int32> &phone2num_pdf_classes,
-                            const std::vector<bool> &share_roots,
-                            const std::vector<bool> &do_split,
-                            const BuildTreeStatsType &stats,
-                            int32 max_leaves_first,
-                            int32 max_leaves_second,
-                            bool cluster_leaves,
-                            int32 P,
-                            std::vector<int32> *leaf_map);
-
-
-/// GenRandStats generates random statistics of the form used by BuildTree.
-/// It tries to do so in such a way that they mimic "real" stats.  The event keys
-/// and their corresponding values are:
-/// - key == -1 == kPdfClass -> pdf-class, generally corresponds to
-///       zero-based position in HMM (0, 1, 2 .. hmm_lengths[phone]-1)
-/// - key == 0 -> phone-id of left-most context phone.
-/// - key == 1 -> phone-id of one-from-left-most context phone.
-/// - key == P-1 -> phone-id of central phone.
-/// - key == N-1 -> phone-id of right-most context phone.
-/// GenRandStats is useful only for testing but it serves to document the format of
-/// stats used by BuildTreeDefault.
-/// if is_ctx_dep[phone] is set to false, GenRandStats will not define the keys for
-/// other than the P-1'th phone.
-
-/// @param dim [in] dimension of features.
-/// @param num_stats [in] approximate number of separate phones-in-context wanted.
-/// @param N [in] context-size (typically 3)
-/// @param P [in] central-phone position in zero-based numbering (typically 1)
-/// @param phone_ids [in] integer ids of phones
-/// @param hmm_lengths [in] lengths of hmm for phone, indexed by phone.
-/// @param is_ctx_dep [in] boolean array indexed by phone, saying whether each phone
-///     is context dependent.
-/// @param ensure_all_phones_covered [in] Boolean argument: if true, GenRandStats
-///     ensures that every phone is seen at least once in the central position (P).
-/// @param stats_out [out] The statistics that this routine outputs.
-
-void GenRandStats(int32 dim, int32 num_stats, int32 N, int32 P,
-                  const std::vector<int32> &phone_ids,
-                  const std::vector<int32> &hmm_lengths,
-                  const std::vector<bool> &is_ctx_dep,
-                  bool ensure_all_phones_covered,
-                  BuildTreeStatsType *stats_out);
-
-
-/// included here because it's used in some tree-building
-/// calling code.  Reads an OpenFst symbl table,
-/// discards the symbols and outputs the integers
-void ReadSymbolTableAsIntegers(std::string filename,
-                               bool include_eps,
-                               std::vector<int32> *syms);
-
-
-
-/**
- *  Outputs sets of phones that are reasonable for questions
- *  to ask in the tree-building algorithm.  These are obtained by tree
- *  clustering of the phones; for each node in the tree, all the leaves
- *  accessible from that node form one of the sets of phones.
- *    @param stats [in] The statistics as used for normal tree-building.
- *    @param phone_sets_in [in] All the phones, pre-partitioned into sets.
- *       The output sets will be various unions of these sets.  These sets
- *       will normally correspond to "real phones", in cases where the phones
- *       have stress and position markings.
- *    @param all_pdf_classes_in [in] All the \ref pdf_class "pdf-classes"
- *      that we consider for clustering.  In the normal case this is the singleton
- *       set {1}, which means that we only consider the central hmm-position
- *       of the standard 3-state HMM, for clustering purposes.
- *    @param P [in] The central position in the phone context window; normally
- *       1 for triphone system.s
- *    @param questions_out [out] The questions (sets of phones) are output to here.
- **/
-void AutomaticallyObtainQuestions(BuildTreeStatsType &stats,
-                                  const std::vector<std::vector<int32> > &phone_sets_in,
-                                  const std::vector<int32> &all_pdf_classes_in,
-                                  int32 P,
-                                  std::vector<std::vector<int32> > *questions_out);
-
-/// This function clusters the phones (or some initially specified sets of phones)
-/// into sets of phones, using a k-means algorithm.  Useful, for example, in building
-/// simple models for purposes of adaptation.
-
-void KMeansClusterPhones(BuildTreeStatsType &stats,
-                         const std::vector<std::vector<int32> > &phone_sets_in,
-                         const std::vector<int32> &all_pdf_classes_in,
-                         int32 P,
-                         int32 num_classes,
-                         std::vector<std::vector<int32> > *sets_out);
-
-/// Reads the roots file (throws on error).  Format is lines like:
-///  "shared split 1 2 3 4",
-///  "not-shared not-split 5",
-/// and so on.  The numbers are indexes of phones.
-void ReadRootsFile(std::istream &is,
-                   std::vector<std::vector<int32> > *phone_sets,
-                   std::vector<bool> *is_shared_root,
-                   std::vector<bool> *is_split_root);
-
-
-/// @}
-
-}// end namespace kaldi
-
-#endif
diff --git a/kaldi_io/src/kaldi/tree/cluster-utils.h b/kaldi_io/src/kaldi/tree/cluster-utils.h
deleted file mode 100644
index 55583a2..0000000
--- a/kaldi_io/src/kaldi/tree/cluster-utils.h
+++ /dev/null
@@ -1,291 +0,0 @@
-// tree/cluster-utils.h
-
-// Copyright 2012   Arnab Ghoshal
-// Copyright 2009-2011  Microsoft Corporation;  Saarland University
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_TREE_CLUSTER_UTILS_H_
-#define KALDI_TREE_CLUSTER_UTILS_H_
-
-#include <vector>
-#include "matrix/matrix-lib.h"
-#include "itf/clusterable-itf.h"
-
-namespace kaldi {
-
-/// \addtogroup clustering_group_simple
-/// @{
-
-/// Returns the total objective function after adding up all the
-/// statistics in the vector (pointers may be NULL).
-BaseFloat SumClusterableObjf(const std::vector<Clusterable*> &vec);
-
-/// Returns the total normalizer (usually count) of the cluster (pointers may be NULL).
-BaseFloat SumClusterableNormalizer(const std::vector<Clusterable*> &vec);
-
-/// Sums stats (ptrs may be NULL). Returns NULL if no non-NULL stats present.
-Clusterable *SumClusterable(const std::vector<Clusterable*> &vec);
-
-/** Fills in any (NULL) holes in "stats" vector, with empty stats, because
- *  certain algorithms require non-NULL stats.  If "stats" nonempty, requires it
- *  to contain at least one non-NULL pointer that we can call Copy() on.
- */
-void EnsureClusterableVectorNotNull(std::vector<Clusterable*> *stats);
-
-
-/** Given stats and a vector "assignments" of the same size (that maps to
- * cluster indices), sums the stats up into "clusters."  It will add to any
- * stats already present in "clusters" (although typically "clusters" will be
- * empty when called), and it will extend with NULL pointers for any unseen
- * indices. Call EnsureClusterableStatsNotNull afterwards if you want to ensure
- * all non-NULL clusters. Pointer in "clusters" are owned by caller. Pointers in
- * "stats" do not have to be non-NULL.
- */
-void AddToClusters(const std::vector<Clusterable*> &stats,
-                   const std::vector<int32> &assignments,
-                   std::vector<Clusterable*> *clusters);
-
-
-/// AddToClustersOptimized does the same as AddToClusters (it sums up the stats
-/// within each cluster, except it uses the sum of all the stats ("total") to
-/// optimize the computation for speed, if possible.  This will generally only be
-/// a significant speedup in the case where there are just two clusters, which
-/// can happen in algorithms that are doing binary splits; the idea is that we
-/// sum up all the stats in one cluster (the one with the fewest points in it),
-/// and then subtract from the total.
-void AddToClustersOptimized(const std::vector<Clusterable*> &stats,
-                            const std::vector<int32> &assignments,
-                            const Clusterable &total,
-                            std::vector<Clusterable*> *clusters);
-
-/// @} end "addtogroup clustering_group_simple"
-
-/// \addtogroup clustering_group_algo
-/// @{
-
-// Note, in the algorithms below, it is assumed that the input "points" (which
-// is std::vector<Clusterable*>) is all non-NULL.
-
-/** A bottom-up clustering algorithm. There are two parameters that control how
- *  many clusters we get: a "max_merge_thresh" which is a threshold for merging
- *  clusters, and a min_clust which puts a floor on the number of clusters we want. Set
- *  max_merge_thresh = large to use the min_clust only, or min_clust to 0 to use
- *  the max_merge_thresh only.
- *
- *  The algorithm is:
- *  \code
- *      while (num-clusters > min_clust && smallest_merge_cost <= max_merge_thresh)
- *          merge the closest two clusters.
- *  \endcode
- *
- *  @param points [in] Points to be clustered (may not contain NULL pointers)
- *  @param thresh [in] Threshold on cost change from merging clusters; clusters
- *               won't be merged if the cost is more than this
- *  @param min_clust [in] Minimum number of clusters desired; we'll stop merging
- *                  after reaching this number.
- *  @param clusters_out [out] If non-NULL, will be set to a vector of size equal
- *                 to the number of output clusters, containing the clustered
- *                 statistics.  Must be empty when called.
- *  @param assignments_out [out] If non-NULL, will be resized to the number of
- *                 points, and each element is the index of the cluster that point
- *                 was assigned to.
- *  @return Returns the total objf change relative to all clusters being separate, which is
- *    a negative.  Note that this is not the same as what the other clustering algorithms return.
- */
-BaseFloat ClusterBottomUp(const std::vector<Clusterable*> &points,
-                          BaseFloat thresh,
-                          int32 min_clust,
-                          std::vector<Clusterable*> *clusters_out,
-                          std::vector<int32> *assignments_out);
-
-/** This is a bottom-up clustering where the points are pre-clustered in a set
- *  of compartments, such that only points in the same compartment are clustered
- *  together. The compartment and pair of points with the smallest merge cost
- *  is selected and the points are clustered. The result stays in the same
- *  compartment. The code does not merge compartments, and hence assumes that
- *  the number of compartments is smaller than the 'min_clust' option.
- *  The clusters in "clusters_out" are newly allocated and owned by the caller.
- */
-BaseFloat ClusterBottomUpCompartmentalized(
-    const std::vector< std::vector<Clusterable*> > &points, BaseFloat thresh,
-    int32 min_clust, std::vector< std::vector<Clusterable*> > *clusters_out,
-    std::vector< std::vector<int32> > *assignments_out);
-
-
-struct RefineClustersOptions {
-  int32 num_iters;  // must be >= 0.  If zero, does nothing.
-  int32 top_n;  // must be >= 2.
-  RefineClustersOptions() : num_iters(100), top_n(5) {}
-  RefineClustersOptions(int32 num_iters_in, int32 top_n_in)
-      : num_iters(num_iters_in), top_n(top_n_in) {}
-  // include Write and Read functions because this object gets written/read as
-  // part of the QuestionsForKeyOptions class.
-  void Write(std::ostream &os, bool binary) const;
-  void Read(std::istream &is, bool binary);
-};
-
-/** RefineClusters is mainly used internally by other clustering algorithms.
- *
- *  It starts with a given assignment of points to clusters and
- *  keeps trying to improve it by moving points from cluster to cluster, up to
- *  a maximum number of iterations.
- *
- *  "clusters" and "assignments" are both input and output variables, and so
- *  both MUST be non-NULL.
- *
- *  "top_n" (>=2) is a pruning value: more is more exact, fewer is faster. The
- *  algorithm initially finds the "top_n" closest clusters to any given point,
- *  and from that point only consider move to those "top_n" clusters. Since
- *  RefineClusters is called multiple times from ClusterKMeans (for instance),
- *  this is not really a limitation.
- */
-BaseFloat RefineClusters(const std::vector<Clusterable*> &points,
-                         std::vector<Clusterable*> *clusters /*non-NULL*/,
-                         std::vector<int32> *assignments /*non-NULL*/,
-                         RefineClustersOptions cfg = RefineClustersOptions());
-
-struct ClusterKMeansOptions {
-  RefineClustersOptions refine_cfg;
-  int32 num_iters;
-  int32 num_tries;  // if >1, try whole procedure >once and pick best.
-  bool verbose;
-  ClusterKMeansOptions()
-      : refine_cfg(), num_iters(20), num_tries(2), verbose(true)  {}
-};
-
-/** ClusterKMeans is a K-means-like clustering algorithm. It starts with
- *  pseudo-random initialization of points to clusters and uses RefineClusters
- *  to iteratively improve the cluster assignments.  It does this for
- *  multiple iterations and picks the result with the best objective function.
- *
- *
- *  ClusterKMeans implicitly uses Rand(). It will not necessarily return
- *  the same value on different calls.  Use sRand() if you want consistent
- *  results.
- *  The algorithm used in ClusterKMeans is a "k-means-like" algorithm that tries
- *  to be as efficient as possible.  Firstly, since the algorithm it uses
- *  includes random initialization, it tries the whole thing cfg.num_tries times
- *  and picks the one with the best objective function.  Each try, it does as
- *  follows: it randomly initializes points to clusters, and then for
- *  cfg.num_iters iterations it calls RefineClusters().  The options to
- *  RefineClusters() are given by cfg.refine_cfg.  Calling RefineClusters once
- *  will always be at least as good as doing one iteration of reassigning points to
- *  clusters, but will generally be quite a bit better (without taking too
- *  much extra time).
- *
- *  @param points [in]  points to be clustered (must be all non-NULL).
- *  @param num_clust [in] number of clusters requested (it will always return exactly
- *                 this many, or will fail if num_clust > points.size()).
- *  @param clusters_out [out] may be NULL; if non-NULL, should be empty when called.
- *          Will be set to a vector of statistics corresponding to the output clusters.
- *  @param assignments_out [out] may be NULL; if non-NULL, will be set to a vector of
- *             same size as "points", which says for each point which cluster
- *              it is assigned to.
- *  @param cfg [in] configuration class specifying options to the algorithm.
- *  @return Returns the objective function improvement versus everything being
- *     in the same cluster.
- *
- */
-BaseFloat ClusterKMeans(const std::vector<Clusterable*> &points,
-                        int32 num_clust,  // exact number of clusters
-                        std::vector<Clusterable*> *clusters_out,  // may be NULL
-                        std::vector<int32> *assignments_out,  // may be NULL
-                        ClusterKMeansOptions cfg = ClusterKMeansOptions());
-
-struct TreeClusterOptions  {
-  ClusterKMeansOptions kmeans_cfg;
-  int32 branch_factor;
-  BaseFloat thresh;  // Objf change: if >0, may be used to control number of leaves.
-  TreeClusterOptions()
-      : kmeans_cfg(), branch_factor(2), thresh(0) {
-    kmeans_cfg.verbose = false;
-  }
-};
-
-/** TreeCluster is a top-down clustering algorithm, using a binary tree (not
- *  necessarily balanced). Returns objf improvement versus having all points
- *  in one cluster.  The algorithm is:
- *     - Initialize to 1 cluster (tree with 1 node).
- *     - Maintain, for each cluster, a "best-binary-split" (using ClusterKMeans
- *       to do so). Always split the highest scoring cluster, until we can do no
- *       more splits.
- *
- *  @param points [in] Data points to be clustered
- *  @param max_clust  [in] Maximum number of clusters (you will get exactly this number,
- *                if there are at least this many points, except if you set the
- *                cfg.thresh value nonzero, in which case that threshold may limit
- *                the number of clusters.
- *  @param clusters_out [out] If non-NULL, will be set to the a vector whose first
- *                (*num_leaves_out) elements are the leaf clusters, and whose
- *                subsequent elements are the nonleaf nodes in the tree, in
- *                topological order with the root node last.  Must be empty vector
- *                when this function is called.
- *  @param assignments_out [out] If non-NULL, will be set to a vector to a vector the
- *               same size as "points", where assignments[i] is the leaf node index i
- *               to which the i'th point gets clustered.
- *  @param clust_assignments_out [out] If non-NULL, will be set to a vector the same size
- *                as clusters_out  which says for each node (leaf or nonleaf), the
- *                index of its parent.  For the root node (which is last),
- *                assignments_out[i] == i.  For each i, assignments_out[i]>=i, i.e.
- *                any node's parent is higher numbered than itself.  If you don't need
- *                this information, consider using instead the ClusterTopDown function.
- *  @param num_leaves_out [out] If non-NULL, will be set to the number of leaf nodes
- *                in the tree.
- *  @param cfg [in] Configuration object that controls clustering behavior.  Most
- *                 important value is "thresh", which provides an alternative mechanism
- *                 [other than max_clust] to limit the number of leaves.
- */
-BaseFloat TreeCluster(const std::vector<Clusterable*> &points,
-                      int32 max_clust,  // max number of leaf-level clusters.
-                      std::vector<Clusterable*> *clusters_out,
-                      std::vector<int32> *assignments_out,
-                      std::vector<int32> *clust_assignments_out,
-                      int32 *num_leaves_out,
-                      TreeClusterOptions cfg = TreeClusterOptions());
-
-
-/**
- *  A clustering algorithm that internally uses TreeCluster,
- *  but does not give you the information about the structure of the tree.
- *  The "clusters_out" and "assignments_out" may be NULL if the outputs are not
- *  needed.
- *
- *  @param points [in]  points to be clustered (must be all non-NULL).
- *  @param max_clust [in] Maximum number of clusters (you will get exactly this number,
- *                if there are at least this many points, except if you set the
- *                cfg.thresh value nonzero, in which case that threshold may limit
- *                the number of clusters.
- *  @param clusters_out [out] may be NULL; if non-NULL, should be empty when called.
- *           Will be set to a vector of statistics corresponding to the output clusters.
- *  @param assignments_out [out] may be NULL; if non-NULL, will be set to a vector of
- *           same size as "points", which says for each point which cluster
- *            it is assigned to.
- *  @param cfg [in] Configuration object that controls clustering behavior.  Most
- *                important value is "thresh", which provides an alternative mechanism
- *                [other than max_clust] to limit the number of leaves.
-*/
-BaseFloat ClusterTopDown(const std::vector<Clusterable*> &points,
-                         int32 max_clust,  // max number of clusters.
-                         std::vector<Clusterable*> *clusters_out,
-                         std::vector<int32> *assignments_out,
-                         TreeClusterOptions cfg = TreeClusterOptions());
-
-/// @} end of "addtogroup clustering_group_algo"
-
-}  // end namespace kaldi.
-
-#endif  // KALDI_TREE_CLUSTER_UTILS_H_
diff --git a/kaldi_io/src/kaldi/tree/clusterable-classes.h b/kaldi_io/src/kaldi/tree/clusterable-classes.h
deleted file mode 100644
index 817d0c6..0000000
--- a/kaldi_io/src/kaldi/tree/clusterable-classes.h
+++ /dev/null
@@ -1,158 +0,0 @@
-// tree/clusterable-classes.h
-
-// Copyright 2009-2011  Microsoft Corporation;  Saarland University
-//                2014  Daniel Povey
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_TREE_CLUSTERABLE_CLASSES_H_
-#define KALDI_TREE_CLUSTERABLE_CLASSES_H_ 1
-
-#include <string>
-#include "itf/clusterable-itf.h"
-#include "matrix/matrix-lib.h"
-
-namespace kaldi {
-
-// Note: see sgmm/sgmm-clusterable.h for an SGMM-based clusterable
-// class.  We didn't include it here, to avoid adding an extra
-// dependency to this directory.
-
-/// \addtogroup clustering_group
-/// @{
-
-/// ScalarClusterable clusters scalars with x^2 loss.
-class ScalarClusterable: public Clusterable {
- public:
-  ScalarClusterable(): x_(0), x2_(0), count_(0) {}
-  explicit ScalarClusterable(BaseFloat x): x_(x), x2_(x*x), count_(1) {}
-  virtual std::string Type() const { return "scalar"; }
-  virtual BaseFloat Objf() const;
-  virtual void SetZero() { count_ = x_ = x2_ = 0.0; }
-  virtual void Add(const Clusterable &other_in);
-  virtual void Sub(const Clusterable &other_in);
-  virtual Clusterable* Copy() const;
-  virtual BaseFloat Normalizer() const {
-    return static_cast<BaseFloat>(count_);
-  }
-
-  // Function to write data to stream. Will organize input later [more complex]
-  virtual void Write(std::ostream &os, bool binary) const;
-  virtual Clusterable* ReadNew(std::istream &is, bool binary) const;
-
-  std::string Info();  // For debugging.
-  BaseFloat Mean() { return (count_ != 0 ? x_/count_ : 0.0); }
-  private:
-  BaseFloat x_;
-  BaseFloat x2_;
-  BaseFloat count_;
-
-  void Read(std::istream &is, bool binary);
-};
-
-
-/// GaussClusterable wraps Gaussian statistics in a form accessible
-/// to generic clustering algorithms.
-class GaussClusterable: public Clusterable {
- public:
-  GaussClusterable(): count_(0.0), var_floor_(0.0) {}
-  GaussClusterable(int32 dim, BaseFloat var_floor):
-      count_(0.0), stats_(2, dim), var_floor_(var_floor) {}
-
-  GaussClusterable(const Vector<BaseFloat> &x_stats,
-                   const Vector<BaseFloat> &x2_stats,
-                   BaseFloat var_floor, BaseFloat count);
-
-  virtual std::string Type() const {  return "gauss"; }
-  void AddStats(const VectorBase<BaseFloat> &vec, BaseFloat weight = 1.0);
-  virtual BaseFloat Objf() const;
-  virtual void SetZero();
-  virtual void Add(const Clusterable &other_in);
-  virtual void Sub(const Clusterable &other_in);
-  virtual BaseFloat Normalizer() const { return count_; }
-  virtual Clusterable *Copy() const;
-  virtual void Scale(BaseFloat f);
-  virtual void Write(std::ostream &os, bool binary) const;
-  virtual Clusterable *ReadNew(std::istream &is, bool binary) const;
-  virtual ~GaussClusterable() {}
-
-  BaseFloat count() const { return count_; }
-  // The next two functions are not const-correct, because of SubVector.
-  SubVector<double> x_stats() const { return stats_.Row(0); }
-  SubVector<double> x2_stats() const { return stats_.Row(1); }
- private:
-  double count_;
-  Matrix<double> stats_; // two rows: sum, then sum-squared.
-  double var_floor_;  // should be common for all objects created.
-
-  void Read(std::istream &is, bool binary);
-};
-
-/// @} end of "addtogroup clustering_group"
-
-inline void GaussClusterable::SetZero() {
-  count_ = 0;
-  stats_.SetZero();
-}
-
-inline GaussClusterable::GaussClusterable(const Vector<BaseFloat> &x_stats,
-                                          const Vector<BaseFloat> &x2_stats,
-                                          BaseFloat var_floor, BaseFloat count):
-    count_(count), stats_(2, x_stats.Dim()), var_floor_(var_floor) {
-  stats_.Row(0).CopyFromVec(x_stats);
-  stats_.Row(1).CopyFromVec(x2_stats);
-}
-
-
-/// VectorClusterable wraps vectors in a form accessible to generic clustering
-/// algorithms.  Each vector is associated with a weight; these could be 1.0.
-/// The objective function (to be maximized) is the negated sum of squared
-/// distances from the cluster center to each vector, times that vector's
-/// weight.
-class VectorClusterable: public Clusterable {
- public:
-  VectorClusterable(): weight_(0.0), sumsq_(0.0) {}
-
-  VectorClusterable(const Vector<BaseFloat> &vector,
-                    BaseFloat weight);
-
-  virtual std::string Type() const {  return "vector"; }
-  // Objf is negated weighted sum of squared distances.
-  virtual BaseFloat Objf() const;
-  virtual void SetZero() { weight_ = 0.0; sumsq_ = 0.0; stats_.Set(0.0); }
-  virtual void Add(const Clusterable &other_in);
-  virtual void Sub(const Clusterable &other_in);
-  virtual BaseFloat Normalizer() const { return weight_; }
-  virtual Clusterable *Copy() const;
-  virtual void Scale(BaseFloat f);
-  virtual void Write(std::ostream &os, bool binary) const;
-  virtual Clusterable *ReadNew(std::istream &is, bool binary) const;
-  virtual ~VectorClusterable() {}
-
- private:
-  double weight_;  // sum of weights of the source vectors.  Never negative.
-  Vector<double> stats_; // Equals the weighted sum of the source vectors.
-  double sumsq_;  // Equals the sum over all sources, of weight_ * vec.vec,
-                  // where vec = stats_ / weight_.  Used in computing
-                  // the objective function.
-  void Read(std::istream &is, bool binary);
-};
-
-
-
-}  // end namespace kaldi.
-
-#endif  // KALDI_TREE_CLUSTERABLE_CLASSES_H_
diff --git a/kaldi_io/src/kaldi/tree/context-dep.h b/kaldi_io/src/kaldi/tree/context-dep.h
deleted file mode 100644
index 307fcd4..0000000
--- a/kaldi_io/src/kaldi/tree/context-dep.h
+++ /dev/null
@@ -1,166 +0,0 @@
-// tree/context-dep.h
-
-// Copyright 2009-2011  Microsoft Corporation
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_TREE_CONTEXT_DEP_H_
-#define KALDI_TREE_CONTEXT_DEP_H_
-
-#include "itf/context-dep-itf.h"
-#include "tree/event-map.h"
-#include "matrix/matrix-lib.h"
-#include "tree/cluster-utils.h"
-
-/*
-  This header provides the declarations for the class ContextDependency, which inherits
-  from the interface class "ContextDependencyInterface" in itf/context-dep-itf.h.
-  This is basically a wrapper around an EventMap.  The EventMap
-  (tree/event-map.h) declares most of the internals of the class, and the building routines are
-  in build-tree.h which uses build-tree-utils.h, which uses cluster-utils.h . */
-
-
-namespace kaldi {
-
-static const EventKeyType kPdfClass = -1;  // The "name" to which we assign the
-// pdf-class (generally corresponds ot position in the HMM, zero-based);
-// must not be used for any other event.  I.e. the value corresponding to
-// this key is the pdf-class (see hmm-topology.h for explanation of what this is).
-
-
-/* ContextDependency is quite a generic decision tree.
-
-   It does not actually do very much-- all the magic is in the EventMap object.
-   All this class does is to encode the phone context as a sequence of events, and
-   pass this to the EventMap object to turn into what it will interpret as a
-   vector of pdfs.
-
-   Different versions of the ContextDependency class that are written in the future may
-   have slightly different interfaces and pass more stuff in as events, to the
-   EventMap object.
-
-   In order to separate the process of training decision trees from the process
-   of actually using them, we do not put any training code into the ContextDependency class.
- */
-class ContextDependency: public ContextDependencyInterface {
- public:
-  virtual int32 ContextWidth() const { return N_; }
-  virtual int32 CentralPosition() const { return P_; }
-
-
-  /// returns success or failure; outputs pdf to pdf_id
-  virtual bool Compute(const std::vector<int32> &phoneseq,
-                       int32 pdf_class, int32 *pdf_id) const;
-
-  virtual int32 NumPdfs() const {
-    // this routine could be simplified to return to_pdf_->MaxResult()+1.  we're a
-    // bit more paranoid than that.
-    if (!to_pdf_) return 0;
-    EventAnswerType max_result = to_pdf_->MaxResult();
-    if (max_result < 0 ) return 0;
-    else return (int32) max_result+1;
-  }
-  virtual ContextDependencyInterface *Copy() const {
-    return new ContextDependency(N_, P_, to_pdf_->Copy());
-  }
-
-  /// Read context-dependency object from disk; throws on error
-  void Read (std::istream &is, bool binary);
-
-  // Constructor with no arguments; will normally be called
-  // prior to Read()
-  ContextDependency(): N_(0), P_(0), to_pdf_(NULL) { }
-
-  // Constructor takes ownership of pointers.
-  ContextDependency(int32 N, int32 P,
-                    EventMap *to_pdf):
-      N_(N), P_(P), to_pdf_(to_pdf) { }
-  void Write (std::ostream &os, bool binary) const;
-
-  ~ContextDependency() { if (to_pdf_ != NULL) delete to_pdf_; }
-
-  const EventMap &ToPdfMap() const { return *to_pdf_; }
-
-  /// GetPdfInfo returns a vector indexed by pdf-id, saying for each pdf which
-  /// pairs of (phone, pdf-class) it can correspond to.  (Usually just one).
-  /// c.f. hmm/hmm-topology.h for meaning of pdf-class.
-
-  void GetPdfInfo(const std::vector<int32> &phones,  // list of phones
-                  const std::vector<int32> &num_pdf_classes,  // indexed by phone,
-                  std::vector<std::vector<std::pair<int32, int32> > > *pdf_info)
-      const;
-
- private:
-  int32 N_;  //
-  int32 P_;
-  EventMap *to_pdf_;  // owned here.
-
-  KALDI_DISALLOW_COPY_AND_ASSIGN(ContextDependency);
-};
-
-/// GenRandContextDependency is mainly of use for debugging.  Phones must be sorted and uniq
-/// on input.
-/// @param phones [in] A vector of phone id's [must be sorted and uniq].
-/// @param ensure_all_covered [in] boolean argument; if true,  GenRandContextDependency
-///        generates a context-dependency object that "works" for all phones [no gaps].
-/// @param num_pdf_classes [out] outputs a vector indexed by phone, of the number
-///          of pdf classes (e.g. states) for that phone.
-/// @return Returns the a context dependency object.
-ContextDependency *GenRandContextDependency(const std::vector<int32> &phones,
-                                            bool ensure_all_covered,
-                                            std::vector<int32> *num_pdf_classes);
-
-/// GenRandContextDependencyLarge is like GenRandContextDependency but generates a larger tree
-/// with specified N and P for use in "one-time" larger-scale tests.
-ContextDependency *GenRandContextDependencyLarge(const std::vector<int32> &phones,
-                                                 int N, int P,
-                                                 bool ensure_all_covered,
-                                                 std::vector<int32> *num_pdf_classes);
-
-// MonophoneContextDependency() returns a new ContextDependency object that
-// corresponds to a monophone system.
-// The map phone2num_pdf_classes maps from the phone id to the number of
-// pdf-classes we have for that phone (e.g. 3, so the pdf-classes would be
-// 0, 1, 2).
-
-ContextDependency*
-MonophoneContextDependency(const std::vector<int32> phones,
-                           const std::vector<int32> phone2num_pdf_classes);
-
-// MonophoneContextDependencyShared is as MonophoneContextDependency but lets
-// you define classes of phones which share pdfs (e.g. different stress-markers of a single
-// phone.)  Each element of phone_classes is a set of phones that are in that class.
-ContextDependency*
-MonophoneContextDependencyShared(const std::vector<std::vector<int32> > phone_classes,
-                                 const std::vector<int32> phone2num_pdf_classes);
-
-
-// Important note:
-// Statistics for training decision trees will be of type:
-// std::vector<std::pair<EventType, Clusterable*> >
-// We don't make this a typedef as it doesn't add clarity.
-// they will be sorted and unique on the EventType member, which
-// itself is sorted and unique on the name (see event-map.h).
-
-// See build-tree.h for functions relating to actually building the decision trees.
-
-
-
-
-}  // namespace Kaldi
-
-
-#endif
diff --git a/kaldi_io/src/kaldi/tree/event-map.h b/kaldi_io/src/kaldi/tree/event-map.h
deleted file mode 100644
index 07fcc2b..0000000
--- a/kaldi_io/src/kaldi/tree/event-map.h
+++ /dev/null
@@ -1,365 +0,0 @@
-// tree/event-map.h
-
-// Copyright 2009-2011  Microsoft Corporation;  Haihua Xu
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_TREE_EVENT_MAP_H_
-#define KALDI_TREE_EVENT_MAP_H_
-
-#include <vector>
-#include <map>
-#include <algorithm>
-#include "base/kaldi-common.h"
-#include "util/stl-utils.h"
-#include "util/const-integer-set.h"
-
-namespace kaldi {
-
-/// \defgroup event_map_group Event maps
-/// \ingroup tree_group
-/// See \ref tree_internals for overview, and specifically \ref treei_event_map.
-
-
-// Note RE negative values: some of this code will not work if things of type
-// EventValueType are negative.  In particular, TableEventMap can't be used if
-// things of EventValueType are negative, and additionally TableEventMap won't
-// be efficient if things of EventValueType take on extremely large values.  The
-// EventKeyType can be negative though.
-
-/// Things of type EventKeyType can take any value.  The code does not assume they are contiguous.
-/// So values like -1, 1000000 and the like are acceptable.
-typedef int32 EventKeyType;
-
-/// Given current code, things of type EventValueType should generally be nonnegative and in a
-/// reasonably small range (e.g. not one million), as we sometimes construct vectors of the size:
-/// [largest value we saw for this key].  This deficiency may be fixed in future [would require
-/// modifying TableEventMap]
-typedef int32 EventValueType;
-
-/// As far as the event-map code itself is concerned, things of type EventAnswerType may take
-/// any value except kNoAnswer (== -1).  However, some specific uses of EventMap (e.g. in
-/// build-tree-utils.h) assume these quantities are nonnegative.
-typedef int32 EventAnswerType;
-
-typedef std::vector<std::pair<EventKeyType, EventValueType> > EventType;
-// It is required to be sorted and have unique keys-- i.e. functions assume this when called
-// with this type.
-
-inline std::pair<EventKeyType, EventValueType> MakeEventPair (EventKeyType k, EventValueType v) {  
-  return std::pair<EventKeyType, EventValueType>(k, v);
-}
-
-void WriteEventType(std::ostream &os, bool binary, const EventType &vec);
-void ReadEventType(std::istream &is, bool binary, EventType *vec);
-
-std::string EventTypeToString(const EventType &evec);  // so we can print events out in error messages.
-
-struct EventMapVectorHash {  // Hashing object for EventMapVector.  Works for both pointers and references.
-  // Not used in event-map.{h, cc}
-  size_t operator () (const EventType &vec);
-  size_t operator () (const EventType *ptr) { return (*this)(*ptr); }
-};
-struct EventMapVectorEqual {  // Equality object for EventType pointers-- test equality of underlying vector.
-  // Not used in event-map.{h, cc}
-  size_t operator () (const EventType *p1, const EventType *p2) { return (*p1 == *p2); }
-};
-
-
-/// A class that is capable of representing a generic mapping from
-/// EventType (which is a vector of (key, value) pairs) to
-/// EventAnswerType which is just an integer.  See \ref tree_internals
-/// for overview.
-class EventMap {
- public:
-  static void Check(const EventType &event);  // will crash if not sorted and unique on key.
-  static bool Lookup(const EventType &event, EventKeyType key, EventValueType *ans);
-
-  // Maps events to the answer type. input must be sorted.
-  virtual bool Map(const EventType &event, EventAnswerType *ans) const = 0;
-
-  // MultiMap maps a partially specified set of events to the set of answers it might
-  // map to.  It appends these to "ans".  "ans" is
-  // **not guaranteed unique at output** if the
-  // tree contains duplicate answers at leaves -- you should sort & uniq afterwards.
-  // e.g.: SortAndUniq(ans).
-  virtual void MultiMap(const EventType &event, std::vector<EventAnswerType> *ans) const = 0;
-
-  // GetChildren() returns the EventMaps that are immediate children of this
-  // EventMap (if they exist), by putting them in *out.  Useful for
-  // determining the structure of the event map.
-  virtual void GetChildren(std::vector<EventMap*> *out) const = 0;
-
-  // This Copy() does a deep copy of the event map.
-  // If new_leaves is nonempty when it reaches a leaf with value l s.t. new_leaves[l] != NULL,
-  // it replaces it with a copy of that EventMap.  This makes it possible to extend and modify
-  // It's the way we do splits of trees, and clustering of trees.  Think about this carefully, because
-  // the EventMap structure does not support modification of an existing tree.  Do not be tempted
-  // to do this differently, because other kinds of mechanisms would get very messy and unextensible.
-  // Copy() is the only mechanism to modify a tree.  It's similar to a kind of function composition.
-  // Copy() does not take ownership of the pointers in new_leaves (it uses the Copy() function of those
-  // EventMaps).
-  virtual EventMap *Copy(const std::vector<EventMap*> &new_leaves) const = 0;
-  
-  EventMap *Copy() const { std::vector<EventMap*> new_leaves; return Copy(new_leaves); }
-
-  // The function MapValues() is intended to be used to map phone-sets between
-  // different integer representations.  For all the keys in the set
-  // "keys_to_map", it will map the corresponding values using the map
-  // "value_map".  Note: these values are the values in the key->value pairs of
-  // the EventMap, which really correspond to phones in the usual case; they are
-  // not the "answers" of the EventMap which correspond to clustered states.  In
-  // case multiple values are mapped to the same value, it will try to deal with
-  // it gracefully where it can, but will crash if, for example, this would
-  // cause problems with the TableEventMap.  It will also crash if any values
-  // used for keys in "keys_to_map" are not mapped by "value_map".  This
-  // function is not currently used.
-  virtual EventMap *MapValues(
-      const unordered_set<EventKeyType> &keys_to_map,
-      const unordered_map<EventValueType,EventValueType> &value_map) const = 0;
-
-  // The function Prune() is like Copy(), except it removes parts of the tree
-  // that return only -1 (it will return NULL if this EventMap returns only -1).
-  // This is a mechanism to remove parts of the tree-- you would first use the
-  // Copy() function with a vector of EventMap*, and for the parts you don't
-  // want, you'd put a ConstantEventMap with -1; you'd then call
-  // Prune() on the result.  This function is not currently used.
-  virtual EventMap *Prune() const = 0;
-  
-  virtual EventAnswerType MaxResult() const {  // child classes may override this for efficiency; here is basic version.
-    // returns -1 if nothing found.
-    std::vector<EventAnswerType> tmp; EventType empty_event;
-    MultiMap(empty_event, &tmp);
-    if (tmp.empty()) {
-      KALDI_WARN << "EventMap::MaxResult(), empty result";
-      return std::numeric_limits<EventAnswerType>::min();
-    }
-    else { return * std::max_element(tmp.begin(), tmp.end()); }
-  }
-
-  /// Write to stream.
-  virtual void Write(std::ostream &os, bool binary) = 0;
-
-  virtual ~EventMap() {}
-
-  /// a Write function that takes care of NULL pointers.
-  static void Write(std::ostream &os, bool binary, EventMap *emap);
-  /// a Read function that reads an arbitrary EventMap; also
-  /// works for NULL pointers.
-  static EventMap *Read(std::istream &is, bool binary);
-};
-
-
-class ConstantEventMap: public EventMap {
- public:
-  virtual bool Map(const EventType &event, EventAnswerType *ans) const {
-    *ans = answer_;
-    return true;
-  }
-
-  virtual void MultiMap(const EventType &,
-                        std::vector<EventAnswerType> *ans) const {
-     ans->push_back(answer_);
-  }
-
-  virtual void GetChildren(std::vector<EventMap*> *out) const { out->clear(); }
-
-  virtual EventMap *Copy(const std::vector<EventMap*> &new_leaves) const {
-    if (answer_ < 0 || answer_ >= (EventAnswerType)new_leaves.size() ||
-        new_leaves[answer_] == NULL)
-      return new ConstantEventMap(answer_);
-    else return new_leaves[answer_]->Copy();
-  }
-
-  virtual EventMap *MapValues(
-      const unordered_set<EventKeyType> &keys_to_map,
-      const unordered_map<EventValueType,EventValueType> &value_map) const {
-    return new ConstantEventMap(answer_);
-  }
-
-  virtual EventMap *Prune() const {
-    return (answer_ == -1 ? NULL : new ConstantEventMap(answer_));
-  }
-  
-  explicit ConstantEventMap(EventAnswerType answer): answer_(answer) { }
-  
-  virtual void Write(std::ostream &os, bool binary);
-  static ConstantEventMap *Read(std::istream &is, bool binary);
- private:
-  EventAnswerType answer_;
-  KALDI_DISALLOW_COPY_AND_ASSIGN(ConstantEventMap);
-};
-
-class TableEventMap: public EventMap {
- public:
-
-  virtual bool Map(const EventType &event, EventAnswerType *ans) const {
-    EventValueType tmp;   *ans = -1;  // means no answer
-    if (Lookup(event, key_, &tmp) && tmp >= 0
-       && tmp < (EventValueType)table_.size() && table_[tmp] != NULL) {
-      return table_[tmp]->Map(event, ans);
-    }
-    return false;
-  }
-
-  virtual void GetChildren(std::vector<EventMap*> *out) const {
-    out->clear();
-    for (size_t i = 0; i<table_.size(); i++)
-      if (table_[i] != NULL) out->push_back(table_[i]);
-  }
-
-  virtual void MultiMap(const EventType &event, std::vector<EventAnswerType> *ans) const {
-    EventValueType tmp;
-    if (Lookup(event, key_, &tmp)) {
-      if (tmp >= 0 && tmp < (EventValueType)table_.size() && table_[tmp] != NULL)
-        return table_[tmp]->MultiMap(event, ans);
-      // else no answers.
-    } else {  // all answers are possible if no such key.
-      for (size_t i = 0;i < table_.size();i++)
-        if (table_[i] != NULL) table_[i]->MultiMap(event, ans);  // append.
-    }
-  }
-
-  virtual EventMap *Prune() const;
-  
-  virtual EventMap *MapValues(
-      const unordered_set<EventKeyType> &keys_to_map,
-      const unordered_map<EventValueType,EventValueType> &value_map) const;
-  
-  /// Takes ownership of pointers.
-  explicit TableEventMap(EventKeyType key, const std::vector<EventMap*> &table): key_(key), table_(table) {}
-  /// Takes ownership of pointers.
-  explicit TableEventMap(EventKeyType key, const std::map<EventValueType, EventMap*> &map_in);
-  /// This initializer creates a ConstantEventMap for each value in the map.
-  explicit TableEventMap(EventKeyType key, const std::map<EventValueType, EventAnswerType> &map_in);
-
-  virtual void Write(std::ostream &os, bool binary);
-  static TableEventMap *Read(std::istream &is, bool binary);
-
-  virtual EventMap *Copy(const std::vector<EventMap*> &new_leaves) const {
-    std::vector<EventMap*> new_table_(table_.size(), NULL);
-    for (size_t i = 0;i<table_.size();i++) if (table_[i]) new_table_[i]=table_[i]->Copy(new_leaves);
-    return new TableEventMap(key_, new_table_);
-  }
-  virtual ~TableEventMap() {
-    DeletePointers(&table_);
-  }
- private:
-  EventKeyType key_;
-  std::vector<EventMap*> table_;
-  KALDI_DISALLOW_COPY_AND_ASSIGN(TableEventMap);
-};
-
-
-
-
-class SplitEventMap: public EventMap {  // A decision tree [non-leaf] node.
- public:
-
-  virtual bool Map(const EventType &event, EventAnswerType *ans) const {
-    EventValueType value;
-    if (Lookup(event, key_, &value)) {
-      // if (std::binary_search(yes_set_.begin(), yes_set_.end(), value)) {
-      if (yes_set_.count(value)) {
-        return yes_->Map(event, ans);
-      }
-      return no_->Map(event, ans);
-    }
-    return false;
-  }
-
-  virtual void MultiMap(const EventType &event, std::vector<EventAnswerType> *ans) const {
-    EventValueType tmp;
-    if (Lookup(event, key_, &tmp)) {
-      if (std::binary_search(yes_set_.begin(), yes_set_.end(), tmp))
-        yes_->MultiMap(event, ans);
-      else
-        no_->MultiMap(event, ans);
-    } else {  // both yes and no contribute.
-      yes_->MultiMap(event, ans);
-      no_->MultiMap(event, ans);
-    }
-  }
-
-  virtual void GetChildren(std::vector<EventMap*> *out) const {
-    out->clear();
-    out->push_back(yes_);
-    out->push_back(no_);
-  }
-
-  virtual EventMap *Copy(const std::vector<EventMap*> &new_leaves) const {
-    return new SplitEventMap(key_, yes_set_, yes_->Copy(new_leaves), no_->Copy(new_leaves));
-  }
-
-  virtual void Write(std::ostream &os, bool binary);
-  static SplitEventMap *Read(std::istream &is, bool binary);
-
-  virtual EventMap *Prune() const;
-  
-  virtual EventMap *MapValues(
-      const unordered_set<EventKeyType> &keys_to_map,
-      const unordered_map<EventValueType,EventValueType> &value_map) const;
-  
-  virtual ~SplitEventMap() { Destroy(); }
-
-  /// This constructor takes ownership of the "yes" and "no" arguments.
-  SplitEventMap(EventKeyType key, const std::vector<EventValueType> &yes_set,
-                EventMap *yes, EventMap *no): key_(key), yes_set_(yes_set), yes_(yes), no_(no) {
-    KALDI_PARANOID_ASSERT(IsSorted(yes_set));
-    KALDI_ASSERT(yes_ != NULL && no_ != NULL);
-  }
-
-
- private:
-  /// This constructor used in the Copy() function.
-  SplitEventMap(EventKeyType key, const ConstIntegerSet<EventValueType> &yes_set,
-                EventMap *yes, EventMap *no): key_(key), yes_set_(yes_set), yes_(yes), no_(no) {
-    KALDI_ASSERT(yes_ != NULL && no_ != NULL);
-  }
-  void Destroy() {
-    delete yes_; delete no_;
-  }
-  EventKeyType key_;
-  //  std::vector<EventValueType> yes_set_;
-  ConstIntegerSet<EventValueType> yes_set_;  // more efficient Map function.
-  EventMap *yes_;  // owned here.
-  EventMap *no_;  // owned here.
-  SplitEventMap &operator = (const SplitEventMap &other);  // Disallow.
-};
-
-/**
-   This function gets the tree structure of the EventMap "map" in a convenient form.
-   If "map" corresponds to a tree structure (not necessarily binary) with leaves
-   uniquely numbered from 0 to num_leaves-1, then the function will return true,
-   output "num_leaves", and set "parent" to a vector of size equal to the number of
-   nodes in the tree (nonleaf and leaf), where each index corresponds to a node
-   and the leaf indices correspond to the values returned by the EventMap from
-   that leaf; for an index i, parent[i] equals the parent of that node in the tree
-   structure, where parent[i] > i, except for the last (root) node where parent[i] == i.
-   If the EventMap does not have this structure (e.g. if multiple different leaf nodes share
-   the same number), then it will return false.
-*/
-
-bool GetTreeStructure(const EventMap &map,
-                      int32 *num_leaves,
-                      std::vector<int32> *parents);
-
-
-/// @} end "addtogroup event_map_group"
-
-}
-
-#endif
diff --git a/kaldi_io/src/kaldi/tree/tree-renderer.h b/kaldi_io/src/kaldi/tree/tree-renderer.h
deleted file mode 100644
index 5e0b0d8..0000000
--- a/kaldi_io/src/kaldi/tree/tree-renderer.h
+++ /dev/null
@@ -1,84 +0,0 @@
-// tree/tree-renderer.h
-
-// Copyright 2012 Vassil Panayotov
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_TREE_TREE_RENDERER_H_
-#define KALDI_TREE_TREE_RENDERER_H_
-
-#include "base/kaldi-common.h"
-#include "tree/event-map.h"
-#include "util/common-utils.h"
-#include "hmm/transition-model.h"
-#include "fst/fstlib.h"
-
-namespace kaldi {
-
-// Parses a decision tree file and outputs its description in GraphViz format
-class TreeRenderer {
- public:
-  const static int32 kEdgeWidth; // normal width of the edges and state contours
-  const static int32 kEdgeWidthQuery; // edge and state width when in query
-  const static std::string kEdgeColor; // normal color for states and edges
-  const static std::string kEdgeColorQuery; // edge and state color when in query
-
-  TreeRenderer(std::istream &is, bool binary, std::ostream &os,
-               fst::SymbolTable &phone_syms, bool use_tooltips)
-      : phone_syms_(phone_syms), is_(is), out_(os), binary_(binary),
-        N_(-1), use_tooltips_(use_tooltips), next_id_(0) {}
-
-  // Renders the tree and if the "query" parameter is not NULL
-  // a distinctly colored trace corresponding to the event.
-  void Render(const EventType *query);
-
- private:
-  // Looks-up the next token from the stream and invokes
-  // the appropriate render method to visualize it
-  void RenderSubTree(const EventType *query, int32 id);
-
-  // Renders a leaf node (constant event map)
-  void RenderConstant(const EventType *query, int32 id);
-
-  // Renders a split event map node and the edges to the nodes
-  // representing YES and NO sets
-  void RenderSplit(const EventType *query, int32 id);
-
-  // Renders a table event map node and the edges to its (non-null) children
-  void RenderTable(const EventType *query, int32 id);
-
-  // Makes a comma-separated string from the elements of a set of identifiers
-  // If the identifiers represent phones, their symbolic representations are used
-  std::string MakeEdgeLabel(const EventKeyType &key,
-                            const ConstIntegerSet<EventValueType> &intset);
-
-  // Writes the GraphViz representation of a non-leaf node to the out stream
-  // A question about a phone from the context window or about pdf-class
-  // is used as a label.
-  void RenderNonLeaf(int32 id, const EventKeyType &key, bool in_query);
-
-  fst::SymbolTable &phone_syms_; // phone symbols to be used as edge labels
-  std::istream &is_; // the stream from which the tree is read
-  std::ostream &out_; // the GraphViz representation is written to this stream
-  bool binary_; // is the input stream binary?
-  int32 N_, P_; // context-width and central position
-  bool use_tooltips_;  // use tooltips(useful in e.g. SVG) instead of labels
-  int32 next_id_; // the first unused GraphViz node ID
-};
-
-} // namespace kaldi
-
-#endif //  KALDI_TREE_TREE_RENDERER_H_
diff --git a/kaldi_io/src/kaldi/util/basic-filebuf.h b/kaldi_io/src/kaldi/util/basic-filebuf.h
deleted file mode 100644
index cf2e079..0000000
--- a/kaldi_io/src/kaldi/util/basic-filebuf.h
+++ /dev/null
@@ -1,1065 +0,0 @@
-///////////////////////////////////////////////////////////////////////////////
-// This is a modified version of the std::basic_filebuf from libc++
-// (http://libcxx.llvm.org/).
-// It allows one to create basic_filebuf from an existing FILE* handle or file
-// descriptor.
-//
-// This file is dual licensed under the MIT and the University of Illinois Open
-// Source License licenses. See LICENSE.TXT for details (included at the
-// bottom).
-///////////////////////////////////////////////////////////////////////////////
-#ifndef KALDI_UTIL_BASIC_FILEBUF_H_
-#define KALDI_UTIL_BASIC_FILEBUF_H_
-
-///////////////////////////////////////////////////////////////////////////////
-#include <fstream>
-#include <cstdio>
-#include <cstring>
-
-///////////////////////////////////////////////////////////////////////////////
-namespace kaldi
-{
-
-///////////////////////////////////////////////////////////////////////////////
-template <typename CharT, typename Traits = std::char_traits<CharT> >
-class basic_filebuf : public std::basic_streambuf<CharT, Traits>
-{
-public:
-    typedef CharT                            char_type;
-    typedef Traits                           traits_type;
-    typedef typename traits_type::int_type   int_type;
-    typedef typename traits_type::pos_type   pos_type;
-    typedef typename traits_type::off_type   off_type;
-    typedef typename traits_type::state_type state_type;
-
-    basic_filebuf();
-    basic_filebuf(basic_filebuf&& rhs);
-    virtual ~basic_filebuf();
-
-    basic_filebuf& operator=(basic_filebuf&& rhs);
-    void swap(basic_filebuf& rhs);
-
-    bool is_open() const;
-    basic_filebuf* open(const char* s, std::ios_base::openmode mode);
-    basic_filebuf* open(const std::string& s, std::ios_base::openmode mode);
-    basic_filebuf* open(int fd, std::ios_base::openmode mode);
-    basic_filebuf* open(FILE* f, std::ios_base::openmode mode);
-    basic_filebuf* close();
-
-    FILE* file() { return this->_M_file; }
-    int fd() { return fileno(this->_M_file); }
-
-protected:
-    int_type underflow() override;
-    int_type pbackfail(int_type c = traits_type::eof()) override;
-    int_type overflow (int_type c = traits_type::eof()) override;
-    std::basic_streambuf<char_type, traits_type>* setbuf(char_type* s, std::streamsize n) override;
-    pos_type seekoff(off_type off, std::ios_base::seekdir way,
-                     std::ios_base::openmode wch = std::ios_base::in | std::ios_base::out) override;
-    pos_type seekpos(pos_type sp,
-                     std::ios_base::openmode wch = std::ios_base::in | std::ios_base::out) override;
-    int sync() override;
-    void imbue(const std::locale& loc) override;
-
-protected:
-    char*       _M_extbuf;
-    const char* _M_extbufnext;
-    const char* _M_extbufend;
-    char _M_extbuf_min[8];
-    size_t _M_ebs;
-    char_type* _M_intbuf;
-    size_t _M_ibs;
-    FILE* _M_file;
-    const std::codecvt<char_type, char, state_type>* _M_cv;
-    state_type _M_st;
-    state_type _M_st_last;
-    std::ios_base::openmode _M_om;
-    std::ios_base::openmode _M_cm;
-    bool _M_owns_eb;
-    bool _M_owns_ib;
-    bool _M_always_noconv;
-
-    const char* _M_get_mode(std::ios_base::openmode mode);
-    bool _M_read_mode();
-    void _M_write_mode();
-};
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-basic_filebuf<CharT, Traits>::basic_filebuf()
-    : _M_extbuf(nullptr),
-      _M_extbufnext(nullptr),
-      _M_extbufend(nullptr),
-      _M_ebs(0),
-      _M_intbuf(nullptr),
-      _M_ibs(0),
-      _M_file(nullptr),
-      _M_cv(nullptr),
-      _M_st(),
-      _M_st_last(),
-      _M_om(std::ios_base::openmode(0)),
-      _M_cm(std::ios_base::openmode(0)),
-      _M_owns_eb(false),
-      _M_owns_ib(false),
-      _M_always_noconv(false)
-{
-    if (std::has_facet<std::codecvt<char_type, char, state_type> >(this->getloc()))
-    {
-        _M_cv = &std::use_facet<std::codecvt<char_type, char, state_type> >(this->getloc());
-        _M_always_noconv = _M_cv->always_noconv();
-    }
-    setbuf(0, 4096);
-}
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-basic_filebuf<CharT, Traits>::basic_filebuf(basic_filebuf&& rhs)
-    : std::basic_streambuf<CharT, Traits>(rhs)
-{
-    if (rhs._M_extbuf == rhs._M_extbuf_min)
-    {
-        _M_extbuf = _M_extbuf_min;
-        _M_extbufnext = _M_extbuf + (rhs._M_extbufnext - rhs._M_extbuf);
-        _M_extbufend = _M_extbuf + (rhs._M_extbufend - rhs._M_extbuf);
-    }
-    else
-    {
-        _M_extbuf = rhs._M_extbuf;
-        _M_extbufnext = rhs._M_extbufnext;
-        _M_extbufend = rhs._M_extbufend;
-    }
-    _M_ebs = rhs._M_ebs;
-    _M_intbuf = rhs._M_intbuf;
-    _M_ibs = rhs._M_ibs;
-    _M_file = rhs._M_file;
-    _M_cv = rhs._M_cv;
-    _M_st = rhs._M_st;
-    _M_st_last = rhs._M_st_last;
-    _M_om = rhs._M_om;
-    _M_cm = rhs._M_cm;
-    _M_owns_eb = rhs._M_owns_eb;
-    _M_owns_ib = rhs._M_owns_ib;
-    _M_always_noconv = rhs._M_always_noconv;
-    if (rhs.pbase())
-    {
-        if (rhs.pbase() == rhs._M_intbuf)
-            this->setp(_M_intbuf, _M_intbuf + (rhs. epptr() - rhs.pbase()));
-        else
-            this->setp((char_type*)_M_extbuf,
-                       (char_type*)_M_extbuf + (rhs. epptr() - rhs.pbase()));
-        this->pbump(rhs. pptr() - rhs.pbase());
-    }
-    else if (rhs.eback())
-    {
-        if (rhs.eback() == rhs._M_intbuf)
-            this->setg(_M_intbuf, _M_intbuf + (rhs.gptr() - rhs.eback()),
-                                  _M_intbuf + (rhs.egptr() - rhs.eback()));
-        else
-            this->setg((char_type*)_M_extbuf,
-                       (char_type*)_M_extbuf + (rhs.gptr() - rhs.eback()),
-                       (char_type*)_M_extbuf + (rhs.egptr() - rhs.eback()));
-    }
-    rhs._M_extbuf = nullptr;
-    rhs._M_extbufnext = nullptr;
-    rhs._M_extbufend = nullptr;
-    rhs._M_ebs = 0;
-    rhs._M_intbuf = nullptr;
-    rhs._M_ibs = 0;
-    rhs._M_file = nullptr;
-    rhs._M_st = state_type();
-    rhs._M_st_last = state_type();
-    rhs._M_om = std::ios_base::openmode(0);
-    rhs._M_cm = std::ios_base::openmode(0);
-    rhs._M_owns_eb = false;
-    rhs._M_owns_ib = false;
-    rhs.setg(0, 0, 0);
-    rhs.setp(0, 0);
-}
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-inline
-basic_filebuf<CharT, Traits>&
-basic_filebuf<CharT, Traits>::operator=(basic_filebuf&& rhs)
-{
-    close();
-    swap(rhs);
-    return *this;
-}
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-basic_filebuf<CharT, Traits>::~basic_filebuf()
-{
-    // try
-    // {
-    //     close();
-    // }
-    // catch (...)
-    // {
-    // }
-    if (_M_owns_eb)
-        delete [] _M_extbuf;
-    if (_M_owns_ib)
-        delete [] _M_intbuf;
-}
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-void
-basic_filebuf<CharT, Traits>::swap(basic_filebuf& rhs)
-{
-    std::basic_streambuf<char_type, traits_type>::swap(rhs);
-    if (_M_extbuf != _M_extbuf_min && rhs._M_extbuf != rhs._M_extbuf_min)
-    {
-        std::swap(_M_extbuf, rhs._M_extbuf);
-        std::swap(_M_extbufnext, rhs._M_extbufnext);
-        std::swap(_M_extbufend, rhs._M_extbufend);
-    }
-    else
-    {
-        ptrdiff_t ln = _M_extbufnext - _M_extbuf;
-        ptrdiff_t le = _M_extbufend - _M_extbuf;
-        ptrdiff_t rn = rhs._M_extbufnext - rhs._M_extbuf;
-        ptrdiff_t re = rhs._M_extbufend - rhs._M_extbuf;
-        if (_M_extbuf == _M_extbuf_min && rhs._M_extbuf != rhs._M_extbuf_min)
-        {
-            _M_extbuf = rhs._M_extbuf;
-            rhs._M_extbuf = rhs._M_extbuf_min;
-        }
-        else if (_M_extbuf != _M_extbuf_min && rhs._M_extbuf == rhs._M_extbuf_min)
-        {
-            rhs._M_extbuf = _M_extbuf;
-            _M_extbuf = _M_extbuf_min;
-        }
-        _M_extbufnext = _M_extbuf + rn;
-        _M_extbufend = _M_extbuf + re;
-        rhs._M_extbufnext = rhs._M_extbuf + ln;
-        rhs._M_extbufend = rhs._M_extbuf + le;
-    }
-    std::swap(_M_ebs, rhs._M_ebs);
-    std::swap(_M_intbuf, rhs._M_intbuf);
-    std::swap(_M_ibs, rhs._M_ibs);
-    std::swap(_M_file, rhs._M_file);
-    std::swap(_M_cv, rhs._M_cv);
-    std::swap(_M_st, rhs._M_st);
-    std::swap(_M_st_last, rhs._M_st_last);
-    std::swap(_M_om, rhs._M_om);
-    std::swap(_M_cm, rhs._M_cm);
-    std::swap(_M_owns_eb, rhs._M_owns_eb);
-    std::swap(_M_owns_ib, rhs._M_owns_ib);
-    std::swap(_M_always_noconv, rhs._M_always_noconv);
-    if (this->eback() == (char_type*)rhs._M_extbuf_min)
-    {
-        ptrdiff_t n = this->gptr() - this->eback();
-        ptrdiff_t e = this->egptr() - this->eback();
-        this->setg((char_type*)_M_extbuf_min,
-                   (char_type*)_M_extbuf_min + n,
-                   (char_type*)_M_extbuf_min + e);
-    }
-    else if (this->pbase() == (char_type*)rhs._M_extbuf_min)
-    {
-        ptrdiff_t n = this->pptr() - this->pbase();
-        ptrdiff_t e = this->epptr() - this->pbase();
-        this->setp((char_type*)_M_extbuf_min,
-                   (char_type*)_M_extbuf_min + e);
-        this->pbump(n);
-    }
-    if (rhs.eback() == (char_type*)_M_extbuf_min)
-    {
-        ptrdiff_t n = rhs.gptr() - rhs.eback();
-        ptrdiff_t e = rhs.egptr() - rhs.eback();
-        rhs.setg((char_type*)rhs._M_extbuf_min,
-                 (char_type*)rhs._M_extbuf_min + n,
-                 (char_type*)rhs._M_extbuf_min + e);
-    }
-    else if (rhs.pbase() == (char_type*)_M_extbuf_min)
-    {
-        ptrdiff_t n = rhs.pptr() - rhs.pbase();
-        ptrdiff_t e = rhs.epptr() - rhs.pbase();
-        rhs.setp((char_type*)rhs._M_extbuf_min,
-                 (char_type*)rhs._M_extbuf_min + e);
-        rhs.pbump(n);
-    }
-}
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-inline
-void
-swap(basic_filebuf<CharT, Traits>& x, basic_filebuf<CharT, Traits>& y)
-{
-    x.swap(y);
-}
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-inline
-bool
-basic_filebuf<CharT, Traits>::is_open() const
-{
-    return _M_file != nullptr;
-}
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-const char* basic_filebuf<CharT, Traits>::_M_get_mode(std::ios_base::openmode mode)
-{
-    switch ((mode & ~std::ios_base::ate) | 0)
-    {
-    case std::ios_base::out:
-    case std::ios_base::out | std::ios_base::trunc:
-        return "w";
-    case std::ios_base::out | std::ios_base::app:
-    case std::ios_base::app:
-        return "a";
-        break;
-    case std::ios_base::in:
-        return "r";
-    case std::ios_base::in  | std::ios_base::out:
-        return "r+";
-    case std::ios_base::in  | std::ios_base::out | std::ios_base::trunc:
-        return "w+";
-    case std::ios_base::in  | std::ios_base::out | std::ios_base::app:
-    case std::ios_base::in  | std::ios_base::app:
-        return "a+";
-    case std::ios_base::out | std::ios_base::binary:
-    case std::ios_base::out | std::ios_base::trunc | std::ios_base::binary:
-        return "wb";
-    case std::ios_base::out | std::ios_base::app | std::ios_base::binary:
-    case std::ios_base::app | std::ios_base::binary:
-        return "ab";
-    case std::ios_base::in  | std::ios_base::binary:
-        return "rb";
-    case std::ios_base::in  | std::ios_base::out | std::ios_base::binary:
-        return "r+b";
-    case std::ios_base::in  | std::ios_base::out | std::ios_base::trunc | std::ios_base::binary:
-        return "w+b";
-    case std::ios_base::in  | std::ios_base::out | std::ios_base::app | std::ios_base::binary:
-    case std::ios_base::in  | std::ios_base::app | std::ios_base::binary:
-        return "a+b";
-    default:
-        return nullptr;
-    }
-}
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-basic_filebuf<CharT, Traits>*
-basic_filebuf<CharT, Traits>::open(const char* s, std::ios_base::openmode mode)
-{
-    basic_filebuf<CharT, Traits>* rt = nullptr;
-    if (_M_file == nullptr)
-    {
-        const char* md= _M_get_mode(mode);
-        if (md)
-        {
-            _M_file = fopen(s, md);
-            if (_M_file)
-            {
-                rt = this;
-                _M_om = mode;
-                if (mode & std::ios_base::ate)
-                {
-                    if (fseek(_M_file, 0, SEEK_END))
-                    {
-                        fclose(_M_file);
-                        _M_file = nullptr;
-                        rt = nullptr;
-                    }
-                }
-            }
-        }
-    }
-    return rt;
-}
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-inline
-basic_filebuf<CharT, Traits>*
-basic_filebuf<CharT, Traits>::open(const std::string& s, std::ios_base::openmode mode)
-{
-    return open(s.c_str(), mode);
-}
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-basic_filebuf<CharT, Traits>*
-basic_filebuf<CharT, Traits>::open(int fd, std::ios_base::openmode mode)
-{
-    const char* md= this->_M_get_mode(mode);
-    if (md)
-    {
-        this->_M_file= fdopen(fd, md);
-        this->_M_om = mode;
-        return this;
-    }
-    else return nullptr;
-}
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-basic_filebuf<CharT, Traits>*
-basic_filebuf<CharT, Traits>::open(FILE* f, std::ios_base::openmode mode)
-{
-    this->_M_file = f;
-    this->_M_om = mode;
-    return this;
-}
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-basic_filebuf<CharT, Traits>*
-basic_filebuf<CharT, Traits>::close()
-{
-    basic_filebuf<CharT, Traits>* rt = nullptr;
-    if (_M_file)
-    {
-        rt = this;
-        std::unique_ptr<FILE, int(*)(FILE*)> h(_M_file, fclose);
-        if (sync())
-            rt = nullptr;
-        if (fclose(h.release()) == 0)
-            _M_file = nullptr;
-        else
-            rt = nullptr;
-    }
-    return rt;
-}
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-typename basic_filebuf<CharT, Traits>::int_type
-basic_filebuf<CharT, Traits>::underflow()
-{
-    if (_M_file == nullptr)
-        return traits_type::eof();
-    bool initial = _M_read_mode();
-    char_type buf;
-    if (this->gptr() == nullptr)
-        this->setg(&buf, &buf+1, &buf+1);
-    const size_t unget_sz = initial ? 0 : std::min<size_t>((this->egptr() - this->eback()) / 2, 4);
-    int_type c = traits_type::eof();
-    if (this->gptr() == this->egptr())
-    {
-        memmove(this->eback(), this->egptr() - unget_sz, unget_sz * sizeof(char_type));
-        if (_M_always_noconv)
-        {
-            size_t nmemb = static_cast<size_t>(this->egptr() - this->eback() - unget_sz);
-            nmemb = fread(this->eback() + unget_sz, 1, nmemb, _M_file);
-            if (nmemb != 0)
-            {
-                this->setg(this->eback(),
-                           this->eback() + unget_sz,
-                           this->eback() + unget_sz + nmemb);
-                c = traits_type::to_int_type(*this->gptr());
-            }
-        }
-        else
-        {
-            memmove(_M_extbuf, _M_extbufnext, _M_extbufend - _M_extbufnext);
-            _M_extbufnext = _M_extbuf + (_M_extbufend - _M_extbufnext);
-            _M_extbufend = _M_extbuf + (_M_extbuf == _M_extbuf_min ? sizeof(_M_extbuf_min) : _M_ebs);
-            size_t nmemb = std::min(static_cast<size_t>(_M_ibs - unget_sz),
-                                    static_cast<size_t>(_M_extbufend - _M_extbufnext));
-            std::codecvt_base::result r;
-            _M_st_last = _M_st;
-            size_t nr = fread((void*)_M_extbufnext, 1, nmemb, _M_file);
-            if (nr != 0)
-            {
-                if (!_M_cv)
-                    throw std::bad_cast();
-                _M_extbufend = _M_extbufnext + nr;
-                char_type*  inext;
-                r = _M_cv->in(_M_st, _M_extbuf, _M_extbufend, _M_extbufnext,
-                              this->eback() + unget_sz,
-                              this->eback() + _M_ibs, inext);
-                if (r == std::codecvt_base::noconv)
-                {
-                    this->setg((char_type*)_M_extbuf, (char_type*)_M_extbuf, (char_type*)_M_extbufend);
-                    c = traits_type::to_int_type(*this->gptr());
-                }
-                else if (inext != this->eback() + unget_sz)
-                {
-                    this->setg(this->eback(), this->eback() + unget_sz, inext);
-                    c = traits_type::to_int_type(*this->gptr());
-                }
-            }
-        }
-    }
-    else
-        c = traits_type::to_int_type(*this->gptr());
-    if (this->eback() == &buf)
-        this->setg(0, 0, 0);
-    return c;
-}
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-typename basic_filebuf<CharT, Traits>::int_type
-basic_filebuf<CharT, Traits>::pbackfail(int_type c)
-{
-    if (_M_file && this->eback() < this->gptr())
-    {
-        if (traits_type::eq_int_type(c, traits_type::eof()))
-        {
-            this->gbump(-1);
-            return traits_type::not_eof(c);
-        }
-        if ((_M_om & std::ios_base::out) ||
-            traits_type::eq(traits_type::to_char_type(c), this->gptr()[-1]))
-        {
-            this->gbump(-1);
-            *this->gptr() = traits_type::to_char_type(c);
-            return c;
-        }
-    }
-    return traits_type::eof();
-}
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-typename basic_filebuf<CharT, Traits>::int_type
-basic_filebuf<CharT, Traits>::overflow(int_type c)
-{
-    if (_M_file == nullptr)
-        return traits_type::eof();
-    _M_write_mode();
-    char_type buf;
-    char_type* pb_save = this->pbase();
-    char_type* epb_save = this->epptr();
-    if (!traits_type::eq_int_type(c, traits_type::eof()))
-    {
-        if (this->pptr() == nullptr)
-            this->setp(&buf, &buf+1);
-        *this->pptr() = traits_type::to_char_type(c);
-        this->pbump(1);
-    }
-    if (this->pptr() != this->pbase())
-    {
-        if (_M_always_noconv)
-        {
-            size_t nmemb = static_cast<size_t>(this->pptr() - this->pbase());
-            if (fwrite(this->pbase(), sizeof(char_type), nmemb, _M_file) != nmemb)
-                return traits_type::eof();
-        }
-        else
-        {
-            char* extbe = _M_extbuf;
-            std::codecvt_base::result r;
-            do
-            {
-                if (!_M_cv)
-                    throw std::bad_cast();
-                const char_type* e;
-                r = _M_cv->out(_M_st, this->pbase(), this->pptr(), e,
-                               _M_extbuf, _M_extbuf + _M_ebs, extbe);
-                if (e == this->pbase())
-                    return traits_type::eof();
-                if (r == std::codecvt_base::noconv)
-                {
-                    size_t nmemb = static_cast<size_t>(this->pptr() - this->pbase());
-                    if (fwrite(this->pbase(), 1, nmemb, _M_file) != nmemb)
-                        return traits_type::eof();
-                }
-                else if (r == std::codecvt_base::ok || r == std::codecvt_base::partial)
-                {
-                    size_t nmemb = static_cast<size_t>(extbe - _M_extbuf);
-                    if (fwrite(_M_extbuf, 1, nmemb, _M_file) != nmemb)
-                        return traits_type::eof();
-                    if (r == std::codecvt_base::partial)
-                    {
-                        this->setp((char_type*)e, this->pptr());
-                        this->pbump(this->epptr() - this->pbase());
-                    }
-                }
-                else
-                    return traits_type::eof();
-            } while (r == std::codecvt_base::partial);
-        }
-        this->setp(pb_save, epb_save);
-    }
-    return traits_type::not_eof(c);
-}
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-std::basic_streambuf<CharT, Traits>*
-basic_filebuf<CharT, Traits>::setbuf(char_type* s, std::streamsize n)
-{
-    this->setg(0, 0, 0);
-    this->setp(0, 0);
-    if (_M_owns_eb)
-        delete [] _M_extbuf;
-    if (_M_owns_ib)
-        delete [] _M_intbuf;
-    _M_ebs = n;
-    if (_M_ebs > sizeof(_M_extbuf_min))
-    {
-        if (_M_always_noconv && s)
-        {
-            _M_extbuf = (char*)s;
-            _M_owns_eb = false;
-        }
-        else
-        {
-            _M_extbuf = new char[_M_ebs];
-            _M_owns_eb = true;
-        }
-    }
-    else
-    {
-        _M_extbuf = _M_extbuf_min;
-        _M_ebs = sizeof(_M_extbuf_min);
-        _M_owns_eb = false;
-    }
-    if (!_M_always_noconv)
-    {
-        _M_ibs = std::max<std::streamsize>(n, sizeof(_M_extbuf_min));
-        if (s && _M_ibs >= sizeof(_M_extbuf_min))
-        {
-            _M_intbuf = s;
-            _M_owns_ib = false;
-        }
-        else
-        {
-            _M_intbuf = new char_type[_M_ibs];
-            _M_owns_ib = true;
-        }
-    }
-    else
-    {
-        _M_ibs = 0;
-        _M_intbuf = 0;
-        _M_owns_ib = false;
-    }
-    return this;
-}
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-typename basic_filebuf<CharT, Traits>::pos_type
-basic_filebuf<CharT, Traits>::seekoff(off_type off, std::ios_base::seekdir way,
-                                      std::ios_base::openmode)
-{
-    if (!_M_cv)
-        throw std::bad_cast();
-    int width = _M_cv->encoding();
-    if (_M_file == nullptr || (width <= 0 && off != 0) || sync())
-        return pos_type(off_type(-1));
-    // width > 0 || off == 0
-    int whence;
-    switch (way)
-    {
-    case std::ios_base::beg:
-        whence = SEEK_SET;
-        break;
-    case std::ios_base::cur:
-        whence = SEEK_CUR;
-        break;
-    case std::ios_base::end:
-        whence = SEEK_END;
-        break;
-    default:
-        return pos_type(off_type(-1));
-    }
-#if _WIN32
-    if (fseek(_M_file, width > 0 ? width * off : 0, whence))
-        return pos_type(off_type(-1));
-    pos_type r = ftell(_M_file);
-#else
-    if (fseeko(_M_file, width > 0 ? width * off : 0, whence))
-        return pos_type(off_type(-1));
-    pos_type r = ftello(_M_file);
-#endif
-    r.state(_M_st);
-    return r;
-}
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-typename basic_filebuf<CharT, Traits>::pos_type
-basic_filebuf<CharT, Traits>::seekpos(pos_type sp, std::ios_base::openmode)
-{
-    if (_M_file == nullptr || sync())
-        return pos_type(off_type(-1));
-#if _WIN32
-    if (fseek(_M_file, sp, SEEK_SET))
-        return pos_type(off_type(-1));
-#else
-    if (fseeko(_M_file, sp, SEEK_SET))
-        return pos_type(off_type(-1));
-#endif
-    _M_st = sp.state();
-    return sp;
-}
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-int
-basic_filebuf<CharT, Traits>::sync()
-{
-    if (_M_file == nullptr)
-        return 0;
-    if (!_M_cv)
-        throw std::bad_cast();
-    if (_M_cm & std::ios_base::out)
-    {
-        if (this->pptr() != this->pbase())
-            if (overflow() == traits_type::eof())
-                return -1;
-        std::codecvt_base::result r;
-        do
-        {
-            char* extbe;
-            r = _M_cv->unshift(_M_st, _M_extbuf, _M_extbuf + _M_ebs, extbe);
-            size_t nmemb = static_cast<size_t>(extbe - _M_extbuf);
-            if (fwrite(_M_extbuf, 1, nmemb, _M_file) != nmemb)
-                return -1;
-        } while (r == std::codecvt_base::partial);
-        if (r == std::codecvt_base::error)
-            return -1;
-        if (fflush(_M_file))
-            return -1;
-    }
-    else if (_M_cm & std::ios_base::in)
-    {
-        off_type c;
-        state_type state = _M_st_last;
-        bool update_st = false;
-        if (_M_always_noconv)
-            c = this->egptr() - this->gptr();
-        else
-        {
-            int width = _M_cv->encoding();
-            c = _M_extbufend - _M_extbufnext;
-            if (width > 0)
-                c += width * (this->egptr() - this->gptr());
-            else
-            {
-                if (this->gptr() != this->egptr())
-                {
-                    const int off =  _M_cv->length(state, _M_extbuf,
-                                                   _M_extbufnext,
-                                                   this->gptr() - this->eback());
-                    c += _M_extbufnext - _M_extbuf - off;
-                    update_st = true;
-                }
-            }
-        }
-#if _WIN32
-        if (fseek(_M_file_, -c, SEEK_CUR))
-            return -1;
-#else
-        if (fseeko(_M_file, -c, SEEK_CUR))
-            return -1;
-#endif
-        if (update_st)
-            _M_st = state;
-        _M_extbufnext = _M_extbufend = _M_extbuf;
-        this->setg(0, 0, 0);
-        _M_cm = std::ios_base::openmode(0);
-    }
-    return 0;
-}
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-void
-basic_filebuf<CharT, Traits>::imbue(const std::locale& loc)
-{
-    sync();
-    _M_cv = &std::use_facet<std::codecvt<char_type, char, state_type> >(loc);
-    bool old_anc = _M_always_noconv;
-    _M_always_noconv = _M_cv->always_noconv();
-    if (old_anc != _M_always_noconv)
-    {
-        this->setg(0, 0, 0);
-        this->setp(0, 0);
-        // invariant, char_type is char, else we couldn't get here
-        if (_M_always_noconv)  // need to dump _M_intbuf
-        {
-            if (_M_owns_eb)
-                delete [] _M_extbuf;
-            _M_owns_eb = _M_owns_ib;
-            _M_ebs = _M_ibs;
-            _M_extbuf = (char*)_M_intbuf;
-            _M_ibs = 0;
-            _M_intbuf = nullptr;
-            _M_owns_ib = false;
-        }
-        else  // need to obtain an _M_intbuf.
-        {     // If _M_extbuf is user-supplied, use it, else new _M_intbuf
-            if (!_M_owns_eb && _M_extbuf != _M_extbuf_min)
-            {
-                _M_ibs = _M_ebs;
-                _M_intbuf = (char_type*)_M_extbuf;
-                _M_owns_ib = false;
-                _M_extbuf = new char[_M_ebs];
-                _M_owns_eb = true;
-            }
-            else
-            {
-                _M_ibs = _M_ebs;
-                _M_intbuf = new char_type[_M_ibs];
-                _M_owns_ib = true;
-            }
-        }
-    }
-}
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-bool
-basic_filebuf<CharT, Traits>::_M_read_mode()
-{
-    if (!(_M_cm & std::ios_base::in))
-    {
-        this->setp(0, 0);
-        if (_M_always_noconv)
-            this->setg((char_type*)_M_extbuf,
-                       (char_type*)_M_extbuf + _M_ebs,
-                       (char_type*)_M_extbuf + _M_ebs);
-        else
-            this->setg(_M_intbuf, _M_intbuf + _M_ibs, _M_intbuf + _M_ibs);
-        _M_cm = std::ios_base::in;
-        return true;
-    }
-    return false;
-}
-
-///////////////////////////////////////////////////////////////////////////////
-template <class CharT, class Traits>
-void
-basic_filebuf<CharT, Traits>::_M_write_mode()
-{
-    if (!(_M_cm & std::ios_base::out))
-    {
-        this->setg(0, 0, 0);
-        if (_M_ebs > sizeof(_M_extbuf_min))
-        {
-            if (_M_always_noconv)
-                this->setp((char_type*)_M_extbuf,
-                           (char_type*)_M_extbuf + (_M_ebs - 1));
-            else
-                this->setp(_M_intbuf, _M_intbuf + (_M_ibs - 1));
-        }
-        else
-            this->setp(0, 0);
-        _M_cm = std::ios_base::out;
-    }
-}
-
-///////////////////////////////////////////////////////////////////////////////
-}
-
-///////////////////////////////////////////////////////////////////////////////
-#endif // KALDI_UTIL_BASIC_FILEBUF_H_
-
-///////////////////////////////////////////////////////////////////////////////
-
-/*
- * ============================================================================
- * libc++ License
- * ============================================================================
- *
- * The libc++ library is dual licensed under both the University of Illinois
- * "BSD-Like" license and the MIT license.  As a user of this code you may
- * choose to use it under either license.  As a contributor, you agree to allow
- * your code to be used under both.
- *
- * Full text of the relevant licenses is included below.
- *
- * ============================================================================
- *
- * University of Illinois/NCSA
- * Open Source License
- *
- * Copyright (c) 2009-2014 by the contributors listed in CREDITS.TXT (included below)
- *
- * All rights reserved.
- *
- * Developed by:
- *
- *     LLVM Team
- *
- *     University of Illinois at Urbana-Champaign
- *
- *     http://llvm.org
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy of
- * this software and associated documentation files (the "Software"), to deal with
- * the Software without restriction, including without limitation the rights to
- * use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
- * of the Software, and to permit persons to whom the Software is furnished to do
- * so, subject to the following conditions:
- *
- *     * Redistributions of source code must retain the above copyright notice,
- *       this list of conditions and the following disclaimers.
- *
- *     * Redistributions in binary form must reproduce the above copyright notice,
- *       this list of conditions and the following disclaimers in the
- *       documentation and/or other materials provided with the distribution.
- *
- *     * Neither the names of the LLVM Team, University of Illinois at
- *       Urbana-Champaign, nor the names of its contributors may be used to
- *       endorse or promote products derived from this Software without specific
- *       prior written permission.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
- * FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL THE
- * CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE
- * SOFTWARE.
- *
- * ==============================================================================
- *
- * Copyright (c) 2009-2014 by the contributors listed in CREDITS.TXT (included below)
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- *
- * ==============================================================================
- *
- * This file is a partial list of people who have contributed to the LLVM/libc++
- * project.  If you have contributed a patch or made some other contribution to
- * LLVM/libc++, please submit a patch to this file to add yourself, and it will be
- * done!
- *
- * The list is sorted by surname and formatted to allow easy grepping and
- * beautification by scripts.  The fields are: name (N), email (E), web-address
- * (W), PGP key ID and fingerprint (P), description (D), and snail-mail address
- * (S).
- *
- * N: Saleem Abdulrasool
- * E: [email protected]
- * D: Minor patches and Linux fixes.
- *
- * N: Dimitry Andric
- * E: [email protected]
- * D: Visibility fixes, minor FreeBSD portability patches.
- *
- * N: Holger Arnold
- * E: [email protected]
- * D: Minor fix.
- *
- * N: Ruben Van Boxem
- * E: vanboxem dot ruben at gmail dot com
- * D: Initial Windows patches.
- *
- * N: David Chisnall
- * E: theraven at theravensnest dot org
- * D: FreeBSD and Solaris ports, libcxxrt support, some atomics work.
- *
- * N: Marshall Clow
- * E: [email protected]
- * E: [email protected]
- * D: C++14 support, patches and bug fixes.
- *
- * N: Bill Fisher
- * E: [email protected]
- * D: Regex bug fixes.
- *
- * N: Matthew Dempsky
- * E: [email protected]
- * D: Minor patches and bug fixes.
- *
- * N: Google Inc.
- * D: Copyright owner and contributor of the CityHash algorithm
- *
- * N: Howard Hinnant
- * E: [email protected]
- * D: Architect and primary author of libc++
- *
- * N: Hyeon-bin Jeong
- * E: [email protected]
- * D: Minor patches and bug fixes.
- *
- * N: Argyrios Kyrtzidis
- * E: [email protected]
- * D: Bug fixes.
- *
- * N: Bruce Mitchener, Jr.
- * E: [email protected]
- * D: Emscripten-related changes.
- *
- * N: Michel Morin
- * E: [email protected]
- * D: Minor patches to is_convertible.
- *
- * N: Andrew Morrow
- * E: [email protected]
- * D: Minor patches and Linux fixes.
- *
- * N: Arvid Picciani
- * E: aep at exys dot org
- * D: Minor patches and musl port.
- *
- * N: Bjorn Reese
- * E: [email protected]
- * D: Initial regex prototype
- *
- * N: Nico Rieck
- * E: [email protected]
- * D: Windows fixes
- *
- * N: Jonathan Sauer
- * D: Minor patches, mostly related to constexpr
- *
- * N: Craig Silverstein
- * E: [email protected]
- * D: Implemented Cityhash as the string hash function on 64-bit machines
- *
- * N: Richard Smith
- * D: Minor patches.
- *
- * N: Joerg Sonnenberger
- * E: [email protected]
- * D: NetBSD port.
- *
- * N: Stephan Tolksdorf
- * E: [email protected]
- * D: Minor <atomic> fix
- *
- * N: Michael van der Westhuizen
- * E: r1mikey at gmail dot com
- *
- * N: Klaas de Vries
- * E: klaas at klaasgaaf dot nl
- * D: Minor bug fix.
- *
- * N: Zhang Xiongpang
- * E: [email protected]
- * D: Minor patches and bug fixes.
- *
- * N: Xing Xue
- * E: [email protected]
- * D: AIX port
- *
- * N: Zhihao Yuan
- * E: [email protected]
- * D: Standard compatibility fixes.
- *
- * N: Jeffrey Yasskin
- * E: [email protected]
- * E: [email protected]
- * D: Linux fixes.
- */
diff --git a/kaldi_io/src/kaldi/util/common-utils.h b/kaldi_io/src/kaldi/util/common-utils.h
deleted file mode 100644
index 9d39f9d..0000000
--- a/kaldi_io/src/kaldi/util/common-utils.h
+++ /dev/null
@@ -1,31 +0,0 @@
-// util/common-utils.h
-
-// Copyright 2009-2011 Microsoft Corporation
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-
-//  http://www.apache.org/licenses/LICENSE-2.0
-
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-#ifndef KALDI_UTIL_COMMON_UTILS_H_
-#define KALDI_UTIL_COMMON_UTILS_H_
-
-#include "base/kaldi-common.h"
-#include "util/parse-options.h"
-#include "util/kaldi-io.h"
-#include "util/simple-io-funcs.h"
-#include "util/kaldi-holder.h"
-#include "util/kaldi-table.h"
-#include "util/table-types.h"
-#include "util/text-utils.h"
-
-#endif
diff --git a/kaldi_io/src/kaldi/util/const-integer-set-inl.h b/kaldi_io/src/kaldi/util/const-integer-set-inl.h
deleted file mode 100644
index 8f92ab2..0000000
--- a/kaldi_io/src/kaldi/util/const-integer-set-inl.h
+++ /dev/null
@@ -1,88 +0,0 @@
-// util/const-integer-set-inl.h
-
-// Copyright 2009-2011     Microsoft Corporation
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-
-#ifndef KALDI_UTIL_CONST_INTEGER_SET_INL_H_
-#define KALDI_UTIL_CONST_INTEGER_SET_INL_H_
-
-// Do not include this file directly.  It is included by const-integer-set.h
-
-
-namespace kaldi {
-
-template<class I>
-void ConstIntegerSet<I>::InitInternal() {
-  KALDI_ASSERT_IS_INTEGER_TYPE(I);
-  quick_set_.clear();  // just in case we previously had data.
-  if (slow_set_.size() == 0) {
-    lowest_member_=(I) 1;
-    highest_member_=(I) 0;
-    contiguous_ = false;
-    quick_ = false;
-  } else {
-    lowest_member_ = slow_set_.front();
-    highest_member_ = slow_set_.back();
-    size_t range = highest_member_ + 1 - lowest_member_;
-    if (range == slow_set_.size()) {
-      contiguous_ = true;
-      quick_=false;
-    } else {
-      contiguous_ = false;
-      if (range < slow_set_.size() * 8 * sizeof(I)) {  // If it would be more compact to store as bool
-        // (assuming 1 bit per element)...
-        quick_set_.resize(range, false);
-        for (size_t i = 0;i < slow_set_.size();i++)
-          quick_set_[slow_set_[i] - lowest_member_] = true;
-        quick_ = true;
-      } else {
-        quick_ = false;
-      }
-    }
-  }
-}
-
-template<class I>
-int ConstIntegerSet<I>::count(I i) const {
-  if (i < lowest_member_ || i > highest_member_) return 0;
-  else {
-    if (contiguous_) return true;
-    if (quick_) return (quick_set_[i-lowest_member_] ? 1 : 0);
-    else {
-      bool ans = std::binary_search(slow_set_.begin(), slow_set_.end(), i);
-      return (ans ? 1 : 0);
-    }
-  }
-}
-
-template<class I>
-void ConstIntegerSet<I>::Write(std::ostream &os, bool binary) const {
-  WriteIntegerVector(os, binary, slow_set_);
-}
-
-template<class I>
-void ConstIntegerSet<I>::Read(std::istream &is, bool binary) {
-  ReadIntegerVector(is, binary, &slow_set_);
-  InitInternal();
-}
-
-
-
-} // end namespace kaldi
-
-#endif
diff --git a/kaldi_io/src/kaldi/util/const-integer-set.h b/kaldi_io/src/kaldi/util/const-integer-set.h
deleted file mode 100644
index ffdce4d..0000000
--- a/kaldi_io/src/kaldi/util/const-integer-set.h
+++ /dev/null
@@ -1,95 +0,0 @@
-// util/const-integer-set.h
-
-// Copyright 2009-2011     Microsoft Corporation
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-
-#ifndef KALDI_UTIL_CONST_INTEGER_SET_H_
-#define KALDI_UTIL_CONST_INTEGER_SET_H_
-#include <vector>
-#include <set>
-#include <algorithm>
-#include <limits>
-#include <cassert>
-#include "util/stl-utils.h"
-
-  /* ConstIntegerSet is a way to efficiently test whether something is in a
-     supplied set of integers.  It can be initialized from a vector or set, but
-     never changed after that. It either uses a sorted vector or an array of
-     bool, depending on the input.  It behaves like a const version of an STL set, with
-     only a subset of the functionality, except all the member functions are
-     upper-case.
-
-     Note that we could get rid of the member slow_set_, but we'd have to
-     do more work to implement an iterator type.  This would save memory.
-  */
-
-namespace kaldi {
-
-template<class I> class ConstIntegerSet {
- public:
-  ConstIntegerSet(): lowest_member_(1), highest_member_(0) { }
-
-  void Init(const std::vector<I> &input) {
-    slow_set_ = input;
-    SortAndUniq(&slow_set_);
-    InitInternal();
-  }
-
-  void Init(const std::set<I> &input) {
-    CopySetToVector(input, &slow_set_);
-    InitInternal();
-  }
-
-  explicit ConstIntegerSet(const std::vector<I> &input): slow_set_(input) {
-    SortAndUniq(&slow_set_);
-    InitInternal();
-  }
-  explicit ConstIntegerSet(const std::set<I> &input) {
-    CopySetToVector(input, &slow_set_);
-    InitInternal();
-  }
-  explicit ConstIntegerSet(const ConstIntegerSet<I> &other): slow_set_(other.slow_set_) {
-    InitInternal();
-  }
-
-  int count(I i) const;  // returns 1 or 0.
-
-  typedef typename std::vector<I>::const_iterator iterator;
-  iterator begin() const { return slow_set_.begin(); }
-  iterator end() const { return slow_set_.end(); }
-  size_t size() const { return slow_set_.size(); }
-  bool empty() const { return slow_set_.empty(); }
-
-  void Write(std::ostream &os, bool binary) const;
-  void Read(std::istream &is, bool binary);
-
- private:
-  I lowest_member_;
-  I highest_member_;
-  bool contiguous_;
-  bool quick_;
-  std::vector<bool> quick_set_;
-  std::vector<I> slow_set_;
-  void InitInternal();
-};
-
-} // end namespace kaldi
-
-#include "const-integer-set-inl.h"
-
-#endif
diff --git a/kaldi_io/src/kaldi/util/edit-distance-inl.h b/kaldi_io/src/kaldi/util/edit-distance-inl.h
deleted file mode 100644
index ebbfb71..0000000
--- a/kaldi_io/src/kaldi/util/edit-distance-inl.h
+++ /dev/null
@@ -1,189 +0,0 @@
-// util/edit-distance-inl.h
-
-// Copyright 2009-2011  Microsoft Corporation;  Haihua Xu;  Yanmin Qian
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-
-//  http://www.apache.org/licenses/LICENSE-2.0
-
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_UTIL_EDIT_DISTANCE_INL_H_
-#define KALDI_UTIL_EDIT_DISTANCE_INL_H_
-#include "util/stl-utils.h"
-
-
-namespace kaldi {
-
-template<class T>
-int32 LevenshteinEditDistance(const std::vector<T> &a,
-                              const std::vector<T> &b) {
-  // Algorithm:
-  //  write A and B for the sequences, with elements a_0 ..
-  //  let |A| = M and |B| = N be the lengths, and have
-  //  elements a_0 ... a_{M-1} and b_0 ... b_{N-1}.
-  //  We are computing the recursion
-  //     E(m, n) = min(  E(m-1, n-1) + (1-delta(a_{m-1}, b_{n-1})),
-  //                    E(m-1, n),
-  //                    E(m, n-1) ).
-  //  where E(m, n) is defined for m = 0..M and n = 0..N and out-of-
-  //  bounds quantities are considered to be infinity (i.e. the
-  //  recursion does not visit them).
-
-  // We do this computation using a vector e of size N+1.
-  // The outer iterations range over m = 0..M.
-
-  int M = a.size(), N = b.size();
-  std::vector<int32> e(N+1);
-  std::vector<int32> e_tmp(N+1);
-  // initialize e.
-  for (size_t i = 0; i < e.size(); i++)
-    e[i] = i;
-  for (int32 m = 1; m <= M; m++) {
-    // computing E(m, .) from E(m-1, .)
-    // handle special case n = 0:
-    e_tmp[0] = e[0] + 1;
-
-    for (int32 n = 1; n <= N; n++) {
-      int32 term1 = e[n-1] + (a[m-1] == b[n-1] ? 0 : 1);
-      int32 term2 = e[n] + 1;
-      int32 term3 = e_tmp[n-1] + 1;
-      e_tmp[n] = std::min(term1, std::min(term2, term3));
-    }
-    e = e_tmp;
-  }
-  return e.back();
-}
-//
-struct error_stats{
-  int32 ins_num;
-  int32 del_num;
-  int32 sub_num;
-  int32 total_cost;  // minimum total cost to the current alignment.
-};
-// Note that both hyp and ref should not contain noise word in
-// the following implementation.
-
-template<class T>
-int32 LevenshteinEditDistance(const std::vector<T> &ref,
-                              const std::vector<T> &hyp,
-                              int32 *ins, int32 *del, int32 *sub) {
-  // temp sequence to remember error type and stats.
-  std::vector<error_stats> e(ref.size()+1);
-  std::vector<error_stats> cur_e(ref.size()+1);
-  // initialize the first hypothesis aligned to the reference at each
-  // position:[hyp_index =0][ref_index]
-  for (size_t i =0; i < e.size(); i ++) {
-    e[i].ins_num = 0;
-    e[i].sub_num = 0;
-    e[i].del_num = i;
-    e[i].total_cost = i;
-  }
-
- // for other alignments
- for (size_t hyp_index = 1; hyp_index <= hyp.size(); hyp_index ++) {
-   cur_e[0] = e[0];
-   cur_e[0].ins_num ++;
-   cur_e[0].total_cost ++;
-   for (size_t ref_index = 1; ref_index <= ref.size(); ref_index ++) {
-
-     int32 ins_err = e[ref_index].total_cost + 1;
-     int32 del_err = cur_e[ref_index-1].total_cost + 1;
-     int32 sub_err = e[ref_index-1].total_cost;
-      if (hyp[hyp_index-1] != ref[ref_index-1])
-       sub_err ++;
-
-     if (sub_err < ins_err && sub_err < del_err) {
-        cur_e[ref_index] =e[ref_index-1];
-        if (hyp[hyp_index-1] != ref[ref_index-1])
-          cur_e[ref_index].sub_num ++;   // substitution error should be increased
-        cur_e[ref_index].total_cost = sub_err;
-     }else if (del_err < ins_err ) {
-        cur_e[ref_index] = cur_e[ref_index-1];
-        cur_e[ref_index].total_cost = del_err;
-        cur_e[ref_index].del_num ++;    // deletion number is increased.
-     }else{
-        cur_e[ref_index] = e[ref_index];
-        cur_e[ref_index].total_cost = ins_err;
-        cur_e[ref_index].ins_num ++;    // insertion number is increased.
-     }
-   }
-   e = cur_e;  // alternate for the next recursion.
- }
-  size_t ref_index = e.size()-1;
-  *ins = e[ref_index].ins_num, *del = e[ref_index].del_num, *sub = e[ref_index].sub_num;
-  return e[ref_index].total_cost;
-}
-
-template<class T>
-int32 LevenshteinAlignment(const std::vector<T> &a,
-                           const std::vector<T> &b,
-                           T eps_symbol,
-                           std::vector<std::pair<T, T> > *output) {
-  // Check inputs:
-  {
-    KALDI_ASSERT(output != NULL);
-    for (size_t i = 0; i < a.size(); i++) KALDI_ASSERT(a[i] != eps_symbol);
-    for (size_t i = 0; i < b.size(); i++) KALDI_ASSERT(b[i] != eps_symbol);
-  }
-  output->clear();
-  // This is very memory-inefficiently implemented using a vector of vectors.
-  size_t M = a.size(), N = b.size();
-  size_t m, n;
-  std::vector<std::vector<int32> > e(M+1);
-  for (m = 0; m <=M; m++) e[m].resize(N+1);
-  for (n = 0; n <= N; n++)
-    e[0][n]  = n;
-  for (m = 1; m <= M; m++) {
-    e[m][0] = e[m-1][0] + 1;
-    for (n = 1; n <= N; n++) {
-      int32 sub_or_ok = e[m-1][n-1] + (a[m-1] == b[n-1] ? 0 : 1);
-      int32 del = e[m-1][n] + 1;  // assumes a == ref, b == hyp.
-      int32 ins = e[m][n-1] + 1;
-      e[m][n] = std::min(sub_or_ok, std::min(del, ins));
-    }
-  }
-  // get time-reversed output first: trace back.
-  m = M; n = N;
-  while (m != 0 || n != 0) {
-    size_t last_m, last_n;
-    if (m == 0) { last_m = m; last_n = n-1; }
-    else if (n == 0) { last_m = m-1; last_n = n; }
-    else {
-      int32 sub_or_ok = e[m-1][n-1] + (a[m-1] == b[n-1] ? 0 : 1);
-      int32 del = e[m-1][n] + 1;  // assumes a == ref, b == hyp.
-      int32 ins = e[m][n-1] + 1;
-      if (sub_or_ok <= std::min(del, ins)) {  // choose sub_or_ok if all else equal.
-        last_m = m-1; last_n = n-1;
-      } else {
-        if (del <= ins) {  // choose del over ins if equal.
-          last_m = m-1; last_n = n;
-        } else {
-          last_m = m; last_n = n-1;
-        }
-      }
-    }
-    T a_sym, b_sym;
-    a_sym = (last_m == m ? eps_symbol : a[last_m]);
-    b_sym = (last_n == n ? eps_symbol : b[last_n]);
-    output->push_back(std::make_pair(a_sym, b_sym));
-    m = last_m;
-    n = last_n;
-  }
-  ReverseVector(output);
-  return e[M][N];
-}
-
-
-}  // end namespace kaldi
-
-#endif // KALDI_UTIL_EDIT_DISTANCE_INL_H_
diff --git a/kaldi_io/src/kaldi/util/edit-distance.h b/kaldi_io/src/kaldi/util/edit-distance.h
deleted file mode 100644
index 6000622..0000000
--- a/kaldi_io/src/kaldi/util/edit-distance.h
+++ /dev/null
@@ -1,63 +0,0 @@
-// util/edit-distance.h
-
-// Copyright 2009-2011     Microsoft Corporation;  Haihua Xu
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-
-#ifndef KALDI_UTIL_EDIT_DISTANCE_H_
-#define KALDI_UTIL_EDIT_DISTANCE_H_
-#include <vector>
-#include <set>
-#include <algorithm>
-#include <limits>
-#include <cassert>
-#include "base/kaldi-types.h"
-
-namespace kaldi {
-
-// Compute the edit-distance between two strings.
-template<class T>
-int32 LevenshteinEditDistance(const std::vector<T> &a,
-                              const std::vector<T> &b);
-
-
-// edit distance calculation with conventional method.
-// note: noise word must be filtered out from the hypothesis and reference sequence
-// before the following procedure conducted.
-template<class T>
-int32 LevenshteinEditDistance(const std::vector<T> &ref,
-                              const std::vector<T> &hyp,
-                              int32 *ins, int32 *del, int32 *sub);
-
-// This version of the edit-distance computation outputs the alignment
-// between the two.  This is a vector of pairs of (symbol a, symbol b).
-// The epsilon symbol (eps_symbol) must not occur in sequences a or b.
-// Where one aligned to no symbol in the other (insertion or deletion),
-// epsilon will be the corresponding member of the pair.
-// It returns the edit-distance between the two strings.
-
-template<class T>
-int32 LevenshteinAlignment(const std::vector<T> &a,
-                           const std::vector<T> &b,
-                           T eps_symbol,
-                           std::vector<std::pair<T, T> > *output);
-
-} // end namespace kaldi
-
-#include "edit-distance-inl.h"
-
-#endif
diff --git a/kaldi_io/src/kaldi/util/hash-list-inl.h b/kaldi_io/src/kaldi/util/hash-list-inl.h
deleted file mode 100644
index 19c2bb6..0000000
--- a/kaldi_io/src/kaldi/util/hash-list-inl.h
+++ /dev/null
@@ -1,183 +0,0 @@
-// util/hash-list-inl.h
-
-// Copyright 2009-2011   Microsoft Corporation
-//                2013   Johns Hopkins University (author: Daniel Povey)
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-
-#ifndef KALDI_UTIL_HASH_LIST_INL_H_
-#define KALDI_UTIL_HASH_LIST_INL_H_
-
-// Do not include this file directly.  It is included by fast-hash.h
-
-
-namespace kaldi {
-
-template<class I, class T> HashList<I, T>::HashList() {
-  list_head_ = NULL;
-  bucket_list_tail_ = static_cast<size_t>(-1);  // invalid.
-  hash_size_ = 0;
-  freed_head_ = NULL;
-}
-
-template<class I, class T> void HashList<I, T>::SetSize(size_t size) {
-  hash_size_ = size;
-  KALDI_ASSERT(list_head_ == NULL && bucket_list_tail_ == static_cast<size_t>(-1));  // make sure empty.
-  if (size > buckets_.size())
-    buckets_.resize(size, HashBucket(0, NULL));
-}
-
-template<class I, class T>
-typename HashList<I, T>::Elem* HashList<I, T>::Clear() {
-  // Clears the hashtable and gives ownership of the currently contained list to the
-  // user.
-  for (size_t cur_bucket = bucket_list_tail_;
-      cur_bucket != static_cast<size_t>(-1);
-      cur_bucket = buckets_[cur_bucket].prev_bucket) {
-    buckets_[cur_bucket].last_elem = NULL;  // this is how we indicate "empty".
-  }
-  bucket_list_tail_ = static_cast<size_t>(-1);
-  Elem *ans = list_head_;
-  list_head_ = NULL;
-  return ans;
-}
-
-template<class I, class T>
-const typename HashList<I, T>::Elem* HashList<I, T>::GetList() const {
-  return list_head_;
-}
-
-template<class I, class T>
-inline void HashList<I, T>::Delete(Elem *e) {
-  e->tail = freed_head_;
-  freed_head_ = e;
-}
-
-template<class I, class T>
-inline typename HashList<I, T>::Elem* HashList<I, T>::Find(I key) {
-  size_t index = (static_cast<size_t>(key) % hash_size_);
-  HashBucket &bucket = buckets_[index];
-  if (bucket.last_elem == NULL) {
-    return NULL;  // empty bucket.
-  } else {
-    Elem *head = (bucket.prev_bucket == static_cast<size_t>(-1) ?
-                  list_head_ :
-                  buckets_[bucket.prev_bucket].last_elem->tail),
-        *tail = bucket.last_elem->tail;
-    for (Elem *e = head; e != tail; e = e->tail)
-      if (e->key == key) return e;
-    return NULL;  // Not found.
-  }
-}
-
-template<class I, class T>
-inline typename HashList<I, T>::Elem* HashList<I, T>::New() {
-  if (freed_head_) {
-    Elem *ans = freed_head_;
-    freed_head_ = freed_head_->tail;
-    return ans;
-  } else {
-    Elem *tmp = new Elem[allocate_block_size_];
-    for (size_t i = 0; i+1 < allocate_block_size_; i++)
-      tmp[i].tail = tmp+i+1;
-    tmp[allocate_block_size_-1].tail = NULL;
-    freed_head_ = tmp;
-    allocated_.push_back(tmp);
-    return this->New();
-  }
-}
-
-template<class I, class T>
-HashList<I, T>::~HashList() {
-  // First test whether we had any memory leak within the
-  // HashList, i.e. things for which the user did not call Delete().
-  size_t num_in_list = 0, num_allocated = 0;
-  for (Elem *e = freed_head_; e != NULL; e = e->tail)
-    num_in_list++;
-  for (size_t i = 0; i < allocated_.size(); i++) {
-    num_allocated += allocate_block_size_;
-    delete[] allocated_[i];
-  }
-  if (num_in_list != num_allocated) {
-    KALDI_WARN << "Possible memory leak: " << num_in_list
-               << " != " << num_allocated
-               << ": you might have forgotten to call Delete on "
-               << "some Elems";
-  }
-}
-
-
-template<class I, class T>
-void HashList<I, T>::Insert(I key, T val) {
-  size_t index = (static_cast<size_t>(key) % hash_size_);
-  HashBucket &bucket = buckets_[index];
-  Elem *elem = New();
-  elem->key = key;
-  elem->val = val;
-
-  if (bucket.last_elem == NULL) {  // Unoccupied bucket.  Insert at
-    // head of bucket list (which is tail of regular list, they go in
-    // opposite directions).
-    if (bucket_list_tail_ == static_cast<size_t>(-1)) {
-      // list was empty so this is the first elem.
-      KALDI_ASSERT(list_head_ == NULL);
-      list_head_ = elem;
-    } else {
-      // link in to the chain of Elems
-      buckets_[bucket_list_tail_].last_elem->tail = elem;
-    }
-    elem->tail = NULL;
-    bucket.last_elem = elem;
-    bucket.prev_bucket = bucket_list_tail_;
-    bucket_list_tail_ = index;
-  } else {
-    // Already-occupied bucket.  Insert at tail of list of elements within
-    // the bucket.
-    elem->tail = bucket.last_elem->tail;
-    bucket.last_elem->tail = elem;
-    bucket.last_elem = elem;
-  }
-}
-
-template<class I, class T>
-void HashList<I, T>::InsertMore(I key, T val) {
-  size_t index = (static_cast<size_t>(key) % hash_size_);
-  HashBucket &bucket = buckets_[index];
-  Elem *elem = New();
-  elem->key = key;
-  elem->val = val;
-
-  KALDI_ASSERT(bucket.last_elem != NULL); // we assume there is already one element
-  if (bucket.last_elem->key == key) { // standard behavior: add as last element
-    elem->tail = bucket.last_elem->tail;
-    bucket.last_elem->tail = elem;
-    bucket.last_elem = elem;
-    return;
-  } 
-  Elem *e = (bucket.prev_bucket == static_cast<size_t>(-1) ?
-             list_head_ : buckets_[bucket.prev_bucket].last_elem->tail);
-  // find place to insert in linked list 
-  while (e != bucket.last_elem->tail && e->key != key) e = e->tail;
-  KALDI_ASSERT(e->key == key); // not found? - should not happen
-  elem->tail = e->tail;
-  e->tail = elem;
-}
-
-
-} // end namespace kaldi
-
-#endif
diff --git a/kaldi_io/src/kaldi/util/hash-list.h b/kaldi_io/src/kaldi/util/hash-list.h
deleted file mode 100644
index 4524759..0000000
--- a/kaldi_io/src/kaldi/util/hash-list.h
+++ /dev/null
@@ -1,140 +0,0 @@
-// util/hash-list.h
-
-// Copyright 2009-2011   Microsoft Corporation
-//                2013   Johns Hopkins University (author: Daniel Povey)
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-
-#ifndef KALDI_UTIL_HASH_LIST_H_
-#define KALDI_UTIL_HASH_LIST_H_
-#include <vector>
-#include <set>
-#include <algorithm>
-#include <limits>
-#include <cassert>
-#include "util/stl-utils.h"
-
-
-/* This header provides utilities for a structure that's used in a decoder (but
-   is quite generic in nature so we implement and test it separately).
-   Basically it's a singly-linked list, but implemented in such a way that we
-   can quickly search for elements in the list.  We give it a slightly richer
-   interface than just a hash and a list.  The idea is that we want to separate
-   the hash part and the list part: basically, in the decoder, we want to have a
-   single hash for the current frame and the next frame, because by the time we
-   need to access the hash for the next frame we no longer need the hash for the
-   previous frame.  So we have an operation that clears the hash but leaves the
-   list structure intact.  We also control memory management inside this object,
-   to avoid repeated new's/deletes.
-
-   See hash-list-test.cc for an example of how to use this object.
-*/
-
-
-namespace kaldi {
-
-template<class I, class T> class HashList {
-
- public:
-  struct Elem {
-    I key;
-    T val;
-    Elem *tail;
-  };
-
-  /// Constructor takes no arguments.  Call SetSize to inform it of the likely size.
-  HashList();
-
-  /// Clears the hash and gives the head of the current list to the user;
-  /// ownership is transferred to the user (the user must call Delete()
-  /// for each element in the list, at his/her leisure).
-  Elem *Clear();
-
-  /// Gives the head of the current list to the user.  Ownership retained in the
-  /// class.  Caution: in December 2013 the return type was changed to const Elem*
-  /// and this function was made const.  You may need to change some types of
-  /// local Elem* variables to const if this produces compilation errors.
-  const Elem *GetList() const;
-
-  /// Think of this like delete().  It is to be called for each Elem in turn
-  /// after you "obtained ownership" by doing Clear().  This is not the opposite of
-  /// Insert, it is the opposite of New.  It's really a memory operation.
-  inline void Delete(Elem *e);
-
-  /// This should probably not be needed to be called directly by the user.  Think of it as opposite
-  /// to Delete();
-  inline Elem *New();
-
-  /// Find tries to find this element in the current list using the hashtable.
-  /// It returns NULL if not present.  The Elem it returns is not owned by the user,
-  /// it is part of the internal list owned by this object, but the user is
-  /// free to modify the "val" element.
-  inline Elem *Find(I key);
-  
-  /// Insert inserts a new element into the hashtable/stored list.  By calling this,
-  /// the user asserts that it is not already present (e.g. Find was called and
-  /// returned NULL).  With current code, calling this if an element already exists will
-  /// result in duplicate elements in the structure, and Find() will find the
-  /// first one that was added.  [but we don't guarantee this behavior].
-  inline void Insert(I key, T val);
-
-  /// Insert inserts another element with same key into the hashtable/stored list.
-  /// By calling this, the user asserts that one element with that key is already present.
-  /// We insert it that way, that all elements with the same key follow each other.
-  /// Find() will return the first one of the elements with the same key.
-  inline void InsertMore(I key, T val);
-
-  /// SetSize tells the object how many hash buckets to allocate (should typically be
-  /// at least twice the number of objects we expect to go in the structure, for fastest
-  /// performance).  It must be called while the hash is empty (e.g. after Clear() or
-  /// after initializing the object, but before adding anything to the hash.
-  void SetSize(size_t sz);
-
-  /// Returns current number of hash buckets.
-  inline size_t Size() { return hash_size_; }
-
-  ~HashList();
- private:
-
-  struct HashBucket {
-    size_t prev_bucket;  // index to next bucket (-1 if list tail).  Note: list of buckets
-    // goes in opposite direction to list of Elems.
-    Elem *last_elem;  // pointer to last element in this bucket (NULL if empty)
-    inline HashBucket(size_t i, Elem *e): prev_bucket(i), last_elem(e) {}
-  };
-
-  Elem *list_head_;  // head of currently stored list.
-  size_t bucket_list_tail_;  // tail of list of active hash buckets.
-
-  size_t hash_size_;  // number of hash buckets.
-
-  std::vector<HashBucket> buckets_;
-
-  Elem *freed_head_;  // head of list of currently freed elements. [ready for allocation]
-
-  std::vector<Elem*> allocated_;  // list of allocated blocks.
-
-  static const size_t allocate_block_size_ = 1024;  // Number of Elements to allocate in one block.  Must be
-  // largish so storing allocated_ doesn't become a problem.
-};
-
-
-} // end namespace kaldi
-
-#include "hash-list-inl.h"
-
-#endif
diff --git a/kaldi_io/src/kaldi/util/kaldi-holder-inl.h b/kaldi_io/src/kaldi/util/kaldi-holder-inl.h
deleted file mode 100644
index 6a66e61..0000000
--- a/kaldi_io/src/kaldi/util/kaldi-holder-inl.h
+++ /dev/null
@@ -1,800 +0,0 @@
-// util/kaldi-holder-inl.h
-
-// Copyright 2009-2011     Microsoft Corporation
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-
-#ifndef KALDI_UTIL_KALDI_HOLDER_INL_H_
-#define KALDI_UTIL_KALDI_HOLDER_INL_H_
-
-#include <algorithm>
-#include "util/kaldi-io.h"
-#include "util/text-utils.h"
-#include "matrix/kaldi-matrix.h"
-
-namespace kaldi {
-
-/// \addtogroup holders
-/// @{
-
-
-// KaldiObjectHolder is valid only for Kaldi objects with
-// copy constructors, default constructors, and "normal"
-// Kaldi Write and Read functions.  E.g. it works for
-// Matrix and Vector.
-template<class KaldiType> class KaldiObjectHolder {
- public:
-  typedef KaldiType T;
-
-  KaldiObjectHolder(): t_(NULL) { }
-
-  static bool Write(std::ostream &os, bool binary, const T &t) {
-    InitKaldiOutputStream(os, binary);  // Puts binary header if binary mode.
-    try {
-      t.Write(os, binary);
-      return os.good();
-    } catch (const std::exception &e) {
-      KALDI_WARN << "Exception caught writing Table object: " << e.what();
-      if (!IsKaldiError(e.what())) { std::cerr << e.what(); }
-      return false;  // Write failure.
-    }
-  }
-
-  void Clear() {
-    if (t_) {
-      delete t_;
-      t_ = NULL;
-    }
-  }
-
-  // Reads into the holder.
-  bool Read(std::istream &is) {
-    if (t_) delete t_;
-    t_ = new T;
-    // Don't want any existing state to complicate the read functioN: get new object.
-    bool is_binary;
-    if (!InitKaldiInputStream(is, &is_binary)) {
-      KALDI_WARN << "Reading Table object, failed reading binary header\n";
-      return false;
-    }
-    try {
-      t_->Read(is, is_binary);
-      return true;
-    } catch (std::exception &e) {
-      KALDI_WARN << "Exception caught reading Table object ";
-      if (!IsKaldiError(e.what())) { std::cerr << e.what(); }
-      delete t_;
-      t_ = NULL;
-      return false;
-    }
-  }
-
-  // Kaldi objects always have the stream open in binary mode for
-  // reading.
-  static bool IsReadInBinary() { return true; }
-
-  const T &Value() const {
-    // code error if !t_.
-    if (!t_) KALDI_ERR << "KaldiObjectHolder::Value() called wrongly.";
-    return *t_;
-  }
-
-  ~KaldiObjectHolder() { if (t_) delete t_; }
- private:
-  KALDI_DISALLOW_COPY_AND_ASSIGN(KaldiObjectHolder);
-  T *t_;
-};
-
-
-// BasicHolder is valid for float, double, bool, and integer
-// types.  There will be a compile time error otherwise, because
-// we make sure that the {Write, Read}BasicType functions do not
-// get instantiated for other types.
-
-template<class BasicType> class BasicHolder {
- public:
-  typedef BasicType T;
-
-  BasicHolder(): t_(static_cast<T>(-1)) { }
-
-  static bool Write(std::ostream &os, bool binary, const T &t) {
-    InitKaldiOutputStream(os, binary);  // Puts binary header if binary mode.
-    try {
-      WriteBasicType(os, binary, t);
-      if (!binary) os << '\n';  // Makes output format more readable and
-      // easier to manipulate.
-      return os.good();
-    } catch (const std::exception &e) {
-      KALDI_WARN << "Exception caught writing Table object: " << e.what();
-      if (!IsKaldiError(e.what())) { std::cerr << e.what(); }
-      return false;  // Write failure.
-    }
-  }
-
-  void Clear() { }
-
-  // Reads into the holder.
-  bool Read(std::istream &is) {
-    bool is_binary;
-    if (!InitKaldiInputStream(is, &is_binary)) {
-      KALDI_WARN << "Reading Table object [integer type], failed reading binary header\n";
-      return false;
-    }
-    try {
-      int c;
-      if (!is_binary) {  // This is to catch errors, the class would work without it..
-        // Eat up any whitespace and make sure it's not newline.
-        while (isspace((c = is.peek())) && c != static_cast<int>('\n')) is.get();
-        if (is.peek() == '\n') {
-          KALDI_WARN << "Found newline but expected basic type.";
-          return false;  // This is just to catch a more-
-          // likely-than average type of error (empty line before the token), since
-          // ReadBasicType will eat it up.
-        }
-      }
-
-      ReadBasicType(is, is_binary, &t_);
-
-      if (!is_binary) {  // This is to catch errors, the class would work without it..
-        // make sure there is a newline.
-        while (isspace((c = is.peek())) && c != static_cast<int>('\n')) is.get();
-        if (is.peek() != '\n') {
-          KALDI_WARN << "BasicHolder::Read, expected newline, got "
-                     << CharToString(is.peek()) << ", position " << is.tellg();
-          return false;
-        }
-        is.get();  // Consume the newline.
-      }
-      return true;
-    } catch (std::exception &e) {
-      KALDI_WARN << "Exception caught reading Table object";
-      if (!IsKaldiError(e.what())) { std::cerr << e.what(); }
-      return false;
-    }
-  }
-
-  // Objects read/written with the Kaldi I/O functions always have the stream
-  // open in binary mode for reading.
-  static bool IsReadInBinary() { return true; }
-
-  const T &Value() const {
-    return t_;
-  }
-
-  ~BasicHolder() { }
- private:
-  KALDI_DISALLOW_COPY_AND_ASSIGN(BasicHolder);
-
-  T t_;
-};
-
-
-/// A Holder for a vector of basic types, e.g.
-/// std::vector<int32>, std::vector<float>, and so on.
-/// Note: a basic type is defined as a type for which ReadBasicType
-/// and WriteBasicType are implemented, i.e. integer and floating
-/// types, and bool.
-template<class BasicType> class BasicVectorHolder {
- public:
-  typedef std::vector<BasicType> T;
-
-  BasicVectorHolder() { }
-
-  static bool Write(std::ostream &os, bool binary, const T &t) {
-    InitKaldiOutputStream(os, binary);  // Puts binary header if binary mode.
-    try {
-      if (binary) {  // need to write the size, in binary mode.
-        KALDI_ASSERT(static_cast<size_t>(static_cast<int32>(t.size())) == t.size());
-        // Or this Write routine cannot handle such a large vector.
-        // use int32 because it's fixed size regardless of compilation.
-        // change to int64 (plus in Read function) if this becomes a problem.
-        WriteBasicType(os, binary, static_cast<int32>(t.size()));
-        for (typename std::vector<BasicType>::const_iterator iter = t.begin();
-            iter != t.end(); ++iter)
-          WriteBasicType(os, binary, *iter);
-
-      } else {
-        for (typename std::vector<BasicType>::const_iterator iter = t.begin();
-            iter != t.end(); ++iter)
-          WriteBasicType(os, binary, *iter);
-        os << '\n';  // Makes output format more readable and
-        // easier to manipulate.  In text mode, this function writes something like
-        // "1 2 3\n".
-      }
-      return os.good();
-    } catch (const std::exception &e) {
-      KALDI_WARN << "Exception caught writing Table object (BasicVector). ";
-      if (!IsKaldiError(e.what())) { std::cerr << e.what(); }
-      return false;  // Write failure.
-    }
-  }
-
-  void Clear() { t_.clear(); }
-
-  // Reads into the holder.
-  bool Read(std::istream &is) {
-    t_.clear();
-    bool is_binary;
-    if (!InitKaldiInputStream(is, &is_binary)) {
-      KALDI_WARN << "Reading Table object [integer type], failed reading binary header\n";
-      return false;
-    }
-    if (!is_binary) {
-      // In text mode, we terminate with newline.
-      std::string line;
-      getline(is, line);  // this will discard the \n, if present.
-      if (is.fail()) {
-        KALDI_WARN << "BasicVectorHolder::Read, error reading line " << (is.eof() ? "[eof]" : "");
-        return false;  // probably eof.  fail in any case.
-      }
-      std::istringstream line_is(line);
-      try {
-        while (1) {
-          line_is >> std::ws;  // eat up whitespace.
-          if (line_is.eof()) break;
-          BasicType bt;
-          ReadBasicType(line_is, false, &bt);
-          t_.push_back(bt);
-        }
-        return true;
-      } catch(std::exception &e) {
-        KALDI_WARN << "BasicVectorHolder::Read, could not interpret line: " << line;
-        if (!IsKaldiError(e.what())) { std::cerr << e.what(); }
-        return false;
-      }
-    } else {  // binary mode.
-      size_t filepos = is.tellg();
-      try {
-        int32 size;
-        ReadBasicType(is, true, &size);
-        t_.resize(size);
-        for (typename std::vector<BasicType>::iterator iter = t_.begin();
-            iter != t_.end();
-            ++iter) {
-          ReadBasicType(is, true, &(*iter));
-        }
-        return true;
-      } catch (...) {
-        KALDI_WARN << "BasicVectorHolder::Read, read error or unexpected data at archive entry beginning at file position " << filepos;
-        return false;
-      }
-    }
-  }
-
-  // Objects read/written with the Kaldi I/O functions always have the stream
-  // open in binary mode for reading.
-  static bool IsReadInBinary() { return true; }
-
-  const T &Value() const {  return t_; }
-
-  ~BasicVectorHolder() { }
- private:
-  KALDI_DISALLOW_COPY_AND_ASSIGN(BasicVectorHolder);
-  T t_;
-};
-
-
-/// BasicVectorVectorHolder is a Holder for a vector of vector of
-/// a basic type, e.g. std::vector<std::vector<int32> >.
-/// Note: a basic type is defined as a type for which ReadBasicType
-/// and WriteBasicType are implemented, i.e. integer and floating
-/// types, and bool.
-template<class BasicType> class BasicVectorVectorHolder {
- public:
-  typedef std::vector<std::vector<BasicType> > T;
-
-  BasicVectorVectorHolder() { }
-
-  static bool Write(std::ostream &os, bool binary, const T &t) {
-    InitKaldiOutputStream(os, binary);  // Puts binary header if binary mode.
-    try {
-      if (binary) {  // need to write the size, in binary mode.
-        KALDI_ASSERT(static_cast<size_t>(static_cast<int32>(t.size())) == t.size());
-        // Or this Write routine cannot handle such a large vector.
-        // use int32 because it's fixed size regardless of compilation.
-        // change to int64 (plus in Read function) if this becomes a problem.
-        WriteBasicType(os, binary, static_cast<int32>(t.size()));
-        for (typename std::vector<std::vector<BasicType> >::const_iterator iter = t.begin();
-            iter != t.end(); ++iter) {
-          KALDI_ASSERT(static_cast<size_t>(static_cast<int32>(iter->size())) == iter->size());
-          WriteBasicType(os, binary, static_cast<int32>(iter->size()));
-          for (typename std::vector<BasicType>::const_iterator iter2=iter->begin();
-              iter2 != iter->end(); ++iter2) {
-            WriteBasicType(os, binary, *iter2);
-          }
-        }
-      } else {  // text mode...
-        // In text mode, we write out something like (for integers):
-        // "1 2 3 ; 4 5 ; 6 ; ; 7 8 9 ;\n"
-        // where the semicolon is a terminator, not a separator
-        // (a separator would cause ambiguity between an
-        // empty list, and a list containing a single empty list).
-        for (typename std::vector<std::vector<BasicType> >::const_iterator iter = t.begin();
-            iter != t.end();
-             ++iter) {
-          for (typename std::vector<BasicType>::const_iterator iter2=iter->begin();
-               iter2 != iter->end(); ++iter2)
-            WriteBasicType(os, binary, *iter2);
-          os << "; ";
-        }
-        os << '\n';
-      }
-      return os.good();
-    } catch (const std::exception &e) {
-      KALDI_WARN << "Exception caught writing Table object. ";
-      if (!IsKaldiError(e.what())) { std::cerr << e.what(); }
-      return false;  // Write failure.
-    }
-  }
-
-  void Clear() { t_.clear(); }
-
-  // Reads into the holder.
-  bool Read(std::istream &is) {
-    t_.clear();
-    bool is_binary;
-    if (!InitKaldiInputStream(is, &is_binary)) {
-      KALDI_WARN << "Failed reading binary header\n";
-      return false;
-    }
-    if (!is_binary) {
-      // In text mode, we terminate with newline.
-      try {  // catching errors from ReadBasicType..
-        std::vector<BasicType> v;  // temporary vector
-        while (1) {
-          int i = is.peek();
-          if (i == -1) {
-            KALDI_WARN << "Unexpected EOF";
-            return false;
-          } else if (static_cast<char>(i) == '\n') {
-            if (!v.empty()) {
-              KALDI_WARN << "No semicolon before newline (wrong format)";
-              return false;
-            } else { is.get(); return true; }
-          } else if (std::isspace(i)) {
-            is.get();
-          } else if (static_cast<char>(i) == ';') {
-            t_.push_back(v);
-            v.clear();
-            is.get();
-          } else {  // some object we want to read...
-            BasicType b;
-            ReadBasicType(is, false, &b);  // throws on error.
-            v.push_back(b);
-          }
-        }
-      } catch(std::exception &e) {
-        KALDI_WARN << "BasicVectorVectorHolder::Read, read error";
-        if (!IsKaldiError(e.what())) { std::cerr << e.what(); }
-        return false;
-      }
-    } else {  // binary mode.
-      size_t filepos = is.tellg();
-      try {
-        int32 size;
-        ReadBasicType(is, true, &size);
-        t_.resize(size);
-        for (typename std::vector<std::vector<BasicType> >::iterator iter = t_.begin();
-            iter != t_.end();
-            ++iter) {
-          int32 size2;
-          ReadBasicType(is, true, &size2);
-          iter->resize(size2);
-          for (typename std::vector<BasicType>::iterator iter2 = iter->begin();
-              iter2 != iter->end();
-              ++iter2)
-            ReadBasicType(is, true, &(*iter2));
-        }
-        return true;
-      } catch (...) {
-        KALDI_WARN << "Read error or unexpected data at archive entry beginning at file position " << filepos;
-        return false;
-      }
-    }
-  }
-
-  // Objects read/written with the Kaldi I/O functions always have the stream
-  // open in binary mode for reading.
-  static bool IsReadInBinary() { return true; }
-
-  const T &Value() const {  return t_; }
-
-  ~BasicVectorVectorHolder() { }
- private:
-  KALDI_DISALLOW_COPY_AND_ASSIGN(BasicVectorVectorHolder);
-  T t_;
-};
-
-
-/// BasicPairVectorHolder is a Holder for a vector of pairs of
-/// a basic type, e.g. std::vector<std::pair<int32> >.
-/// Note: a basic type is defined as a type for which ReadBasicType
-/// and WriteBasicType are implemented, i.e. integer and floating
-/// types, and bool.
-template<class BasicType> class BasicPairVectorHolder {
- public:
-  typedef std::vector<std::pair<BasicType, BasicType> > T;
-
-  BasicPairVectorHolder() { }
-  
-  static bool Write(std::ostream &os, bool binary, const T &t) {
-    InitKaldiOutputStream(os, binary);  // Puts binary header if binary mode.
-    try {
-      if (binary) {  // need to write the size, in binary mode.
-        KALDI_ASSERT(static_cast<size_t>(static_cast<int32>(t.size())) == t.size());
-        // Or this Write routine cannot handle such a large vector.
-        // use int32 because it's fixed size regardless of compilation.
-        // change to int64 (plus in Read function) if this becomes a problem.
-        WriteBasicType(os, binary, static_cast<int32>(t.size()));
-        for (typename T::const_iterator iter = t.begin();
-            iter != t.end(); ++iter) {
-          WriteBasicType(os, binary, iter->first);
-          WriteBasicType(os, binary, iter->second);
-        }
-      } else {  // text mode...
-        // In text mode, we write out something like (for integers):
-        // "1 2 ; 4 5 ; 6 7 ; 8 9 \n"
-        // where the semicolon is a separator, not a terminator.
-        for (typename T::const_iterator iter = t.begin();
-             iter != t.end();) {
-          WriteBasicType(os, binary, iter->first);
-          WriteBasicType(os, binary, iter->second);
-          ++iter;
-          if (iter != t.end())
-            os << "; ";
-        }
-        os << '\n';
-      }
-      return os.good();
-    } catch (const std::exception &e) {
-      KALDI_WARN << "Exception caught writing Table object. ";
-      if (!IsKaldiError(e.what())) { std::cerr << e.what(); }
-      return false;  // Write failure.
-    }
-  }
-  
-  void Clear() { t_.clear(); }
-
-  // Reads into the holder.
-  bool Read(std::istream &is) {
-    t_.clear();
-    bool is_binary;
-    if (!InitKaldiInputStream(is, &is_binary)) {
-      KALDI_WARN << "Reading Table object [integer type], failed reading binary header\n";
-      return false;
-    }
-    if (!is_binary) {
-      // In text mode, we terminate with newline.
-      try {  // catching errors from ReadBasicType..
-        std::vector<BasicType> v;  // temporary vector
-        while (1) {
-          int i = is.peek();
-          if (i == -1) {
-            KALDI_WARN << "Unexpected EOF";
-            return false;
-          } else if (static_cast<char>(i) == '\n') {
-            if (t_.empty() && v.empty()) {
-              is.get();
-              return true;
-            } else if (v.size() == 2) {
-              t_.push_back(std::make_pair(v[0], v[1]));
-              is.get();
-              return true;
-            } else {
-              KALDI_WARN << "Unexpected newline, reading vector<pair<?> >; got "
-                         << v.size() << " elements, expected 2.";
-              return false;
-            }
-          } else if (std::isspace(i)) {
-            is.get();
-          } else if (static_cast<char>(i) == ';') {
-            if (v.size() != 2) {
-              KALDI_WARN << "Wrong input format, reading vector<pair<?> >; got "
-                         << v.size() << " elements, expected 2.";
-              return false;
-            }
-            t_.push_back(std::make_pair(v[0], v[1]));
-            v.clear();
-            is.get();
-          } else {  // some object we want to read...
-            BasicType b;
-            ReadBasicType(is, false, &b);  // throws on error.
-            v.push_back(b);
-          }
-        }
-      } catch(std::exception &e) {
-        KALDI_WARN << "BasicPairVectorHolder::Read, read error";
-        if (!IsKaldiError(e.what())) { std::cerr << e.what(); }
-        return false;
-      }
-    } else {  // binary mode.
-      size_t filepos = is.tellg();
-      try {
-        int32 size;
-        ReadBasicType(is, true, &size);
-        t_.resize(size);
-        for (typename T::iterator iter = t_.begin();
-            iter != t_.end();
-            ++iter) {
-          ReadBasicType(is, true, &(iter->first));
-          ReadBasicType(is, true, &(iter->second));
-        }
-        return true;
-      } catch (...) {
-        KALDI_WARN << "BasicVectorHolder::Read, read error or unexpected data at archive entry beginning at file position " << filepos;
-        return false;
-      }
-    }
-  }
-
-  // Objects read/written with the Kaldi I/O functions always have the stream
-  // open in binary mode for reading.
-  static bool IsReadInBinary() { return true; }
-
-  const T &Value() const {  return t_; }
-
-  ~BasicPairVectorHolder() { }
- private:
-  KALDI_DISALLOW_COPY_AND_ASSIGN(BasicPairVectorHolder);
-  T t_;
-};
-
-
-
-
-// We define a Token as a nonempty, printable, whitespace-free std::string.
-// The binary and text formats here are the same (newline-terminated)
-// and as such we don't bother with the binary-mode headers.
-class TokenHolder {
- public:
-  typedef std::string T;
-
-  TokenHolder() {}
-
-  static bool Write(std::ostream &os, bool, const T &t) {  // ignore binary-mode.
-    KALDI_ASSERT(IsToken(t));
-    os << t << '\n';
-    return os.good();
-  }
-
-  void Clear() { t_.clear(); }
-
-  // Reads into the holder.
-  bool Read(std::istream &is) {
-    is >> t_;
-    if (is.fail()) return false;
-    char c;
-    while (isspace(c = is.peek()) && c!= '\n') is.get();
-    if (is.peek() != '\n') {
-      KALDI_ERR << "TokenHolder::Read, expected newline, got char " << CharToString(is.peek())
-                << ", at stream pos " << is.tellg();
-      return false;
-    }
-    is.get();  // get '\n'
-    return true;
-  }
-
-
-  // Since this is fundamentally a text format, read in text mode (would work
-  // fine either way, but doing it this way will exercise more of the code).
-  static bool IsReadInBinary() { return false; }
-
-  const T &Value() const { return t_; }
-
-  ~TokenHolder() { }
- private:
-  KALDI_DISALLOW_COPY_AND_ASSIGN(TokenHolder);
-  T t_;
-};
-
-// A Token is a nonempty, whitespace-free std::string.
-// Class TokenVectorHolder is a Holder class for vectors of these.
-class TokenVectorHolder {
- public:
-  typedef std::vector<std::string> T;
-
-  TokenVectorHolder() { }
-
-  static bool Write(std::ostream &os, bool, const T &t) {  // ignore binary-mode.
-    for (std::vector<std::string>::const_iterator iter = t.begin();
-        iter != t.end();
-        ++iter) {
-      KALDI_ASSERT(IsToken(*iter));  // make sure it's whitespace-free, printable and nonempty.
-      os << *iter << ' ';
-    }
-    os << '\n';
-    return os.good();
-  }
-
-  void Clear() { t_.clear(); }
-
-
-  // Reads into the holder.
-  bool Read(std::istream &is) {
-    t_.clear();
-
-    // there is no binary/non-binary mode.
-
-    std::string line;
-    getline(is, line);  // this will discard the \n, if present.
-    if (is.fail()) {
-      KALDI_WARN << "BasicVectorHolder::Read, error reading line " << (is.eof() ? "[eof]" : "");
-      return false;  // probably eof.  fail in any case.
-    }
-    const char *white_chars = " \t\n\r\f\v";
-    SplitStringToVector(line, white_chars, true, &t_);  // true== omit empty strings e.g.
-    // between spaces.
-    return true;
-  }
-
-  // Read in text format since it's basically a text-mode thing.. doesn't really matter,
-  // it would work either way since we ignore the extra '\r'.
-  static bool IsReadInBinary() { return false; }
-
-  const T &Value() const { return t_; }
-
- private:
-  KALDI_DISALLOW_COPY_AND_ASSIGN(TokenVectorHolder);
-  T t_;
-};
-
-
-class HtkMatrixHolder {
- public:
-  typedef std::pair<Matrix<BaseFloat>, HtkHeader> T;
-
-  HtkMatrixHolder() {}
-
-  static bool Write(std::ostream &os, bool binary, const T &t) {
-    if (!binary)
-      KALDI_ERR << "Non-binary HTK-format write not supported.";
-    bool ans = WriteHtk(os, t.first, t.second);
-    if (!ans)
-      KALDI_WARN << "Error detected writing HTK-format matrix.";
-    return ans;
-  }
-
-  void Clear() { t_.first.Resize(0, 0); }
-
-  // Reads into the holder.
-  bool Read(std::istream &is) {
-    bool ans = ReadHtk(is, &t_.first, &t_.second);
-    if (!ans) {
-      KALDI_WARN << "Error detected reading HTK-format matrix.";
-      return false;
-    }
-    return ans;
-  }
-
-  // HTK-format matrices only read in binary.
-  static bool IsReadInBinary() { return true; }
-
-  const T &Value() const { return t_; }
-
-
-  // No destructor.
- private:
-  KALDI_DISALLOW_COPY_AND_ASSIGN(HtkMatrixHolder);
-  T t_;
-};
-
-// SphinxMatrixHolder can be used to read and write feature files in
-// CMU Sphinx format. 13-dimensional big-endian features are assumed.
-// The ultimate reference is SphinxBase's source code (for example see
-// feat_s2mfc_read() in src/libsphinxbase/feat/feat.c).
-// We can't fully automate the detection of machine/feature file endianess
-// mismatch here, because for this Sphinx relies on comparing the feature
-// file's size with the number recorded in its header. We are working with
-// streams, however(what happens if this is a Kaldi archive?). This should
-// be no problem, because the usage help of Sphinx' "wave2feat" for example
-// says that Sphinx features are always big endian.
-// Note: the kFeatDim defaults to 13, see forward declaration in kaldi-holder.h
-template<int kFeatDim> class SphinxMatrixHolder {
- public:
-  typedef Matrix<BaseFloat> T;
-
-  SphinxMatrixHolder() {}
-
-  void Clear() { feats_.Resize(0, 0); }
-
-  // Writes Sphinx-format features
-  static bool Write(std::ostream &os, bool binary, const T &m) {
-    if (!binary) {
-      KALDI_WARN << "SphinxMatrixHolder can't write Sphinx features in text ";
-      return false;
-    }
-
-    int32 size = m.NumRows() * m.NumCols();
-    if (MachineIsLittleEndian())
-      KALDI_SWAP4(size);
-    os.write((char*) &size, sizeof(size)); // write the header
-
-    for (MatrixIndexT i = 0; i < m.NumRows(); i++) {
-      float32 tmp[m.NumCols()];
-      for (MatrixIndexT j = 0; j < m.NumCols(); j++) {
-        tmp[j] = static_cast<float32>(m(i, j));
-        if (MachineIsLittleEndian())
-          KALDI_SWAP4(tmp[j]);
-      }
-      os.write((char*) tmp, sizeof(tmp));
-    }
-
-    return true;
-  }
-
-  // Reads the features into a Kaldi Matrix
-  bool Read(std::istream &is) {
-    int32 nmfcc;
-
-    is.read((char*) &nmfcc, sizeof(nmfcc));
-    if (MachineIsLittleEndian())
-      KALDI_SWAP4(nmfcc);
-    KALDI_VLOG(2) << "#feats: " << nmfcc;
-    int32 nfvec = nmfcc / kFeatDim;
-    if ((nmfcc % kFeatDim) != 0) {
-      KALDI_WARN << "Sphinx feature count is inconsistent with vector length ";
-      return false;
-    }
-
-    feats_.Resize(nfvec, kFeatDim);
-    for (MatrixIndexT i = 0; i < feats_.NumRows(); i++) {
-      if (sizeof(BaseFloat) == sizeof(float32)) {
-        is.read((char*) feats_.RowData(i), kFeatDim * sizeof(float32));
-        if (!is.good()) {
-          KALDI_WARN << "Unexpected error/EOF while reading Sphinx features ";
-          return false;
-        }
-        if (MachineIsLittleEndian()) {
-          for (MatrixIndexT j=0; j < kFeatDim; j++)
-            KALDI_SWAP4(feats_(i, j));
-        }
-      } else { // KALDI_DOUBLEPRECISION=1
-        float32 tmp[kFeatDim];
-        is.read((char*) tmp, sizeof(tmp));
-        if (!is.good()) {
-          KALDI_WARN << "Unexpected error/EOF while reading Sphinx features ";
-          return false;
-        }
-        for (MatrixIndexT j=0; j < kFeatDim; j++) {
-          if (MachineIsLittleEndian())
-            KALDI_SWAP4(tmp[j]);
-          feats_(i, j) = static_cast<BaseFloat>(tmp[j]);
-        }
-      }
-    }
-
-    return true;
-  }
-
-  // Only read in binary
-  static bool IsReadInBinary() { return true; }
-
-  const T &Value() const { return feats_; }
-
- private:
-  KALDI_DISALLOW_COPY_AND_ASSIGN(SphinxMatrixHolder);
-  T feats_;
-};
-
-
-/// @} end "addtogroup holders"
-
-} // end namespace kaldi
-
-
-
-#endif
diff --git a/kaldi_io/src/kaldi/util/kaldi-holder.h b/kaldi_io/src/kaldi/util/kaldi-holder.h
deleted file mode 100644
index 95f1183..0000000
--- a/kaldi_io/src/kaldi/util/kaldi-holder.h
+++ /dev/null
@@ -1,207 +0,0 @@
-// util/kaldi-holder.h
-
-// Copyright 2009-2011     Microsoft Corporation
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-
-#ifndef KALDI_UTIL_KALDI_HOLDER_H_
-#define KALDI_UTIL_KALDI_HOLDER_H_
-
-#include <algorithm>
-#include "util/kaldi-io.h"
-#include "util/text-utils.h"
-#include "matrix/kaldi-vector.h"
-
-namespace kaldi {
-
-
-// The Table class uses a Holder class to wrap objects, and make them behave
-// in a "normalized" way w.r.t. reading and writing, so the Table class can
-// be template-ized without too much trouble. Look below this
-// comment (search for GenericHolder) to see what it looks like.
-//
-//  Requirements of the holder class:
-//
-// They can only contain objects that can be read/written without external
-// information; other objects cannot be stored in this type of archive.
-//
-// In terms of what functions it should have, see GenericHolder below.
-// It is just for documentation.
-//
-// (1) Requirements of the Read and Write functions
-//
-// The Read and Write functions should have the property that in a longer
-// file, if the Read function is started from where the Write function started
-// writing, it should go to where the Write function stopped writing, in either
-// text or binary mode (but it's OK if it doesn't eat up trailing space).
-//
-//     [Desirable property: when writing in text mode the output should contain
-//      exactly one newline, at the end of the output; this makes it easier to manipulate]
-//
-//     [Desirable property for classes: the output should just be a binary-mode
-//      header (if in binary mode and it's a Kaldi object, or no header
-//      othewise), and then the output of Object.Write().  This means that when
-//      written to individual files with the scp: type of wspecifier, we can read
-//      the individual files in the "normal" Kaldi way by reading the binary
-//      header and then the object.]
-//
-//
-// The Write function takes a 'binary' argument.  In general, each object will
-// have two formats: text and binary.  However, it's permitted to throw() if
-// asked to read in the text format if there is none.  The file will be open, if
-// the file system has binary/text modes, in the corresponding mode.  However,
-// the object should have a file-mode in which it can read either text or binary
-// output.  It announces this via the static IsReadInBinary() function.  This
-// will generally be the binary mode and it means that where necessary, in text
-// formats, we must ignore \r characters.
-//
-// Memory requirements: if it allocates memory, the destructor should
-// free that memory.  Copying and assignment of Holder objects may be
-// disallowed as the Table code never does this.
-
-
-/// GenericHolder serves to document the requirements of the Holder interface;
-/// it's not intended to be used.
-template<class SomeType> class GenericHolder {
- public:
-  typedef SomeType T;
-
-  /// Must have a constructor that takes no arguments.
-  GenericHolder() { }
-
-  /// Write writes this object of type T.  Possibly also writes a binary-mode
-  /// header so that the Read function knows which mode to read in (since the
-  /// Read function does not get this information).  It's a static member so we
-  /// can write those not inside this class (can use this function with Value()
-  /// to write from this class).  The Write method may throw if it cannot write
-  /// the object in the given (binary/non-binary) mode.  The holder object can
-  /// assume the stream has been opened in the given mode (where relevant).  The
-  /// object can write the data how it likes.
-  static bool Write(std::ostream &os, bool binary, const T &t);
-  
-  /// Reads into the holder.  Must work out from the stream (which will be opened
-  /// on Windows in binary mode if the IsReadInBinary() function of this class
-  /// returns true, and text mode otherwise) whether the actual data is binary or
-  /// not (usually via reading the Kaldi binary-mode header).  We put the
-  /// responsibility for reading the Kaldi binary-mode header in the Read
-  /// function (rather than making the binary mode an argument to this function),
-  /// so that for non-Kaldi binary files we don't have to write the header, which
-  /// would prevent the file being read by non-Kaldi programs (e.g. if we write
-  /// to individual files using an scp).
-  ///
-  /// Read must deallocate any existing data we have here, if applicable (must
-  /// not assume the object was newly constructed).
-  ///
-  /// Returns true on success.
-  bool Read(std::istream &is);
-
-  /// IsReadInBinary() will return true if the object wants the file to be
-  /// opened in binary for reading (if the file system has binary/text modes),
-  /// and false otherwise.  Static function.  Kaldi objects always return true
-  /// as they always read in binary mode.  Note that we must be able to read, in
-  /// this mode, objects written in both text and binary mode by Write (which
-  /// may mean ignoring "\r" characters).  I doubt we will ever want this
-  /// function to return false.
-  static bool IsReadInBinary() { return true; }
-
-  /// Returns the value of the object held here.  Will only
-  /// ever be called if Read() has been previously called and it returned
-  /// true (so OK to throw exception if no object was read).
-  const T &Value() const { return t_; } // if t is a pointer, would return *t_;
-
-  /// The Clear() function doesn't have to do anything.  Its purpose is to
-  /// allow the object to free resources if they're no longer needed.
-  void Clear() { }
-
-  /// If the object held pointers, the destructor would free them.
-  ~GenericHolder() { }
-
- private:
-  KALDI_DISALLOW_COPY_AND_ASSIGN(GenericHolder);
-  T t_;  // t_ may alternatively be of type T*.
-};
-
-
-// See kaldi-holder-inl.h for examples of some actual Holder
-// classes and templates.
-
-
-// The following two typedefs should probably be in their own file, but they're
-// here until there are enough of them to warrant their own header.
-
-
-/// \addtogroup holders
-/// @{
-
-/// KaldiObjectHolder works for Kaldi objects that have the "standard" Read and Write
-/// functions, and a copy constructor.
-template<class KaldiType> class KaldiObjectHolder;
-
-/// BasicHolder is valid for float, double, bool, and integer
-/// types.  There will be a compile time error otherwise, because
-/// we make sure that the {Write, Read}BasicType functions do not
-/// get instantiated for other types.
-template<class BasicType> class BasicHolder;
-
-
-// A Holder for a vector of basic types, e.g.
-// std::vector<int32>, std::vector<float>, and so on.
-// Note: a basic type is defined as a type for which ReadBasicType
-// and WriteBasicType are implemented, i.e. integer and floating
-// types, and bool.
-template<class BasicType> class BasicVectorHolder;
-
-
-// A holder for vectors of vectors of basic types, e.g.
-// std::vector<std::vector<int32> >, and so on.
-// Note: a basic type is defined as a type for which ReadBasicType
-// and WriteBasicType are implemented, i.e. integer and floating
-// types, and bool.
-template<class BasicType> class BasicVectorVectorHolder;
-
-// A holder for vectors of pairsof basic types, e.g.
-// std::vector<std::vector<int32> >, and so on.
-// Note: a basic type is defined as a type for which ReadBasicType
-// and WriteBasicType are implemented, i.e. integer and floating
-// types, and bool.  Text format is (e.g. for integers),
-// "1 12 ; 43 61 ; 17 8 \n"
-template<class BasicType> class BasicPairVectorHolder;
-
-/// We define a Token (not a typedef, just a word) as a nonempty, printable,
-/// whitespace-free std::string.  The binary and text formats here are the same
-/// (newline-terminated) and as such we don't bother with the binary-mode headers.
-class TokenHolder;
-
-/// Class TokenVectorHolder is a Holder class for vectors of Tokens (T == std::string).
-class TokenVectorHolder;
-
-/// A class for reading/writing HTK-format matrices.
-/// T == std::pair<Matrix<BaseFloat>, HtkHeader>
-class HtkMatrixHolder;
-
-/// A class for reading/writing Sphinx format matrices.
-template<int kFeatDim=13> class SphinxMatrixHolder;
-
-
-/// @} end "addtogroup holders"
-
-
-} // end namespace kaldi
-
-#include "kaldi-holder-inl.h"
-
-#endif
diff --git a/kaldi_io/src/kaldi/util/kaldi-io-inl.h b/kaldi_io/src/kaldi/util/kaldi-io-inl.h
deleted file mode 100644
index 7df7505..0000000
--- a/kaldi_io/src/kaldi/util/kaldi-io-inl.h
+++ /dev/null
@@ -1,45 +0,0 @@
-// util/kaldi-io-inl.h
-
-// Copyright 2009-2011 Microsoft Corporation
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-
-//  http://www.apache.org/licenses/LICENSE-2.0
-
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-#ifndef KALDI_UTIL_KALDI_IO_INL_H_
-#define KALDI_UTIL_KALDI_IO_INL_H_
-
-
-namespace kaldi {
-
-bool Input::Open(const std::string &rxfilename, bool *binary) {
-  return OpenInternal(rxfilename, true, binary);
-}
-
-bool Input::OpenTextMode(const std::string &rxfilename) {
-  return OpenInternal(rxfilename, false, NULL);
-}
-
-bool Input::IsOpen() {
-  return impl_ != NULL;
-}
-
-bool Output::IsOpen() {
-  return impl_ != NULL;
-}
-
-
-}  // end namespace kaldi.
-
-
-#endif
diff --git a/kaldi_io/src/kaldi/util/kaldi-io.h b/kaldi_io/src/kaldi/util/kaldi-io.h
deleted file mode 100644
index f2c7563..0000000
--- a/kaldi_io/src/kaldi/util/kaldi-io.h
+++ /dev/null
@@ -1,264 +0,0 @@
-// util/kaldi-io.h
-
-// Copyright 2009-2011  Microsoft Corporation;  Jan Silovsky
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-
-//  http://www.apache.org/licenses/LICENSE-2.0
-
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-#ifndef KALDI_UTIL_KALDI_IO_H_
-#define KALDI_UTIL_KALDI_IO_H_
-
-#include <cctype>  // For isspace.
-#include <limits>
-#include <string>
-#include "base/kaldi-common.h"
-#ifdef _MSC_VER
-# include <fcntl.h>
-# include <io.h>
-#endif
-
-
-
-namespace kaldi {
-
-class OutputImplBase;  // Forward decl; defined in a .cc file
-class InputImplBase;  // Forward decl; defined in a .cc file
-
-/// \addtogroup io_group
-/// @{
-
-// The Output and Input classes handle stream-opening for "extended" filenames
-// that include actual files, standard-input/standard-output, pipes, and
-// offsets into actual files.  They also handle reading and writing the
-// binary-mode headers for Kaldi files, where applicable.  The classes have
-// versions of the Open routines that throw and do not throw, depending whether
-// the calling code wants to catch the errors or not; there are also versions
-// that write (or do not write) the Kaldi binary-mode header that says if it's
-// binary mode.  Generally files that contain Kaldi objects will have the header
-// on, so we know upon reading them whether they have the header.  So you would
-// use the OpenWithHeader routines for these (or the constructor); but other
-// types of objects (e.g. FSTs) would have files without a header so you would
-// use OpenNoHeader.
-
-// We now document the types of extended filenames that we use.
-//
-// A "wxfilename"  is an extended filename for writing.  It can take three forms:
-// (1) Filename: e.g.    "/some/filename", "./a/b/c", "c:\Users\dpovey\My Documents\\boo"
-//          (whatever the actual file-system interprets)
-// (2) Standard output:  "" or "-"
-// (3) A pipe: e.g.  "gunzip -c /tmp/abc.gz |"
-//
-//
-// A "rxfilename" is an extended filename for reading.  It can take four forms:
-// (1) An actual filename, whatever the file-system can read, e.g. "/my/file".
-// (2) Standard input: "" or "-"
-// (3) A pipe: e.g. "| gzip -c > /tmp/abc.gz"
-// (4) An offset into a file, e.g.: "/mnt/blah/data/1.ark:24871"
-//   [these are created by the Table and TableWriter classes; I may also write
-//    a program that creates them for arbitrary files]
-//
-
-
-// Typical usage:
-// ...
-// bool binary;
-// MyObject.Write(Output(some_filename, binary).Stream(), binary);
-//
-// ... more extensive example:
-// {
-//    Output ko(some_filename, binary);
-//    MyObject1.Write(ko.Stream(), binary);
-//    MyObject2.Write(ko.Stream(), binary);
-// }
-
-
-
-enum OutputType {
-  kNoOutput,
-  kFileOutput,
-  kStandardOutput,
-  kPipeOutput
-};
-
-/// ClassifyWxfilename interprets filenames as follows:
-///  - kNoOutput: invalid filenames (leading or trailing space, things that look
-///     like wspecifiers and rspecifiers or like pipes to read from with leading |.
-///  - kFileOutput: Normal filenames
-///  - kStandardOutput: The empty string or "-", interpreted as standard output
-///  - kPipeOutput: pipes, e.g. "gunzip -c some_file.gz |"  
-OutputType ClassifyWxfilename(const std::string &wxfilename);
-
-enum InputType {
-  kNoInput,
-  kFileInput,
-  kStandardInput,
-  kOffsetFileInput,
-  kPipeInput
-};
-
-/// ClassifyRxfilenames interprets filenames for reading as follows:
-///  - kNoInput: invalid filenames (leading or trailing space, things that
-///       look like wspecifiers and rspecifiers or pipes to write to
-///       with trailing |.
-///  - kFileInput: normal filenames
-///  - kStandardInput: the empty string or "-"
-///  - kPipeInput: e.g. "| gzip -c > blah.gz"
-///  - kOffsetFileInput: offsets into files, e.g.  /some/filename:12970
-InputType ClassifyRxfilename(const std::string &rxfilename);
-
-
-class Output {
- public:
-  // The normal constructor, provided for convenience.
-  // Equivalent to calling with default constructor then Open()
-  // with these arguments.
-  Output(const std::string &filename, bool binary, bool write_header = true);
-
-  Output(): impl_(NULL) {};
-
-  /// This opens the stream, with the given mode (binary or text).  It returns
-  /// true on success and false on failure.  However, it will throw if something
-  /// was already open and could not be closed (to avoid this, call Close()
-  /// first.  if write_header == true and binary == true, it writes the Kaldi
-  /// binary-mode header ('\0' then 'B').  You may call Open even if it is
-  /// already open; it will close the existing stream and reopen (however if
-  /// closing the old stream failed it will throw).
-  bool Open(const std::string &wxfilename, bool binary, bool write_header);
-
-  inline bool IsOpen();  // return true if we have an open stream.  Does not imply
-  // stream is good for writing.
-
-  std::ostream &Stream();  // will throw if not open; else returns stream.
-
-  // Close closes the stream. Calling Close is never necessary unless you
-  // want to avoid exceptions being thrown.  There are times when calling
-  // Close will hurt efficiency (basically, when using offsets into files,
-  // and using the same Input object),
-  // but most of the time the user won't be doing this directly, it will
-  // be done in kaldi-table.{h, cc}, so you don't have to worry about it.
-  bool Close();
-
-  // This will throw if stream could not be closed (to check error status,
-  // call Close()).
-  ~Output();
-
- private:
-  OutputImplBase *impl_;  // non-NULL if open.
-  std::string filename_;
-  KALDI_DISALLOW_COPY_AND_ASSIGN(Output);
-};
-
-
-// bool binary_in;
-// Input ki(some_filename, &binary_in);
-// MyObject.Read(ki, binary_in);
-//
-// ... more extensive example:
-//
-// {
-//    bool binary_in;
-//    Input ki(some_filename, &binary_in);
-//    MyObject1.Read(ki.Stream(), &binary_in);
-//    MyObject2.Write(ki.Stream(), &binary_in);
-// }
-// Note that to catch errors you need to use try.. catch.
-// Input communicates errors by throwing exceptions.
-
-
-// Input interprets four kinds of filenames:
-//  (1) Normal filenames
-//  (2) The empty string or "-", interpreted as standard output
-//  (3) Pipes, e.g. "| gzip -c > some_file.gz"
-//  (4) Offsets into [real] files, e.g. "/my/filename:12049"
-// The last one has no correspondence in Output.
-
-
-class Input {
- public:
-  /// The normal constructor.  Opens the stream in binary mode.
-  /// Equivalent to calling the default constructor followed by Open(); then, if
-  /// binary != NULL, it calls ReadHeader(), putting the output in "binary"; it
-  /// throws on error.
-  Input(const std::string &rxfilename, bool *contents_binary = NULL);
-
-  Input(): impl_(NULL) {}
-
-  // Open opens the stream for reading (the mode, where relevant, is binary; use
-  // OpenTextMode for text-mode, we made this a separate function rather than a
-  // boolean argument, to avoid confusion with Kaldi's text/binary distinction,
-  // since reading in the file system's text mode is unusual.)  If
-  // contents_binary != NULL, it reads the binary-mode header and puts it in the
-  // "binary" variable.  Returns true on success.  If it returns false it will
-  // not be open.  You may call Open even if it is already open; it will close
-  // the existing stream and reopen (however if closing the old stream failed it
-  // will throw).
-  inline bool Open(const std::string &rxfilename, bool *contents_binary = NULL);
-
-  // As Open but (if the file system has text/binary modes) opens in text mode;
-  // you shouldn't ever have to use this as in Kaldi we read even text files in
-  // binary mode (and ignore the \r).
-  inline bool OpenTextMode(const std::string &rxfilename);
-
-  // Return true if currently open for reading and Stream() will
-  // succeed.  Does not guarantee that the stream is good.
-  inline bool IsOpen();
-
-  // It is never necessary or helpful to call Close, except if
-  // you are concerned about to many filehandles being open.
-  // Close does not throw.
-  void Close();
-
-  // Returns the underlying stream. Throws if !IsOpen()
-  std::istream &Stream();
-
-  // Destructor does not throw: input streams may legitimately fail so we
-  // don't worry about the status when we close them.
-  ~Input();
- private:
-  bool OpenInternal(const std::string &rxfilename, bool file_binary, bool *contents_binary);
-  InputImplBase *impl_;
-  KALDI_DISALLOW_COPY_AND_ASSIGN(Input);
-};
-
-template <class C> inline void ReadKaldiObject(const std::string &filename,
-                                               C *c) {
-  bool binary_in;
-  Input ki(filename, &binary_in);
-  c->Read(ki.Stream(), binary_in);
-}
-
-template <class C> inline void WriteKaldiObject(const C &c,
-                                                const std::string &filename,
-                                                bool binary) {
-  Output ko(filename, binary);
-  c.Write(ko.Stream(), binary);
-}
-
-/// PrintableRxfilename turns the rxfilename into a more human-readable
-/// form for error reporting, i.e. it does quoting and escaping and
-/// replaces "" or "-" with "standard input".
-std::string PrintableRxfilename(std::string rxfilename);
-
-/// PrintableWxfilename turns the filename into a more human-readable
-/// form for error reporting, i.e. it does quoting and escaping and
-/// replaces "" or "-" with "standard output".
-std::string PrintableWxfilename(std::string wxfilename);
-
-/// @}
-
-}  // end namespace kaldi.
-
-#include "kaldi-io-inl.h"
-
-#endif
diff --git a/kaldi_io/src/kaldi/util/kaldi-pipebuf.h b/kaldi_io/src/kaldi/util/kaldi-pipebuf.h
deleted file mode 100644
index 43e5a2e..0000000
--- a/kaldi_io/src/kaldi/util/kaldi-pipebuf.h
+++ /dev/null
@@ -1,90 +0,0 @@
-// util/kaldi-pipebuf.h
-
-// Copyright 2009-2011  Ondrej Glembek
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-
-//  http://www.apache.org/licenses/LICENSE-2.0
-
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-
-/** @file kaldi-pipebuf.h
- *  This is an Kaldi C++ Library header.
- */
-
-#ifndef KALDI_UTIL_KALDI_PIPEBUF_H_
-#define KALDI_UTIL_KALDI_PIPEBUF_H_
-
-#if defined(_LIBCPP_VERSION)  // libc++
-#include "basic-filebuf.h"
-#else
-#include <fstream>
-#endif
-
-namespace kaldi
-{
-// This class provides a way to initialize a filebuf with a FILE* pointer
-// directly; it will not close the file pointer when it is deleted.
-// The C++ standard does not allow implementations of C++ to provide
-// this constructor within basic_filebuf, which makes it hard to deal
-// with pipes using completely native C++.  This is a workaround
-
-#ifdef _MSC_VER
-#elif defined(_LIBCPP_VERSION)  // libc++
-template<class CharType, class Traits = std::char_traits<CharType> >
-class basic_pipebuf : public basic_filebuf<CharType, Traits>
-{
- public:
-  typedef basic_pipebuf<CharType, Traits>   ThisType;
-
- public:
-  basic_pipebuf(FILE *fptr, std::ios_base::openmode mode)
-      : basic_filebuf<CharType, Traits>() {
-    this->open(fptr, mode);
-    if (!this->is_open()) {
-      KALDI_WARN << "Error initializing pipebuf";  // probably indicates
-      // code error, if the fptr was good.
-      return;
-    }
-  }
-};  // class basic_pipebuf
-#else
-template<class CharType, class Traits = std::char_traits<CharType> >
-class basic_pipebuf : public std::basic_filebuf<CharType, Traits>
-{
- public:
-  typedef basic_pipebuf<CharType, Traits>   ThisType;
-
- public:
-  basic_pipebuf(FILE *fptr, std::ios_base::openmode mode)
-      : std::basic_filebuf<CharType, Traits>() {
-    this->_M_file.sys_open(fptr, mode);
-    if (!this->is_open()) {
-      KALDI_WARN << "Error initializing pipebuf";  // probably indicates
-      // code error, if the fptr was good.
-      return;
-    }
-    this->_M_mode = mode;
-    this->_M_buf_size = BUFSIZ;
-    this->_M_allocate_internal_buffer();
-    this->_M_reading = false;
-    this->_M_writing = false;
-    this->_M_set_buffer(-1);
-  }
-};  // class basic_pipebuf
-#endif // _MSC_VER
-
-};  // namespace kaldi
-
-#endif // KALDI_UTIL_KALDI_PIPEBUF_H_
-
diff --git a/kaldi_io/src/kaldi/util/kaldi-table-inl.h b/kaldi_io/src/kaldi/util/kaldi-table-inl.h
deleted file mode 100644
index 6b73c88..0000000
--- a/kaldi_io/src/kaldi/util/kaldi-table-inl.h
+++ /dev/null
@@ -1,2246 +0,0 @@
-// util/kaldi-table-inl.h
-
-// Copyright 2009-2011    Microsoft Corporation
-//                2013    Johns Hopkins University (author: Daniel Povey)
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-
-#ifndef KALDI_UTIL_KALDI_TABLE_INL_H_
-#define KALDI_UTIL_KALDI_TABLE_INL_H_
-
-#include <algorithm>
-#include "util/kaldi-io.h"
-#include "util/text-utils.h"
-#include "util/stl-utils.h" // for StringHasher.
-
-
-namespace kaldi {
-
-/// \addtogroup table_impl_types
-/// @{
-
-template<class Holder> class SequentialTableReaderImplBase {
- public:
-  typedef typename Holder::T T;
-  // note that Open takes rxfilename not rspecifier.
-  virtual bool Open(const std::string &rxfilename) = 0;
-  virtual bool Done() const = 0;
-  virtual bool IsOpen() const = 0;
-  virtual std::string Key() = 0;
-  virtual const T &Value() = 0;
-  virtual void FreeCurrent() = 0;
-  virtual void Next() = 0;
-  virtual bool Close() = 0;
-  SequentialTableReaderImplBase() { }
-  virtual ~SequentialTableReaderImplBase() { }
- private:
-  KALDI_DISALLOW_COPY_AND_ASSIGN(SequentialTableReaderImplBase);  
-};
-
-
-// This is the implementation for SequentialTableReader
-// when it's actually a script file.
-template<class Holder>  class SequentialTableReaderScriptImpl:
-      public SequentialTableReaderImplBase<Holder> {
- public:
-  typedef typename Holder::T T;
-
-  SequentialTableReaderScriptImpl(): state_(kUninitialized) { }
-
-  virtual bool Open(const std::string &rspecifier) {
-    if (state_ != kUninitialized)
-      if (! Close()) // call Close() yourself to suppress this exception.
-        KALDI_ERR << "TableReader::Open, error closing previous input: "
-                  << "rspecifier was " << rspecifier_;
-    bool binary;
-    rspecifier_ = rspecifier;
-    RspecifierType rs = ClassifyRspecifier(rspecifier, &script_rxfilename_,
-                                           &opts_);
-    KALDI_ASSERT(rs == kScriptRspecifier);
-    if (!script_input_.Open(script_rxfilename_, &binary)) {  // Failure on Open
-      KALDI_WARN << "Failed to open script file "
-                 << PrintableRxfilename(script_rxfilename_);
-      state_ = kUninitialized;
-      return false;
-    } else {  // Open succeeded.
-      if (binary) {  // script file should not be binary file..
-        state_ = kError;  // bad script file.
-        script_input_.Close();
-        return false;
-      } else {
-        state_ = kFileStart;
-        Next();
-        if (state_ == kError) {
-          script_input_.Close();
-          return false;
-        }
-        if (opts_.permissive) {  // Next() will have preloaded.
-          KALDI_ASSERT(state_ == kLoadSucceeded || state_ == kEof);
-        } else {
-          KALDI_ASSERT(state_ == kHaveScpLine || state_ == kEof);
-        }
-        return true;  // Success.
-      }
-    }
-  }
-
-  virtual bool IsOpen() const {
-    switch (state_) {
-      case kEof: case kError: case kHaveScpLine: case kLoadSucceeded: case kLoadFailed: return true;
-      case kUninitialized:  return false;
-      default: KALDI_ERR << "IsOpen() called on invalid object.";  // kFileStart is not valid
-        // state for user to call something on.
-        return false;
-    }
-  }
-
-  virtual bool Done() const {
-    switch (state_) {
-      case kHaveScpLine: return false;
-      case kLoadSucceeded: case kLoadFailed: return false;
-        // These cases are because we want LoadCurrent()
-        // to be callable after Next() and to not change the Done() status [only Next() should change
-        // the Done() status].
-      case kEof: case kError: return true;  // Error condition, like Eof, counts as Done(); the destructor
-        // or Close() will inform the user of the error.
-      default: KALDI_ERR << "Done() called on TableReader object at the wrong time.";
-        return false;
-    }
-  }
-
-  virtual std::string Key() {
-    // Valid to call this whenever Done() returns false.
-    switch (state_) {
-      case kHaveScpLine: case kLoadSucceeded: case kLoadFailed: break;
-      default:
-        // coding error.
-        KALDI_ERR << "Key() called on TableReader object at the wrong time.";
-    }
-    return key_;
-  }
-  const T &Value() {
-    StateType orig_state = state_;
-    if (state_ == kHaveScpLine) LoadCurrent();  // Takes
-    // state_ to kLoadSucceeded or kLoadFailed.
-    if (state_ == kLoadFailed) {  // this can happen due to
-      // a file listed in an scp file not existing, or
-      // read failure, failure of a command, etc.
-      if (orig_state == kHaveScpLine)
-        KALDI_ERR << "TableReader: failed to load object from "
-                  << PrintableRxfilename(data_rxfilename_)
-                  << " (to suppress this error, add the permissive "
-                  << "(p, ) option to the rspecifier.";
-
-      else // orig_state_ was kLoadFailed, which only could have happened
-        // if the user called FreeCurrent().
-        KALDI_ERR << "TableReader: you called Value() after FreeCurrent().";
-    } else if (state_ != kLoadSucceeded) {
-      // This would be a coding error.
-      KALDI_ERR << "TableReader: Value() called at the wrong time.";
-    }
-    return holder_.Value();
-  }
-  void FreeCurrent() {
-    if (state_ == kLoadSucceeded) {
-      holder_.Clear();
-      state_ = kLoadFailed;
-    } else {
-      KALDI_WARN << "TableReader: FreeCurrent called at the wrong time.";
-    }
-  }
-  void Next() {
-    while (1) {
-      NextScpLine();
-      if (Done()) return;
-      if (opts_.permissive) {
-        // Permissive mode means, when reading scp files, we treat keys whose scp entry
-        // cannot be read as nonexistent.  This means trying to read.
-        if (LoadCurrent()) return;  // Success.
-        // else try the next scp line.
-      } else {
-        return;  // We go the next key; Value() will crash if we can't
-        // read the scp line.
-      }
-    }
-  }
-
-  virtual bool Close() {
-    // Close() will succeed if the stream was not in an error
-    // state.  To clean up, it also closes the Input objects if
-    // they're open.
-    if (script_input_.IsOpen())
-      script_input_.Close();
-    if (data_input_.IsOpen())
-      data_input_.Close();
-    if (state_ == kLoadSucceeded)
-      holder_.Clear();
-    if (!this->IsOpen())
-      KALDI_ERR << "Close() called on input that was not open.";
-    StateType old_state = state_;
-    state_ = kUninitialized;
-    if (old_state == kError) {
-      if (opts_.permissive) {
-        KALDI_WARN << "Close() called on scp file with read error, ignoring the "
-            "error because permissive mode specified.";
-        return true;
-      } else  return false;  // User will do something with the error status.
-    } else  return true;
-  }
-
-  virtual ~SequentialTableReaderScriptImpl() {
-    if (state_ == kError)
-      KALDI_ERR << "TableReader: reading script file failed: from scp "
-                << PrintableRxfilename(script_rxfilename_);
-    // If you don't want this exception to be thrown you can
-    // call Close() and check the status.
-    if (state_ == kLoadSucceeded)
-      holder_.Clear();
-  }
- private:  
-  bool LoadCurrent() {
-    // Attempts to load object whose rxfilename is on the current scp line.
-    if (state_ != kHaveScpLine)
-      KALDI_ERR << "TableReader: LoadCurrent() called at the wrong time.";
-    bool ans;
-    // note, NULL means it doesn't read the binary-mode header
-    if (Holder::IsReadInBinary()) ans = data_input_.Open(data_rxfilename_, NULL);
-    else ans = data_input_.OpenTextMode(data_rxfilename_);
-    if (!ans) {
-      // May want to make this warning a VLOG at some point
-      KALDI_WARN << "TableReader: failed to open file "
-                 << PrintableRxfilename(data_rxfilename_);
-      state_ = kLoadFailed;
-      return false;
-    } else {
-      if (holder_.Read(data_input_.Stream())) {
-        state_ = kLoadSucceeded;
-        return true;
-      } else {  // holder_ will not contain data.
-        KALDI_WARN << "TableReader: failed to load object from "
-                   << PrintableRxfilename(data_rxfilename_);
-        state_ = kLoadFailed;
-        return false;
-      }
-    }
-  }
-
-  // Reads the next line in the script file.
-  void NextScpLine() {
-    switch (state_) {
-      case kLoadSucceeded: holder_.Clear(); break;
-      case kHaveScpLine: case kLoadFailed: case kFileStart: break;
-      default:
-        // No other states are valid to call Next() from.
-        KALDI_ERR << "Reading script file: Next called wrongly.";
-    }
-    std::string line;
-    if (getline(script_input_.Stream(), line)) {
-      SplitStringOnFirstSpace(line, &key_, &data_rxfilename_);
-      if (!key_.empty() && !data_rxfilename_.empty()) {
-        // Got a valid line.
-        state_ = kHaveScpLine;
-      } else {
-        // Got an invalid line.
-        state_ = kError;  // we can't make sense of this
-        // scp file and will now die.
-      }
-    } else {
-      state_ = kEof;  // nothing more in the scp file.
-      // Might as well close the input streams as don't need them.
-      script_input_.Close();
-      if (data_input_.IsOpen())
-        data_input_.Close();
-    }
-  }
-
-
-  Input script_input_;  // Input object for the .scp file
-  Input data_input_;   // Input object for the entries in
-  // the script file.
-  Holder holder_;  // Holds the object.
-  bool binary_;  // Binary-mode archive.
-  std::string key_;
-  std::string rspecifier_;
-  std::string script_rxfilename_;  // of the script file.
-  RspecifierOptions opts_;  // options.
-  std::string data_rxfilename_;  // of the file we're reading.
-  enum StateType {
-    //       [The state of the reading process]               [does holder_ [is script_inp_
-    //                                                         have object]   open]
-    kUninitialized,  // Uninitialized or closed.                    no         no
-    kEof,     // We did Next() and found eof in script file.       no         no
-    kError,   // Some other error                                  no         yes
-    kHaveScpLine,  // Just called Open() or Next() and have a       no         yes
-    // line of the script file but no data.
-    kLoadSucceeded,  // Called LoadCurrent() and it succeeded.     yes         yes
-    kLoadFailed,  // Called LoadCurrent() and it failed,           no         yes
-    // or the user called FreeCurrent().. note,
-    // if when called by user we are in this state,
-    // it means the user called FreeCurrent().
-    kFileStart,        // [state we only use internally]           no         yes
-  } state_;
- private:
-};
-
-
-// This is the implementation for SequentialTableReader
-// when it's an archive.  Note that the archive format is:
-// key1 [space] object1 key2 [space]
-// object2 ... eof.
-// "object1" is the output of the Holder::Write function and will
-// typically contain a binary header (in binary mode) and then
-// the output of object.Write(os, binary).
-// The archive itself does not care whether it is in binary
-// or text mode, for reading purposes.
-
-template<class Holder>  class SequentialTableReaderArchiveImpl:
-      public SequentialTableReaderImplBase<Holder> {
- public:
-  typedef typename Holder::T T;
-
-  SequentialTableReaderArchiveImpl(): state_(kUninitialized) { }
-
-  virtual bool Open(const std::string &rspecifier) {
-    if (state_ != kUninitialized) {
-      if (! Close()) {  // call Close() yourself to suppress this exception.
-        if (opts_.permissive)
-          KALDI_WARN << "TableReader::Open, error closing previous input "
-              "(only warning, since permissive mode).";
-        else
-          KALDI_ERR << "TableReader::Open, error closing previous input.";
-      }
-    }
-    rspecifier_ = rspecifier;
-    RspecifierType rs = ClassifyRspecifier(rspecifier,
-                                           &archive_rxfilename_,
-                                           &opts_);
-    KALDI_ASSERT(rs == kArchiveRspecifier);
-
-    bool ans;
-    // NULL means don't expect binary-mode header
-    if (Holder::IsReadInBinary())
-      ans = input_.Open(archive_rxfilename_, NULL);
-    else
-      ans = input_.OpenTextMode(archive_rxfilename_);
-    if (!ans) {  // header.
-      KALDI_WARN << "TableReader: failed to open stream "
-                 << PrintableRxfilename(archive_rxfilename_);
-      state_ = kUninitialized;  // Failure on Open
-      return false;  // User should print the error message.
-    }
-    state_ = kFileStart;
-    Next();
-    if (state_ == kError) {
-      KALDI_WARN << "Error beginning to read archive file (wrong filename?): "
-                 << PrintableRxfilename(archive_rxfilename_);
-      input_.Close();
-      state_ = kUninitialized;
-      return false;
-    }
-    KALDI_ASSERT(state_ == kHaveObject || state_ == kEof);
-    return true;
-  }
-
-  virtual void Next() {
-    switch (state_) {
-      case kHaveObject:
-        holder_.Clear(); break;
-      case kFileStart: case kFreedObject:
-        break;
-      default:
-        KALDI_ERR << "TableReader: Next() called wrongly.";
-    }
-    std::istream &is = input_.Stream();
-    is.clear();  // Clear any fail bits that may have been set... just in case
-    // this happened in the Read function.
-    is >> key_;  // This eats up any leading whitespace and gets the string.
-    if (is.eof()) {
-      state_ = kEof;
-      return;
-    }
-    if (is.fail()) {  // This shouldn't really happen, barring file-system errors.
-      KALDI_WARN << "Error reading archive "
-                 << PrintableRxfilename(archive_rxfilename_);
-      state_ = kError;
-      return;
-    }
-    int c;
-    if ((c = is.peek()) != ' ' && c != '\t' && c != '\n') {  // We expect a space ' ' after the key.
-      // We also allow tab [which is consumed] and newline [which is not], just
-      // so we can read archives generated by scripts that may not be fully
-      // aware of how this format works.
-      KALDI_WARN << "Invalid archive file format: expected space after key "
-                 << key_ << ", got character "
-                 << CharToString(static_cast<char>(is.peek())) << ", reading "
-                 << PrintableRxfilename(archive_rxfilename_);
-      state_ = kError;
-      return;
-    }
-    if (c != '\n') is.get();  // Consume the space or tab.
-    if (holder_.Read(is)) {
-      state_ = kHaveObject;
-      return;
-    } else {
-      KALDI_WARN << "Object read failed, reading archive "
-                 << PrintableRxfilename(archive_rxfilename_);
-      state_ = kError;
-      return;
-    }
-  }
-
-  virtual bool IsOpen() const {
-    switch (state_) {
-      case kEof: case kError: case kHaveObject: case kFreedObject: return true;
-      case kUninitialized: return false;
-      default: KALDI_ERR << "IsOpen() called on invalid object.";  // kFileStart is not valid
-        // state for user to call something on.
-        return false;
-    }
-  }
-
-  virtual bool Done() const {
-    switch (state_) {
-      case kHaveObject:
-        return false;
-      case kEof: case kError:
-        return true;  // Error-state counts as Done(), but destructor
-        // will fail (unless you check the status with Close()).
-      default:
-        KALDI_ERR << "Done() called on TableReader object at the wrong time.";
-        return false;
-    }
-  }
-
-  virtual std::string Key() {
-    // Valid to call this whenever Done() returns false
-    switch (state_) {
-      case kHaveObject: break;  // only valid case.
-      default:
-        // coding error.
-        KALDI_ERR << "Key() called on TableReader object at the wrong time.";
-    }
-    return key_;
-  }
-  const T &Value() {
-    switch (state_) {
-      case kHaveObject:
-        break;  // only valid case.
-      default:
-        // coding error.
-        KALDI_ERR << "Value() called on TableReader object at the wrong time.";
-    }
-    return holder_.Value();
-  }
-  virtual void FreeCurrent() {
-    if (state_ == kHaveObject) {
-      holder_.Clear();
-      state_ = kFreedObject;
-    } else
-      KALDI_WARN << "TableReader: FreeCurernt called at the wrong time.";
-  }
-
-  virtual bool Close() {
-    if (! this->IsOpen())
-      KALDI_ERR << "Close() called on TableReader twice or otherwise wrongly.";
-    if (input_.IsOpen())
-      input_.Close();
-    if (state_ == kHaveObject)
-      holder_.Clear();
-    bool ans;
-    if (opts_.permissive) {
-      ans = true;  // always return success.
-      if (state_ == kError)
-        KALDI_WARN << "Error detected closing TableReader for archive "
-                   << PrintableRxfilename(archive_rxfilename_) << " but ignoring "
-                   << "it as permissive mode specified.";
-    } else
-      ans = (state_ != kError);  // If error state, user should detect it.
-    state_ = kUninitialized;
-    return ans;
-  }
-
-  virtual ~SequentialTableReaderArchiveImpl() {
-    if (state_ == kError) {
-      if (opts_.permissive)
-        KALDI_WARN << "Error detected closing TableReader for archive "
-                   << PrintableRxfilename(archive_rxfilename_) << " but ignoring "
-                   << "it as permissive mode specified.";
-      else
-        KALDI_ERR << "TableReader: error detected closing archive "
-                  << PrintableRxfilename(archive_rxfilename_);
-    }
-    // If you don't want this exception to be thrown you can
-    // call Close() and check the status.
-    if (state_ == kHaveObject)
-      holder_.Clear();
-  }
- private:
-  Input input_;  // Input object for the archive
-  Holder holder_;     // Holds the object.
-  std::string key_;
-  std::string rspecifier_;
-  std::string archive_rxfilename_;
-  RspecifierOptions opts_;
-  enum {  //  [The state of the reading process]               [does holder_ [is input_
-    //                                                         have object]   open]
-    kUninitialized,  // Uninitialized or closed.                    no         no
-    kFileStart,      // [state we use internally: just opened.]    no         yes
-    kEof,     // We did Next() and found eof in archive            no         no
-    kError,   // Some other error                                  no         no
-    kHaveObject,  // We read the key and the object after it.       yes        yes
-    kFreedObject,  // The user called FreeCurrent().                no         yes
-  } state_;
-};
-
-
-template<class Holder>
-SequentialTableReader<Holder>::SequentialTableReader(const std::string &rspecifier): impl_(NULL) {
-  if (rspecifier != "" && !Open(rspecifier))
-    KALDI_ERR << "Error constructing TableReader: rspecifier is " << rspecifier;
-}
-
-template<class Holder>
-bool SequentialTableReader<Holder>::Open(const std::string &rspecifier) {
-  if (IsOpen())
-    if (!Close())
-      KALDI_ERR << "Could not close previously open object.";
-  // now impl_ will be NULL.
-
-  RspecifierType wt = ClassifyRspecifier(rspecifier, NULL, NULL);
-  switch (wt) {
-    case kArchiveRspecifier:
-      impl_ = new SequentialTableReaderArchiveImpl<Holder>();
-      break;
-    case kScriptRspecifier:
-      impl_ = new SequentialTableReaderScriptImpl<Holder>();
-      break;
-    case kNoRspecifier: default:
-      KALDI_WARN << "Invalid rspecifier " << rspecifier;
-      return false;
-  }
-  if (!impl_->Open(rspecifier)) {
-    delete impl_;
-    impl_ = NULL;
-    return false;  // sub-object will have printed warnings.
-  }
-  else return true;
-}
-
-template<class Holder>
-bool SequentialTableReader<Holder>::Close() {
-  CheckImpl();  
-  bool ans = impl_->Close();
-  delete impl_;  // We don't keep around empty impl_ objects.
-  impl_ = NULL;
-  return ans;
-}
-
-
-template<class Holder>
-bool SequentialTableReader<Holder>::IsOpen() const {
-  return (impl_ != NULL);  // Because we delete the object whenever
-  // that object is not open.  Thus, the IsOpen functions of the
-  // Impl objects are not really needed.
-}
-
-template<class Holder>
-std::string SequentialTableReader<Holder>::Key() {
-  CheckImpl();
-  return impl_->Key();  // this call may throw if called wrongly in other ways,
-  // e.g. eof.
-}
-
-
-template<class Holder>
-void SequentialTableReader<Holder>::FreeCurrent() {
-  CheckImpl();
-  impl_->FreeCurrent();
-}
-
-
-template<class Holder>
-const typename SequentialTableReader<Holder>::T &
-SequentialTableReader<Holder>::Value() {
-  CheckImpl();
-  return impl_->Value();  // This may throw (if LoadCurrent() returned false you are safe.).
-}
-
-
-template<class Holder>
-void SequentialTableReader<Holder>::Next() {
-  CheckImpl();
-  impl_->Next();
-}
-
-template<class Holder>
-bool SequentialTableReader<Holder>::Done() {
-  CheckImpl();
-  return impl_->Done();
-}
-
-
-template<class Holder>
-SequentialTableReader<Holder>::~SequentialTableReader() {
-  if (impl_)  delete impl_;
-  // Destructor of impl_ may throw.
-}
-
-
-
-template<class Holder> class TableWriterImplBase {
- public:
-  typedef typename Holder::T T;
-
-  virtual bool Open(const std::string &wspecifier) = 0;
-
-  // Write returns true on success, false on failure, but
-  // some errors may not be detected until we call Close().
-  // It throws (via KALDI_ERR) if called wrongly.  We could
-  // have just thrown on all errors, since this is what
-  // TableWriter does; it was designed this way because originally
-  // TableWriter::Write returned an exit status.
-  virtual bool Write(const std::string &key, const T &value) = 0;
-
-  // Flush will flush any archive; it does not return error status,
-  //  any errors will be reported on the next Write or Close.
-  virtual void Flush() = 0;
-
-  virtual bool Close() = 0;
-
-  virtual bool IsOpen() const = 0;
-
-  // May throw on write error if Close was not called.
-  virtual ~TableWriterImplBase() { }
-
-  TableWriterImplBase() { }
- private:
-  KALDI_DISALLOW_COPY_AND_ASSIGN(TableWriterImplBase);
-};
-
-
-// The implementation of TableWriter we use when writing directly
-// to an archive with no associated scp.
-template<class Holder>
-class TableWriterArchiveImpl: public TableWriterImplBase<Holder> {
- public:
-  typedef typename Holder::T T;
-
-  virtual bool Open(const std::string &wspecifier) {
-    switch (state_) {
-      case kUninitialized:
-        break;
-      case kWriteError:
-        KALDI_ERR << "TableWriter: opening stream, already open with write error.";
-      case kOpen: default:
-        if (!Close())  // throw because this error may not have been previously
-          // detected by the user.
-          KALDI_ERR << "TableWriter: opening stream, error closing previously open stream.";
-    }
-    wspecifier_ = wspecifier;
-    WspecifierType ws = ClassifyWspecifier(wspecifier,
-                                           &archive_wxfilename_,
-                                           NULL,
-                                           &opts_);
-    KALDI_ASSERT(ws == kArchiveWspecifier);  // or wrongly called.
-
-    if (output_.Open(archive_wxfilename_, opts_.binary, false)) {  // false means no binary header.
-      state_ = kOpen;
-      return true;
-    } else {
-      // stream will not be open.  User will report this error
-      // (we return bool), so don't bother printing anything.
-      state_ = kUninitialized;
-      return false;
-    }
-  }
-
-  virtual bool IsOpen() const {
-    switch (state_) {
-      case kUninitialized: return false;
-      case kOpen: case kWriteError: return true;
-      default: KALDI_ERR << "IsOpen() called on TableWriter in invalid state.";
-    }
-    return false;
-  }
-
-  // Write returns true on success, false on failure, but
-  // some errors may not be detected till we call Close().
-  virtual bool Write(const std::string &key, const T &value) {
-    switch (state_) {
-      case kOpen: break;
-      case kWriteError:
-        // user should have known from the last
-        // call to Write that there was a problem.
-        KALDI_WARN << "TableWriter: attempting to write to invalid stream.";
-        return false;
-      case kUninitialized: default:
-        KALDI_ERR << "TableWriter: Write called on invalid stream";
-
-    }
-    // state is now kOpen or kWriteError.
-    if (!IsToken(key)) // e.g. empty string or has spaces...
-      KALDI_ERR << "TableWriter: using invalid key " << key;
-    output_.Stream() << key << ' ';
-    if (!Holder::Write(output_.Stream(), opts_.binary, value)) {
-      KALDI_WARN << "TableWriter: write failure to "
-                 << PrintableWxfilename(archive_wxfilename_);
-      state_ = kWriteError;
-      return false;
-    }
-    if (state_ == kWriteError) return false;  // Even if this Write seems to have
-    // succeeded, we fail because a previous Write failed and the archive may be
-    // corrupted and unreadable.
-
-    if (opts_.flush)
-      Flush();
-    return true;
-  }
-
-  // Flush will flush any archive; it does not return error status,
-  //  any errors will be reported on the next Write or Close.
-  virtual void Flush() {
-    switch (state_) {
-      case kWriteError: case kOpen:
-        output_.Stream().flush();  // Don't check error status.
-        return;
-      default:
-        KALDI_WARN << "TableWriter: Flush called on not-open writer.";
-    }
-  }
-
-  virtual bool Close() {
-    if (!this->IsOpen() || !output_.IsOpen())
-      KALDI_ERR << "TableWriter: Close called on a stream that was not open." << this->IsOpen() << ", " << output_.IsOpen();
-    bool close_success = output_.Close();
-    if (!close_success) {
-      KALDI_WARN << "TableWriter: error closing stream: wspecifier is "
-                 << wspecifier_;
-      state_ = kUninitialized;
-      return false;
-    }
-    if (state_ == kWriteError) {
-      KALDI_WARN << "TableWriter: closing writer in error state: wspecifier is "
-                 << wspecifier_;
-      state_ = kUninitialized;
-      return false;
-    }
-    state_ = kUninitialized;
-    return true;
-  }
-
-  TableWriterArchiveImpl(): state_(kUninitialized) {}
-
-  // May throw on write error if Close was not called.
-  virtual ~TableWriterArchiveImpl() {
-    if (!IsOpen()) return;
-    else if (!Close())
-      KALDI_ERR << "At TableWriter destructor: Write failed or stream close "
-                << "failed: wspecifier is "<<  wspecifier_;
-  }
-
- private:
-  Output output_;
-  WspecifierOptions opts_;
-  std::string wspecifier_;
-  std::string archive_wxfilename_;
-  enum {               // is stream open?
-    kUninitialized,    // no
-    kOpen,             // yes
-    kWriteError,       // yes
-  } state_;
-};
-
-
-
-
-// The implementation of TableWriter we use when writing to
-// individual files (more generally, wxfilenames) specified
-// in an scp file that we read.
-
-// Note: the code for this class is similar to RandomAccessTableReaderScriptImpl;
-// try to keep them in sync.
-
-template<class Holder>
-class TableWriterScriptImpl: public TableWriterImplBase<Holder> {
- public:
-  typedef typename Holder::T T;
-
-  TableWriterScriptImpl(): last_found_(0), state_(kUninitialized) {}
-
-  virtual bool Open(const std::string &wspecifier) {
-    switch (state_) {
-      case kReadScript:
-        KALDI_ERR << " Opening already open TableWriter: call Close first.";
-      case kUninitialized: case kNotReadScript:
-        break;
-    }
-    wspecifier_ = wspecifier;
-    WspecifierType ws = ClassifyWspecifier(wspecifier,
-                                           NULL,
-                                           &script_rxfilename_,
-                                           &opts_);
-    KALDI_ASSERT(ws == kScriptWspecifier);  // or wrongly called.
-    KALDI_ASSERT(script_.empty());  // no way it could be nonempty at this point.
-
-    if (! ReadScriptFile(script_rxfilename_,
-                         true,  // print any warnings
-                         &script_)) {  // error reading script file or invalid format
-      state_ = kNotReadScript;
-      return false;  // no need to print further warnings.  user gets the error.
-    }
-    std::sort(script_.begin(), script_.end());
-    for (size_t i = 0; i+1 < script_.size(); i++) {
-      if (script_[i].first.compare(script_[i+1].first) >= 0) {
-        // script[i] not < script[i+1] in lexical order...
-        KALDI_WARN << "Script file " << PrintableRxfilename(script_rxfilename_)
-                   << " contains duplicate key " << script_[i].first;
-        state_ = kNotReadScript;
-        return false;
-      }
-    }
-    state_ = kReadScript;
-    return true;
-  }
-
-  virtual bool IsOpen() const {  return (state_ == kReadScript);  }
-
-  virtual bool Close() {
-    if (!IsOpen())
-      KALDI_ERR << "Close() called on TableWriter that was not open.";
-    state_ = kUninitialized;
-    last_found_ = 0;
-    script_.clear();
-    return true;
-  }
-
-  // Write returns true on success, false on failure, but
-  // some errors may not be detected till we call Close().
-  virtual bool Write(const std::string &key, const T &value) {
-    if (!IsOpen())
-      KALDI_ERR << "TableWriter: Write called on invalid stream";
-
-    if (!IsToken(key)) // e.g. empty string or has spaces...
-      KALDI_ERR << "TableWriter: using invalid key " << key;
-
-    std::string wxfilename;
-    if (!LookupFilename(key, &wxfilename)) {
-      if (opts_.permissive) {
-        return true; // In permissive mode, it's as if we're writing to /dev/null
-                     // for missing keys.
-      } else {
-        KALDI_WARN << "TableWriter: script file "
-                   << PrintableRxfilename(script_rxfilename_)
-                   << " has no entry for key "<<key;
-        return false;
-      }
-    }
-    Output output;
-    if (!output.Open(wxfilename, opts_.binary, false)) {
-      // Open in the text/binary mode (on Windows) given by member var. "binary"
-      // (obtained from wspecifier), but do not put the binary-mode header (it
-      // will be written, if needed, by the Holder::Write function.)
-      KALDI_WARN << "TableWriter: failed to open stream: "
-                 << PrintableWxfilename(wxfilename);
-      return false;
-    }
-    if (!Holder::Write(output.Stream(), opts_.binary, value)
-        || !output.Close()) {
-      KALDI_WARN << "TableWriter: failed to write data to "
-                 << PrintableWxfilename(wxfilename);
-      return false;
-    }
-    return true;
-  }
-
-  // Flush does nothing in this implementation, there is nothing to flush.
-  virtual void Flush() { }
-
-
-  virtual ~TableWriterScriptImpl() {
-    // Nothing to do in destructor.
-  }
-
- private:
-  // Note: this function is almost the same as in RandomAccessTableReaderScriptImpl.
-  bool LookupFilename(const std::string &key, std::string *wxfilename) {
-    // First, an optimization: if we're going consecutively, this will
-    // make the lookup very fast.
-    last_found_++;
-    if (last_found_ < script_.size() && script_[last_found_].first == key) {
-      *wxfilename = script_[last_found_].second;
-      return true;
-    }
-    std::pair<std::string, std::string> pr(key, "");  // Important that ""
-    // compares less than or equal to any string, so lower_bound points to the
-    // element that has the same key.
-    typedef typename std::vector<std::pair<std::string, std::string> >::const_iterator 
-        IterType;
-    IterType iter = std::lower_bound(script_.begin(), script_.end(), pr);
-    if (iter != script_.end() && iter->first == key) {
-      last_found_ = iter - script_.begin();
-      *wxfilename = iter->second;
-      return true;
-    } else {
-      return false;
-    }
-  }
-
-
-  WspecifierOptions opts_;
-  std::string wspecifier_;
-  std::string script_rxfilename_;
-
-  // the script_ variable contains pairs of (key, filename), sorted using
-  // std::sort.  This can be used with binary_search to look up filenames for
-  // writing.  If this becomes inefficient we can use std::unordered_map (but I
-  // suspect this wouldn't be significantly faster & would use more memory).
-  // If memory becomes a problem here, the user should probably be passing
-  // only the relevant part of the scp file rather than expecting us to get too
-  // clever in the code.
-  std::vector<std::pair<std::string, std::string> > script_;
-  size_t last_found_;  // This is for an optimization used in LookupFilename.
-
-  enum {
-    kUninitialized,
-    kReadScript,
-    kNotReadScript,  // read of script failed.
-  } state_;
-};
-
-
-// The implementation of TableWriter we use when writing directly
-// to an archive plus an associated scp.
-template<class Holder>
-class TableWriterBothImpl: public TableWriterImplBase<Holder> {
- public:
-  typedef typename Holder::T T;
-
-  virtual bool Open(const std::string &wspecifier) {
-    switch (state_) {
-      case kUninitialized:
-        break;
-      case kWriteError:
-        KALDI_ERR << "TableWriter: opening stream, already open with write error.";
-      case kOpen: default:
-        if (!Close())  // throw because this error may not have been previously detected by user.
-          KALDI_ERR << "TableWriter: opening stream, error closing previously open stream.";
-    }
-    wspecifier_ = wspecifier;
-    WspecifierType ws = ClassifyWspecifier(wspecifier,
-                                           &archive_wxfilename_,
-                                           &script_wxfilename_,
-                                           &opts_);
-    KALDI_ASSERT(ws == kBothWspecifier);  // or wrongly called.
-    if (ClassifyWxfilename(archive_wxfilename_) != kFileOutput)
-      KALDI_WARN << "When writing to both archive and script, the script file "
-          "will generally not be interpreted correctly unless the archive is "
-          "an actual file: wspecifier = " << wspecifier;
-
-    if (!archive_output_.Open(archive_wxfilename_, opts_.binary, false)) {  // false means no binary header.
-      state_ = kUninitialized;
-      return false;
-    }
-    if (!script_output_.Open(script_wxfilename_, false, false)) {  // first false means text mode:
-      // script files always text-mode.   second false means don't write header (doesn't matter
-      // for text mode).
-      archive_output_.Close();  // Don't care about status: error anyway.
-      state_ = kUninitialized;
-      return false;
-    }
-    state_ = kOpen;
-    return true;
-  }
-
-  virtual bool IsOpen() const {
-    switch (state_) {
-      case kUninitialized: return false;
-      case kOpen: case kWriteError: return true;
-      default: KALDI_ERR << "IsOpen() called on TableWriter in invalid state.";
-    }
-    return false;
-  }
-
-  void MakeFilename(typename std::ostream::pos_type streampos, std::string *output) const {
-    std::ostringstream ss;
-    ss << ':' << streampos;
-    KALDI_ASSERT(ss.str() != ":-1");
-    *output = archive_wxfilename_ + ss.str();
-    
-    // e.g. /some/file:12302.
-    // Note that we warned if archive_wxfilename_ is not an actual filename;
-    // the philosophy is we give the user rope and if they want to hang
-    // themselves, with it, fine.
-  }
-
-  // Write returns true on success, false on failure, but
-  // some errors may not be detected till we call Close().
-  virtual bool Write(const std::string &key, const T &value) {
-    switch (state_) {
-      case kOpen: break;
-      case kWriteError:
-        // user should have known from the last
-        // call to Write that there was a problem.  Warn about it.
-        KALDI_WARN << "TableWriter: writing to non-open TableWriter object.";
-        return false;
-      case kUninitialized: default:
-        KALDI_ERR << "TableWriter: Write called on invalid stream";
-    }
-    // state is now kOpen or kWriteError.
-    if (!IsToken(key)) // e.g. empty string or has spaces...
-      KALDI_ERR << "TableWriter: using invalid key " << key;
-    std::ostream &archive_os = archive_output_.Stream();
-    archive_os << key << ' ';
-    typename std::ostream::pos_type archive_os_pos = archive_os.tellp();
-    // position at start of Write() to archive.  We will record this in the script file.
-    std::string offset_rxfilename;  // rxfilename with offset into the archive,
-    // e.g. some_archive_name.ark:431541423
-    MakeFilename(archive_os_pos, &offset_rxfilename);
-
-    // Write to the script file first.
-    // The idea is that we want to get all the information possible into the
-    // script file, to make it easier to unwind errors later.
-    std::ostream &script_os = script_output_.Stream();
-    script_output_.Stream() << key << ' ' << offset_rxfilename << '\n';
-
-    if (!Holder::Write(archive_output_.Stream(), opts_.binary, value)) {
-      KALDI_WARN << "TableWriter: write failure to"
-                 << PrintableWxfilename(archive_wxfilename_);
-      state_ = kWriteError;
-      return false;
-    }
-
-    if (script_os.fail()) {
-      KALDI_WARN << "TableWriter: write failure to script file detected: "
-                 << PrintableWxfilename(script_wxfilename_);
-      state_ = kWriteError;
-      return false;
-    }
-
-    if (archive_os.fail()) {
-      KALDI_WARN << "TableWriter: write failure to archive file detected: "
-                 << PrintableWxfilename(archive_wxfilename_);
-      state_ = kWriteError;
-      return false;
-    }
-
-    if (state_ == kWriteError) return false;  // Even if this Write seems to have
-    // succeeded, we fail because a previous Write failed and the archive may be
-    // corrupted and unreadable.
-
-    if (opts_.flush)
-      Flush();
-    return true;
-  }
-
-  // Flush will flush any archive; it does not return error status,
-  //  any errors will be reported on the next Write or Close.
-  virtual void Flush() {
-    switch (state_) {
-      case kWriteError: case kOpen:
-        archive_output_.Stream().flush();  // Don't check error status.
-        script_output_.Stream().flush();  // Don't check error status.
-        return;
-      default:
-        KALDI_WARN << "TableWriter: Flush called on not-open writer.";
-    }
-  }
-
-  virtual bool Close() {
-    if (!this->IsOpen())
-      KALDI_ERR << "TableWriter: Close called on a stream that was not open.";
-    bool close_success = true;
-    if (archive_output_.IsOpen())
-      if (!archive_output_.Close()) close_success = false;
-    if (script_output_.IsOpen())
-      if (!script_output_.Close()) close_success = false;
-    bool ans = close_success && (state_ != kWriteError);
-    state_ = kUninitialized;
-    return ans;
-  }
-
-  TableWriterBothImpl(): state_(kUninitialized) {}
-
-  // May throw on write error if Close() was not called.
-  // User can get the error status by calling Close().
-  virtual ~TableWriterBothImpl() {
-    if (!IsOpen()) return;
-    else if (!Close())
-      KALDI_ERR << "At TableWriter destructor: Write failed or stream close failed: "
-                << wspecifier_;
-  }
-
- private:
-  Output archive_output_;
-  Output script_output_;
-  WspecifierOptions opts_;
-  std::string archive_wxfilename_;
-  std::string script_wxfilename_;
-  std::string wspecifier_;
-  enum {               // is stream open?
-    kUninitialized,    // no
-    kOpen,             // yes
-    kWriteError,       // yes
-  } state_;
-};
-
-
-template<class Holder>
-TableWriter<Holder>::TableWriter(const std::string &wspecifier): impl_(NULL) {
-  if (wspecifier != "" && !Open(wspecifier)) {
-    KALDI_ERR << "TableWriter: failed to write to "
-              << wspecifier;
-  }
-}
-
-template<class Holder>
-bool TableWriter<Holder>::IsOpen() const {
-  return (impl_ != NULL);
-}
-
-
-template<class Holder>
-bool TableWriter<Holder>::Open(const std::string &wspecifier) {
-
-  if (IsOpen()) {
-    if (!Close()) // call Close() yourself to suppress this exception.
-      KALDI_ERR << "TableWriter::Open, failed to close previously open writer.";
-  }
-  KALDI_ASSERT(impl_ == NULL);
-  WspecifierType wtype = ClassifyWspecifier(wspecifier, NULL, NULL, NULL);
-  switch (wtype) {
-    case kBothWspecifier:
-      impl_ = new TableWriterBothImpl<Holder>();
-      break;
-    case kArchiveWspecifier:
-      impl_ = new TableWriterArchiveImpl<Holder>();
-      break;
-    case kScriptWspecifier:
-      impl_ = new TableWriterScriptImpl<Holder>();
-      break;
-    case kNoWspecifier: default:
-      KALDI_WARN << "ClassifyWspecifier: invalid wspecifier " << wspecifier;
-      return false;
-  }
-  if (impl_->Open(wspecifier)) return true;
-  else {  // The class will have printed a more specific warning.
-    delete impl_;
-    impl_ = NULL;
-    return false;
-  }
-}
-
-template<class Holder>
-void TableWriter<Holder>::Write(const std::string &key,
-                                const T &value) const {
-  CheckImpl();
-  if (!impl_->Write(key, value))
-    KALDI_ERR << "Error in TableWriter::Write";
-  // More specific warning will have
-  // been printed in the Write function.
-}
-
-template<class Holder>
-void TableWriter<Holder>::Flush() {
-  CheckImpl();
-  impl_->Flush();
-}
-
-template<class Holder>
-bool TableWriter<Holder>::Close() {
-  CheckImpl();
-  bool ans = impl_->Close();
-  delete impl_;  // We don't keep around non-open impl_ objects [c.f. definition of IsOpen()]
-  impl_ = NULL;
-  return ans;
-}
-
-template<class Holder>
-TableWriter<Holder>::~TableWriter() {
-  if (IsOpen() && !Close()) {
-    KALDI_ERR << "Error closing TableWriter [in destructor].";
-  }
-}
-
-
-// Types of RandomAccessTableReader:
-// In principle, we would like to have four types of RandomAccessTableReader:
-//  the 4 combinations  [scp, archive], [seekable, not-seekable],
-// where if something is seekable we only store a file offset.  However,
-// it seems sufficient for now to only implement two of these, in both
-// cases assuming it's not seekable so we never store file offsets and always
-// store either the scp line or the data in the archive.  The reasons are:
-// (1)
-// For scp files, storing the actual entry is not that much more expensive
-// than storing the file offsets (since the entries are just filenames), and
-// avoids a lot of fseek operations that might be expensive.
-// (2)
-// For archive files, there is no real reason, if you have the archive file
-// on disk somewhere, why you wouldn't access it via its associated scp.
-// [i.e. write it as ark, scp].  The main reason to read archives directly
-// is if they are part of a pipe, and in this case it's not seekable, so
-// we implement only this case.
-//
-// Note that we will rarely in practice have to keep in memory everything in
-// the archive, as long as things are only read once from the archive (the
-// "o, " or "once" option) and as long as we keep our keys in sorted order; to take
-// advantage of this we need the "s, " (sorted) option, so we would read archives
-// as e.g. "s, o, ark:-" (this is the rspecifier we would use if it was the
-// standard input and these conditions held).
-
-template<class Holder> class RandomAccessTableReaderImplBase {
- public:
-  typedef typename Holder::T T;
-
-  virtual bool Open(const std::string &rspecifier) = 0;
-
-  virtual bool HasKey(const std::string &key) = 0;
-
-  virtual const T &Value(const std::string &key) = 0;
-
-  virtual bool Close() = 0;
-
-  virtual ~RandomAccessTableReaderImplBase() {}
-};
-
-
-// Implementation of RandomAccessTableReader for a script file; for simplicity we
-// just read it in all in one go, as it's unlikely someone would generate this
-// from a pipe.  In principle we could read it on-demand as for the archives, but
-// this would probably be overkill.
-
-// Note: the code for this this class is similar to TableWriterScriptImpl:
-// try to keep them in sync.
-template<class Holder>
-class RandomAccessTableReaderScriptImpl:
-      public RandomAccessTableReaderImplBase<Holder> {
-
- public:
-  typedef typename Holder::T T;
-
-  RandomAccessTableReaderScriptImpl(): last_found_(0), state_(kUninitialized) {}
-
-  virtual bool Open(const std::string &rspecifier) {
-    switch (state_) {
-      case kNotHaveObject: case kHaveObject: case kGaveObject:
-        KALDI_ERR << " Opening already open RandomAccessTableReader: call Close first.";
-      case kUninitialized: case kNotReadScript:
-        break;
-    }
-    rspecifier_ = rspecifier;
-    RspecifierType rs = ClassifyRspecifier(rspecifier,
-                                           &script_rxfilename_,
-                                           &opts_);
-    KALDI_ASSERT(rs == kScriptRspecifier);  // or wrongly called.
-    KALDI_ASSERT(script_.empty());  // no way it could be nonempty at this point.
-
-    if (! ReadScriptFile(script_rxfilename_,
-                        true,  // print any warnings
-                        &script_)) {  // error reading script file or invalid format
-      state_ = kNotReadScript;
-      return false;  // no need to print further warnings.  user gets the error.
-    }
-
-    rspecifier_ = rspecifier;
-    // If opts_.sorted, the user has asserted that the keys are already sorted.
-    // Although we could easily sort them, we want to let the user know of this
-    // mistake.  This same mistake could have serious effects if used with an
-    // archive rather than a script.
-    if (!opts_.sorted)
-      std::sort(script_.begin(), script_.end());
-    for (size_t i = 0; i+1 < script_.size(); i++) {
-      if (script_[i].first.compare(script_[i+1].first) >= 0) {
-        // script[i] not < script[i+1] in lexical order...
-        bool same = (script_[i].first == script_[i+1].first);
-        KALDI_WARN << "Script file " << PrintableRxfilename(script_rxfilename_)
-                   << (same ? " contains duplicate key: " :
-                       " is not sorted (remove s, option or add ns, option): key is ")
-                   << script_[i].first;
-        state_ = kNotReadScript;
-        return false;
-      }
-    }
-    state_ = kNotHaveObject;
-    return true;
-  }
-
-  virtual bool IsOpen() const {
-    return  (state_ == kNotHaveObject || state_ == kHaveObject ||
-             state_ == kGaveObject);
-  }
-
-  virtual bool Close() {
-    if (!IsOpen())
-      KALDI_ERR << "Close() called on RandomAccessTableReader that was not open.";
-    holder_.Clear();
-    state_ = kUninitialized;
-    last_found_ = 0;
-    script_.clear();
-    current_key_ = "";
-    // This one cannot fail because any errors of a "global"
-    // nature would have been detected when we did Open().
-    // With archives it's different.
-    return true;
-  }
-
-  virtual bool HasKey(const std::string &key) {
-    bool preload = opts_.permissive;
-    // In permissive mode, we have to check that we can read
-    // the scp entry before we assert that the key is there.
-    return HasKeyInternal(key, preload);
-  }
-
-
-  // Write returns true on success, false on failure, but
-  // some errors may not be detected till we call Close().
-  virtual const T&  Value(const std::string &key) {
-
-    if (!IsOpen())
-      KALDI_ERR << "Value() called on non-open object.";
-
-    if (!((state_ == kHaveObject || state_ == kGaveObject)
-          && key == current_key_)) {  // Not already stored...
-      bool has_key = HasKeyInternal(key, true);  // preload.
-      if (!has_key)
-        KALDI_ERR << "Could not get item for key " << key
-                  << ", rspecifier is " << rspecifier_ << "[to ignore this, "
-                  << "add the p, (permissive) option to the rspecifier.";
-      KALDI_ASSERT(state_ == kHaveObject && key == current_key_);
-    }
-
-    if (state_ == kHaveObject) {
-      state_ = kGaveObject;
-      if (opts_.once) MakeTombstone(key);  // make sure that future lookups fail.
-      return holder_.Value();
-    } else {  // state_ == kGaveObject
-      if (opts_.once)
-        KALDI_ERR << "Value called twice for the same key and ,o (once) option "
-                  << "is used: rspecifier is " << rspecifier_;
-      return holder_.Value();
-    }
-  }
-
-  virtual ~RandomAccessTableReaderScriptImpl() {
-    if (state_ == kHaveObject || state_ == kGaveObject)
-      holder_.Clear();
-  }
-
- private:
-  // HasKeyInternal when called with preload == false just tells us whether the
-  // key is in the scp.  With preload == true, which happens when the ,p
-  // (permissive) option is given in the rspecifier, it will also check that we
-  // can preload the object from disk (loading from the rxfilename in the scp),
-  // and only return true if we can.  This function is called both from HasKey
-  // and from Value().
-  virtual bool HasKeyInternal(const std::string &key, bool preload) {
-    switch (state_) {
-      case kUninitialized: case kNotReadScript:
-        KALDI_ERR << "HasKey called on RandomAccessTableReader object that is not open.";
-      case kHaveObject: case kGaveObject:
-        if (key == current_key_)
-          return true;
-        break;
-      default: break;
-    }
-    KALDI_ASSERT(IsToken(key));
-    size_t key_pos = 0; // set to zero to suppress warning
-    bool ans = LookupKey(key, &key_pos);
-    if (!ans) return false;
-    else {
-      // First do a check regarding the "once" option.
-      if (opts_.once && script_[key_pos].second == "") {  // A "tombstone"; user is asking about
-        // already-read key.
-        KALDI_ERR << "HasKey called on key whose value was already read, and "
-            " you specified the \"once\" option (o, ): try removing o, or adding no, :"
-            " rspecifier is " << rspecifier_;
-      }
-      if (!preload)
-        return true;  // we have the key.
-      else {  // preload specified, so we have to pre-load the object before returning true.
-        if (!input_.Open(script_[key_pos].second)) {
-          KALDI_WARN << "Error opening stream "
-                     << PrintableRxfilename(script_[key_pos].second);
-          return false;
-        } else {
-          // Make sure holder empty.
-          if (state_ == kHaveObject || state_ == kGaveObject)
-            holder_.Clear();
-          if (holder_.Read(input_.Stream())) {
-            state_ = kHaveObject;
-            current_key_ = key;
-            return true;
-          } else {
-            KALDI_WARN << "Error reading object from "
-                "stream " << PrintableRxfilename(script_[key_pos].second);
-            state_ = kNotHaveObject;
-            return false;
-          }
-        }
-      }
-    }
-  }
-  void MakeTombstone(const std::string &key) {
-    size_t offset;
-    if (!LookupKey(key, &offset))
-      KALDI_ERR << "RandomAccessTableReader object in inconsistent state.";
-    else
-      script_[offset].second = "";
-  }
-  bool LookupKey(const std::string &key, size_t *script_offset) {
-    // First, an optimization: if we're going consecutively, this will
-    // make the lookup very fast.  Since we may call HasKey and then
-    // Value(), which both may look up the key, we test if either the
-    // current or next position are correct.
-    if (last_found_ < script_.size() && script_[last_found_].first == key) {
-      *script_offset = last_found_;
-      return true;
-    }
-    last_found_++;
-    if (last_found_ < script_.size() && script_[last_found_].first == key) {
-      *script_offset = last_found_;
-      return true;
-    }
-    std::pair<std::string, std::string> pr(key, "");  // Important that ""
-    // compares less than or equal to any string, so lower_bound points to the
-    // element that has the same key.
-    typedef typename std::vector<std::pair<std::string, std::string> >::const_iterator 
-        IterType;
-    IterType iter = std::lower_bound(script_.begin(), script_.end(), pr);
-    if (iter != script_.end() && iter->first == key) {
-      last_found_ = *script_offset = iter - script_.begin();
-      return true;
-    } else {
-      return false;
-    }
-  }
-
-
-  Input input_;  // Use the same input_ object for reading each file, in case
-  // the scp specifies offsets in an archive (so we can keep the same file open).
-  RspecifierOptions opts_;
-  std::string rspecifier_;  // rspecifier used to open it; used in debug messages
-  std::string script_rxfilename_;  // filename of script.
-
-  std::string current_key_;  // Key of object in holder_
-  Holder holder_;
-
-  // the script_ variable contains pairs of (key, filename), sorted using
-  // std::sort.  This can be used with binary_search to look up filenames for
-  // writing.  If this becomes inefficient we can use std::unordered_map (but I
-  // suspect this wouldn't be significantly faster & would use more memory).
-  // If memory becomes a problem here, the user should probably be passing
-  // only the relevant part of the scp file rather than expecting us to get too
-  // clever in the code.
-  std::vector<std::pair<std::string, std::string> > script_;
-  size_t last_found_;  // This is for an optimization used in FindFilename.
-
-  enum {  //           [Do we have          [Does holder_
-    //                script_ set up?]      contain object?]
-    kUninitialized,  //     no                     no
-    kNotReadScript,  //     no                     no
-    kNotHaveObject,  //     yes                    no
-    kHaveObject,   //     yes                    yes
-    kGaveObject,   //     yes                    yes
-    // [kGaveObject is as kHaveObject but we note that the
-    //  user has already read it; this is for checking that
-    // if "once" is specified, the user actually only reads
-    // it once.
-  } state_;
-
-};
-
-
-
-
-// This is the base-class (with some implemented functions) for the
-// implementations of RandomAccessTableReader when it's an archive.  This
-// base-class handles opening the files, storing the state of the reading
-// process, and loading objects.  This is the only case in which we have
-// an intermediate class in the hierarchy between the virtual ImplBase
-// class and the actual Impl classes.
-// The child classes vary in the assumptions regarding sorting, etc.
-
-template<class Holder>  class RandomAccessTableReaderArchiveImplBase:
-      public RandomAccessTableReaderImplBase<Holder> {
- public:
-  typedef typename Holder::T T;
-
-  RandomAccessTableReaderArchiveImplBase(): holder_(NULL), state_(kUninitialized) { }
-
-  virtual bool Open(const std::string &rspecifier) {
-    if (state_ != kUninitialized) {
-      if (! this->Close()) // call Close() yourself to suppress this exception.
-        KALDI_ERR << "TableReader::Open, error closing previous input.";
-    }
-    rspecifier_ = rspecifier;
-    RspecifierType rs = ClassifyRspecifier(rspecifier, &archive_rxfilename_,
-                                           &opts_);
-    KALDI_ASSERT(rs == kArchiveRspecifier);
-
-    // NULL means don't expect binary-mode header
-    bool ans;
-    if (Holder::IsReadInBinary())
-      ans = input_.Open(archive_rxfilename_, NULL);
-    else
-      ans = input_.OpenTextMode(archive_rxfilename_);
-    if (!ans) {  // header.
-      KALDI_WARN << "TableReader: failed to open stream "
-                 << PrintableRxfilename(archive_rxfilename_);
-      state_ = kUninitialized;  // Failure on Open
-      return false;  // User should print the error message.
-    } else {
-      state_ = kNoObject;
-    }
-    return true;
-  }
-
-  // ReadNextObject() requires that the state be kNoObject,
-  // and it will try read the next object.  If it succeeds,
-  // it sets the state to kHaveObject, and
-  // cur_key_ and holder_ have the key and value.  If it fails,
-  // it sets the state to kError or kEof.
-  void ReadNextObject() {
-    if (state_ != kNoObject)
-      KALDI_ERR << "TableReader: ReadNextObject() called from wrong state.";  // Code error
-    // somewhere in this class or a child class.
-    std::istream &is = input_.Stream();
-    is.clear();  // Clear any fail bits that may have been set... just in case
-    // this happened in the Read function.
-    is >> cur_key_;  // This eats up any leading whitespace and gets the string.
-    if (is.eof()) {
-      state_ = kEof;
-      return;
-    }
-    if (is.fail()) {  // This shouldn't really happen, barring file-system errors.
-      KALDI_WARN << "Error reading archive: rspecifier is " << rspecifier_;
-      state_ = kError;
-      return;
-    }
-    int c;
-    if ((c = is.peek()) != ' ' && c != '\t' && c != '\n') {  // We expect a space ' ' after the key.
-      // We also allow tab, just so we can read archives generated by scripts that may
-      // not be fully aware of how this format works.
-      KALDI_WARN << "Invalid archive file format: expected space after key " <<cur_key_
-                 <<", got character "
-                 << CharToString(static_cast<char>(is.peek())) << ", reading archive "
-                 << PrintableRxfilename(archive_rxfilename_);
-      state_ = kError;
-      return;
-    }
-    if (c != '\n') is.get();  // Consume the space or tab.
-    holder_ = new Holder;
-    if (holder_->Read(is)) {
-      state_ = kHaveObject;
-      return;
-    } else {
-      KALDI_WARN << "Object read failed, reading archive "
-                 << PrintableRxfilename(archive_rxfilename_);
-      state_ = kError;
-      delete holder_;
-      holder_ = NULL;
-      return;
-    }
-  }
-
-  virtual bool IsOpen() const {
-    switch (state_) {
-      case kEof: case kError: case kHaveObject: case kNoObject: return true;
-      case kUninitialized: return false;
-      default: KALDI_ERR << "IsOpen() called on invalid object.";
-        return false;
-    }
-  }
-
-  // Called by the child-class virutal Close() functions; does the
-  // shared parts of the cleanup.
-  bool CloseInternal() {
-    if (! this->IsOpen())
-      KALDI_ERR << "Close() called on TableReader twice or otherwise wrongly.";
-    if (input_.IsOpen())
-      input_.Close();
-    if (state_ == kHaveObject) {
-      KALDI_ASSERT(holder_ != NULL);
-      delete holder_;
-      holder_ = NULL;
-    } else KALDI_ASSERT(holder_ == NULL);
-    bool ans = (state_ != kError);
-    state_ = kUninitialized;
-    if (!ans && opts_.permissive) {
-      KALDI_WARN << "Error state detected closing reader.  "
-                 << "Ignoring it because you specified permissive mode.";
-      return true;
-    }
-    return ans;
-  }
-
-  ~RandomAccessTableReaderArchiveImplBase() {
-    // The child class has the responsibility to call CloseInternal().
-    KALDI_ASSERT(state_ == kUninitialized && holder_ == NULL);
-  }
- private:
-  Input input_;       // Input object for the archive
- protected:
-  // The variables below are accessed by child classes.
-
-  std::string cur_key_;   // current key (if state == kHaveObject).
-  Holder *holder_;     // Holds the object we just read (if state == kHaveObject)
-
-  std::string rspecifier_;
-  std::string archive_rxfilename_;
-  RspecifierOptions opts_;
-
-  enum {  //  [The state of the reading process]               [does holder_ [is input_
-    //                                                         have object]   open]
-    kUninitialized,  // Uninitialized or closed                     no         no
-    kNoObject,      // Do not have object in holder_               no         yes
-    kHaveObject,    // Have object in holder_                      yes        yes
-    kEof,           // End of file                                 no         yes
-    kError,         // Some kind of error-state in the reading.    no         yes
-  } state_;
-
-};
-
-
-// RandomAccessTableReaderDSortedArchiveImpl (DSorted for "doubly sorted") is the
-// implementation for random-access reading of archives when both the archive,
-// and the calling code, are in sorted order (i.e. we ask for the keys in sorted
-// order).  This is when the s and cs options are both given.  It only ever has
-// to keep one object in memory.  It inherits from
-// RandomAccessTableReaderArchiveImplBase which implements the common parts of
-// RandomAccessTableReader that are used when it's an archive we're reading from.
-
-template<class Holder>  class RandomAccessTableReaderDSortedArchiveImpl:
-      public RandomAccessTableReaderArchiveImplBase<Holder> {
-  using RandomAccessTableReaderArchiveImplBase<Holder>::kUninitialized;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::kHaveObject;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::kNoObject;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::kEof;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::kError;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::state_;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::opts_;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::cur_key_;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::holder_;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::rspecifier_;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::archive_rxfilename_;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::ReadNextObject;
- public:
-  typedef typename Holder::T T;
-
-  RandomAccessTableReaderDSortedArchiveImpl() { }
-
-  virtual bool Close() {
-    // We don't have anything additional to clean up, so just
-    // call generic base-class one.
-    return this->CloseInternal();
-  }
-
-  virtual bool HasKey(const std::string &key) {
-    return FindKeyInternal(key);
-  }
-  virtual const T & Value(const std::string &key) {
-    if (FindKeyInternal(key)) {
-      KALDI_ASSERT(this->state_ == kHaveObject && key == this->cur_key_
-                   && holder_ != NULL);
-      return this->holder_->Value();
-    } else {
-      KALDI_ERR << "Value() called but no such key " << key
-                << " in archive " << PrintableRxfilename(archive_rxfilename_);
-      return *(const T*)NULL;  // keep compiler happy.
-    }
-  }
-
-  virtual ~RandomAccessTableReaderDSortedArchiveImpl() {
-    if (this->IsOpen())
-      if (!Close()) // more specific warning will already have been printed.
-        // we are in some kind of error state & user did not find out by
-        // calling Close().
-        KALDI_ERR << "Error closing RandomAccessTableReader: rspecifier is "
-                  << rspecifier_;
-  }
- private:
-  // FindKeyInternal tries to find the key by calling "ReadNextObject()"
-  // as many times as necessary till we get to it.  It is called from
-  // both FindKey and Value().
-  bool FindKeyInternal(const std::string &key) {
-    // First check that the user is calling us right: should be
-    // in sorted order.  If not, error.
-    if (!last_requested_key_.empty()) {
-      if (key.compare(last_requested_key_) < 0) {  // key < last_requested_key_
-        KALDI_ERR << "You provided the \"cs\" option "
-                  << "but are not calling with keys in sorted order: "
-                  << key << " < " << last_requested_key_ << ": rspecifier is "
-                  << rspecifier_;
-      }
-    }
-    // last_requested_key_ is just for debugging of order of calling.
-    last_requested_key_ = key;
-
-    if (state_ == kNoObject)
-      ReadNextObject();  // This can only happen
-      // once, the first time someone calls HasKey() or Value().  We don't
-      // do it in the initializer to stop the program hanging too soon,
-      // if reading from a pipe.
-
-    if (state_ == kEof || state_ == kError) return false;
-
-    if (state_ == kUninitialized)
-      KALDI_ERR << "Trying to access a RandomAccessTableReader object that is not open.";
-
-    std::string last_key_;  // To check that
-    // the archive we're reading is in sorted order.
-    while (1) {
-      KALDI_ASSERT(state_ == kHaveObject);
-      int compare = key.compare(cur_key_);
-      if (compare == 0) {  // key == key_
-        return true;  // we got it..
-      } else if (compare < 0) {  // key < cur_key_, so we already read past the
-        // place where we want to be.  This implies that we will never find it
-        // [due to the sorting etc., this means it just isn't in the archive].
-        return false;
-      } else {  // compare > 0, key > cur_key_.  We need to read further ahead.
-        last_key_ = cur_key_;
-        // read next object.. we have to set state to kNoObject first.
-        KALDI_ASSERT(holder_ != NULL);
-        delete holder_;
-        holder_ = NULL;
-        state_ = kNoObject;
-        ReadNextObject();
-        if (state_ != kHaveObject)
-          return false;  // eof or read error.
-        if (cur_key_.compare(last_key_) <= 0) {
-          KALDI_ERR << "You provided the \"s\" option "
-                    << " (sorted order), but keys are out of order or duplicated: "
-                    << last_key_ << " is followed by " << cur_key_
-                    << ": rspecifier is " << rspecifier_;
-        }
-      }
-    }
-  }
-
-  /// Last string provided to HasKey() or Value();
-  std::string last_requested_key_;
-
-
-};
-
-// RandomAccessTableReaderSortedArchiveImpl is for random-access reading of
-// archives when the user specified the sorted (s) option but not the
-// called-sorted (cs) options.
-template<class Holder>  class RandomAccessTableReaderSortedArchiveImpl:
-      public RandomAccessTableReaderArchiveImplBase<Holder> {
-  using RandomAccessTableReaderArchiveImplBase<Holder>::kUninitialized;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::kHaveObject;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::kNoObject;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::kEof;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::kError;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::state_;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::opts_;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::cur_key_;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::holder_;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::rspecifier_;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::archive_rxfilename_;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::ReadNextObject;
-
- public:
-  typedef typename Holder::T T;
-
-  RandomAccessTableReaderSortedArchiveImpl():
-      last_found_index_(static_cast<size_t>(-1)),
-      pending_delete_(static_cast<size_t>(-1)) { }
-
-  virtual bool Close() {
-    for (size_t i = 0; i < seen_pairs_.size(); i++)
-      if (seen_pairs_[i].second)
-        delete seen_pairs_[i].second;
-    seen_pairs_.clear();
-
-    pending_delete_ = static_cast<size_t>(-1);
-    last_found_index_ = static_cast<size_t>(-1);
-
-    return this->CloseInternal();
-  }
-  virtual bool HasKey(const std::string &key) {
-    HandlePendingDelete();
-    size_t index;
-    bool ans = FindKeyInternal(key, &index);
-    if (ans && opts_.once && seen_pairs_[index].second == NULL) {
-      // Just do a check RE the once option. "&&opts_.once" is for
-      // efficiency since this can only happen in that case.
-      KALDI_ERR << "Error: HasKey called after Value() already called for "
-                << " that key, and once (o) option specified: rspecifier is "
-                << rspecifier_;
-    }
-    return ans;
-  }
-  virtual const T & Value(const std::string &key) {
-    HandlePendingDelete();
-    size_t index;
-    if (FindKeyInternal(key, &index)) {
-      if (seen_pairs_[index].second == NULL) {  // can happen if opts.once_
-        KALDI_ERR << "Error: Value() called more than once for key "
-                  << key << " and once (o) option specified: rspecifier is "
-                  << rspecifier_;
-      }
-      if (opts_.once)
-        pending_delete_ = index;  // mark this index to be deleted on next call.
-      return seen_pairs_[index].second->Value();
-    } else {
-      KALDI_ERR << "Value() called but no such key " << key
-                << " in archive " << PrintableRxfilename(archive_rxfilename_);
-      return *(const T*)NULL;  // keep compiler happy.
-    }
-  }
-  virtual ~RandomAccessTableReaderSortedArchiveImpl() {
-    if (this->IsOpen())
-      if (!Close()) // more specific warning will already have been printed.
-        // we are in some kind of error state & user did not find out by
-        // calling Close().
-        KALDI_ERR << "Error closing RandomAccessTableReader: rspecifier is "
-                  << rspecifier_;
-  }
- private:
-  void HandlePendingDelete() {
-    const size_t npos = static_cast<size_t>(-1);
-    if (pending_delete_ != npos) {
-      KALDI_ASSERT(pending_delete_ < seen_pairs_.size());
-      KALDI_ASSERT(seen_pairs_[pending_delete_].second != NULL);
-      delete seen_pairs_[pending_delete_].second;
-      seen_pairs_[pending_delete_].second = NULL;
-      pending_delete_ = npos;
-    }
-  }
-
-  // FindKeyInternal tries to find the key in the array "seen_pairs_".
-  // If it is not already there, it reads ahead as far as necessary
-  // to determine whether we have the key or not.  On success it returns
-  // true and puts the index into the array seen_pairs_, into "index";
-  // on failure it returns false.
-  // It will leave the state as either kNoObject, kEof or kError.
-  // FindKeyInternal does not do any checking about whether you are asking
-  // about a key that has been already given (with the "once" option).
-  // That is the user's responsibility.
-
-  bool FindKeyInternal(const std::string &key, size_t *index) {
-    // First, an optimization in case the previous call was for the
-    // same key, and we found it.
-    if (last_found_index_ < seen_pairs_.size()
-       && seen_pairs_[last_found_index_].first == key) {
-      *index = last_found_index_;
-      return true;
-    }
-
-    if (state_ == kUninitialized)
-      KALDI_ERR << "Trying to access a RandomAccessTableReader object that is not open.";
-    
-    // Step one is to see whether we have to read ahead for the object..
-    // Note, the possible states right now are kNoObject, kEof or kError.
-    // We are never in the state kHaveObject except just after calling
-    // ReadNextObject().
-    bool looped = false;
-    while (state_ == kNoObject &&
-          (seen_pairs_.empty() || key.compare(seen_pairs_.back().first) > 0)) {
-      looped = true;
-      // Read this as:
-      //  while ( the stream is potentially good for reading &&
-      //        ([got no keys] || key > most_recent_key) ) { ...
-      //     Try to read a new object.
-      // Note that the keys in seen_pairs_ are ordered from least to greatest.
-      ReadNextObject();
-      if (state_ == kHaveObject) {  // Successfully read object.
-        if (!seen_pairs_.empty() && // This is just a check.
-           cur_key_.compare(seen_pairs_.back().first) <= 0) {
-          // read the expression above as: !( cur_key_ > previous_key).
-          // it means we are not in sorted order [the user specified that we
-          // are, or we would not be using this implementation].
-          KALDI_ERR << "You provided the sorted (s) option but keys in archive "
-                    << PrintableRxfilename(archive_rxfilename_) << " are not "
-                    << "in sorted order: " << seen_pairs_.back().first
-                    << " is followed by " << cur_key_;
-        }
-        KALDI_ASSERT(holder_ != NULL);
-        seen_pairs_.push_back(std::make_pair(cur_key_, holder_));
-        holder_ = NULL;
-        state_ = kNoObject;
-      }
-    }
-    if (looped) {  // We only need to check the last element of the seen_pairs_ array,
-      // since we would not have read more after getting "key".
-      if (!seen_pairs_.empty() && seen_pairs_.back().first == key) {
-        last_found_index_ = *index = seen_pairs_.size() - 1;
-        return true;
-      } else return false;
-    }
-    // Now we have do an actual binary search in the seen_pairs_ array.
-    std::pair<std::string, Holder*> pr(key, static_cast<Holder*>(NULL));
-    typename std::vector<std::pair<std::string, Holder*> >::iterator
-        iter = std::lower_bound(seen_pairs_.begin(), seen_pairs_.end(),
-                                pr, PairCompare());
-    if (iter != seen_pairs_.end() &&
-       key == iter->first) {
-      last_found_index_ = *index = (iter - seen_pairs_.begin());
-      return true;
-    } else return false;
-  }
-
-  // These are the pairs of (key, object) we have read.  We keep all the keys we
-  // have read but the actual objects (if they are stored with pointers inside
-  // the Holder object) may be deallocated if once == true, and the Holder
-  // pointer set to NULL.
-  std::vector<std::pair<std::string, Holder*> > seen_pairs_;
-  size_t last_found_index_;  // An optimization s.t. if FindKeyInternal called twice with
-  // same key (as it often will), it doesn't have to do the key search twice.
-  size_t pending_delete_;  // If opts_.once == true, this is the index of
-  // element of seen_pairs_ that is pending deletion.
-  struct PairCompare {
-    // PairCompare is the Less-than operator for the pairs of(key, Holder).
-    // compares the keys.
-    inline bool operator() (const std::pair<std::string, Holder*> &pr1,
-                            const std::pair<std::string, Holder*> &pr2) {
-      return  (pr1.first.compare(pr2.first) < 0);
-    }
-  };
-};
-
-
-
-// RandomAccessTableReaderUnsortedArchiveImpl is for random-access reading of
-// archives when the user does not specify the sorted (s) option (in this case
-// the called-sorted, or "cs" option, is ignored).  This is the least efficient
-// of the random access archive readers, in general, but it can be as efficient
-// as the others, in speed, memory and latency, if the "once" option is specified
-// and it happens that the keys of the archive are the same as the keys the code
-// is called with (to HasKey() and Value()), and in the same order.  However, if
-// you ask it for a key that's not present it will have to read the archive till
-// the end and store it all in memory.
-
-template<class Holder>  class RandomAccessTableReaderUnsortedArchiveImpl:
-      public RandomAccessTableReaderArchiveImplBase<Holder> {
-  using RandomAccessTableReaderArchiveImplBase<Holder>::kUninitialized;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::kHaveObject;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::kNoObject;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::kEof;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::kError;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::state_;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::opts_;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::cur_key_;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::holder_;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::rspecifier_;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::archive_rxfilename_;
-  using RandomAccessTableReaderArchiveImplBase<Holder>::ReadNextObject;
-
-  typedef typename Holder::T T;
-
- public:
-  RandomAccessTableReaderUnsortedArchiveImpl(): to_delete_iter_(map_.end()),
-                                                to_delete_iter_valid_(false)
-                                                 {
-    map_.max_load_factor(0.5);  // make it quite empty -> quite efficient.
-    // default seems to be 1.
-  }
-
-  virtual bool Close() {
-    for (typename MapType::iterator iter = map_.begin();
-        iter != map_.end();
-        ++iter) {
-      if (iter->second)
-        delete iter->second;
-    }
-    map_.clear();
-    first_deleted_string_ = "";
-    to_delete_iter_valid_ = false;
-    return this->CloseInternal();
-  }
-
-  virtual bool HasKey(const std::string &key) {
-    HandlePendingDelete();
-    return FindKeyInternal(key, NULL);
-  }
-  virtual const T & Value(const std::string &key) {
-    HandlePendingDelete();
-    const T *ans_ptr = NULL;
-    if (FindKeyInternal(key, &ans_ptr))
-      return *ans_ptr;
-    else
-      KALDI_ERR << "Value() called but no such key " << key
-                << " in archive " << PrintableRxfilename(archive_rxfilename_);
-    return *(const T*)NULL;  // keep compiler happy.
-  }
-  virtual ~RandomAccessTableReaderUnsortedArchiveImpl() {
-    if (this->IsOpen())
-      if (!Close()) // more specific warning will already have been printed.
-        // we are in some kind of error state & user did not find out by
-        // calling Close().
-        KALDI_ERR << "Error closing RandomAccessTableReader: rspecifier is "
-                  << rspecifier_;
-  }
- private:
-  void HandlePendingDelete() {
-    if (to_delete_iter_valid_) {
-      to_delete_iter_valid_ = false;
-      delete to_delete_iter_->second;  // Delete Holder object.
-      if (first_deleted_string_.length() == 0)
-        first_deleted_string_ = to_delete_iter_->first;
-      map_.erase(to_delete_iter_);  // delete that element.
-    }
-  }
-
-  // FindKeyInternal tries to find the key in the map "map_"
-  // If it is not already there, it reads ahead either until it finds the
-  // key, or until end of file.  If called with value_ptr == NULL,
-  // it assumes it's called from HasKey() and just returns true or false
-  // and doesn't otherwise have side effects.  If called with value_ptr != 
-  // NULL, it assumes it's called from Value().  Thus, it will crash
-  // if it cannot find the key.  If it can find it it puts its address in
-  // *value_ptr, and if opts_once == true it will mark that element of the
-  // map to be deleted.
-
-  bool FindKeyInternal(const std::string &key, const T **value_ptr = NULL) {
-    typename MapType::iterator iter = map_.find(key);
-    if (iter != map_.end()) {  // Found in the map...
-      if (value_ptr == NULL) {  // called from HasKey
-        return true;  // this is all we have to do.
-      } else {
-        *value_ptr = &(iter->second->Value());
-        if (opts_.once) {  // value won't be needed again, so mark
-          // for deletion.
-          to_delete_iter_ = iter;  // pending delete.
-          KALDI_ASSERT(!to_delete_iter_valid_);
-          to_delete_iter_valid_ = true;
-        }
-        return true;
-      }
-    }
-    while (state_ == kNoObject) {
-      ReadNextObject();
-      if (state_ == kHaveObject) {  // Successfully read object.
-        state_ = kNoObject;  // we are about to transfer ownership
-        // of the object in holder_ to map_.
-        // Insert it into map_.
-        std::pair<typename MapType::iterator, bool> pr =
-            map_.insert(typename MapType::value_type(cur_key_, holder_));
-
-        if (!pr.second) {  // Was not inserted-- previous element w/ same key
-          delete holder_;  // map was not changed, no ownership transferred.
-          holder_ = NULL;
-          KALDI_ERR << "Error in RandomAccessTableReader: duplicate key "
-                    << cur_key_ << " in archive " << archive_rxfilename_;
-        }
-        holder_ = NULL;  // ownership transferred to map_.
-        if (cur_key_ == key) {  // the one we wanted..
-          if (value_ptr == NULL) {  // called from HasKey
-            return true;
-          } else {  // called from Value()
-            *value_ptr = &(pr.first->second->Value());  // this gives us the
-            // Value() from the Holder in the map.
-            if (opts_.once) {  // mark for deletion, as won't be needed again.
-              to_delete_iter_ = pr.first;
-              KALDI_ASSERT(!to_delete_iter_valid_);
-              to_delete_iter_valid_ = true;
-            }
-            return true;
-          }
-        }
-      }
-    }
-    if (opts_.once && key == first_deleted_string_) {
-      KALDI_ERR << "You specified the once (o) option but "
-                << "you are calling using key " << key
-                << " more than once: rspecifier is " << rspecifier_;
-    }
-    return false;  // We read the entire archive (or got to error state) and didn't
-    // find it.
-  }
-
-  typedef unordered_map<std::string, Holder*, StringHasher>  MapType;
-  MapType map_;
-
-  typename MapType::iterator to_delete_iter_;
-  bool to_delete_iter_valid_;
-
-  std::string first_deleted_string_;  // keep the first string we deleted
-  // from map_ (if opts_.once == true).  It's for an inexact spot-check that the
-  // "once" option isn't being used incorrectly.
-
-};
-
-
-
-
-
-template<class Holder>
-RandomAccessTableReader<Holder>::RandomAccessTableReader(const std::string &rspecifier):
-    impl_(NULL) {
-  if (rspecifier != "" && !Open(rspecifier))
-    KALDI_ERR << "Error opening RandomAccessTableReader object "
-        " (rspecifier is: " << rspecifier << ")";
-}
-
-template<class Holder>
-bool RandomAccessTableReader<Holder>::Open(const std::string &rspecifier) {
-  if (IsOpen())
-    KALDI_ERR << "Already open.";
-  RspecifierOptions opts;
-  RspecifierType rs = ClassifyRspecifier(rspecifier, NULL, &opts);
-  switch (rs) {
-    case kScriptRspecifier:
-      impl_ = new RandomAccessTableReaderScriptImpl<Holder>();
-      break;
-    case kArchiveRspecifier:
-      if (opts.sorted) {
-        if (opts.called_sorted) // "doubly" sorted case.
-          impl_ = new RandomAccessTableReaderDSortedArchiveImpl<Holder>();
-        else
-          impl_ = new RandomAccessTableReaderSortedArchiveImpl<Holder>();
-      } else impl_ = new RandomAccessTableReaderUnsortedArchiveImpl<Holder>();
-      break;
-    case kNoRspecifier: default:
-      KALDI_WARN << "Invalid rspecifier: "
-                 << rspecifier;
-      return false;
-  }
-  if (impl_->Open(rspecifier))
-    return true;
-  else {
-    // Warning will already have been printed.
-    delete impl_;
-    impl_ = NULL;
-    return false;
-  }
-}
-
-template<class Holder>
-bool RandomAccessTableReader<Holder>::HasKey(const std::string &key) {
-  CheckImpl();
-  if (!IsToken(key))
-    KALDI_ERR << "Invalid key \"" << key << '"';
-  return impl_->HasKey(key);
-}
-
-
-template<class Holder>
-const typename RandomAccessTableReader<Holder>::T&
-RandomAccessTableReader<Holder>::Value(const std::string &key) {
-  CheckImpl();  
-  return impl_->Value(key);
-}
-
-template<class Holder>
-bool RandomAccessTableReader<Holder>::Close() {
-  CheckImpl();
-  bool ans =impl_->Close();
-  delete impl_;
-  impl_ = NULL;
-  return ans;
-}
-
-template<class Holder>
-RandomAccessTableReader<Holder>::~RandomAccessTableReader() {
-  if (IsOpen() && !Close()) // call Close() yourself to stop this being thrown.
-    KALDI_ERR << "failure detected in destructor.";
-}
-
-template<class Holder>
-void SequentialTableReader<Holder>::CheckImpl() const {
-  if (!impl_) {
-    KALDI_ERR << "Trying to use empty SequentialTableReader (perhaps you "
-              << "passed the empty string as an argument to a program?)";
-  }
-}
-
-template<class Holder>
-void RandomAccessTableReader<Holder>::CheckImpl() const {
-  if (!impl_) {
-    KALDI_ERR << "Trying to use empty RandomAccessTableReader (perhaps you "
-              << "passed the empty string as an argument to a program?)";
-  }
-}
-
-template<class Holder>
-void TableWriter<Holder>::CheckImpl() const {
-  if (!impl_) {
-    KALDI_ERR << "Trying to use empty TableWriter (perhaps you "
-              << "passed the empty string as an argument to a program?)";
-  }
-}
-
-template<class Holder>
-RandomAccessTableReaderMapped<Holder>::RandomAccessTableReaderMapped(
-    const std::string &table_rxfilename,
-    const std::string &utt2spk_rxfilename):
-    reader_(table_rxfilename), token_reader_(table_rxfilename.empty() ? "" :
-                                             utt2spk_rxfilename),
-    utt2spk_rxfilename_(utt2spk_rxfilename) { }
-
-template<class Holder>
-bool RandomAccessTableReaderMapped<Holder>::Open(
-    const std::string &table_rxfilename,
-    const std::string &utt2spk_rxfilename) {
-  if (reader_.IsOpen()) reader_.Close();
-  if (token_reader_.IsOpen()) token_reader_.Close();
-  KALDI_ASSERT(!table_rxfilename.empty());
-  if (!reader_.Open(table_rxfilename)) return false; // will have printed
-  // warning internally, probably.
-  if (!utt2spk_rxfilename.empty()) {
-    if (!token_reader_.Open(utt2spk_rxfilename)) {
-      reader_.Close();
-      return false;
-    }
-  }
-  return true;
-}
-
-
-template<class Holder>
-bool RandomAccessTableReaderMapped<Holder>::HasKey(const std::string &utt) {
-  // We don't check IsOpen, we let the call go through to the member variable
-  // (reader_), which will crash with a more informative error message than
-  // we can give here, as we don't any longer know the rxfilename.
-  if (token_reader_.IsOpen()) { // We need to map the key from utt to spk.
-    if (!token_reader_.HasKey(utt))
-      KALDI_ERR << "Attempting to read key " << utt << ", which is not present "
-                << "in utt2spk map or similar map being read from "
-                << PrintableRxfilename(utt2spk_rxfilename_);
-    const std::string &spk = token_reader_.Value(utt);
-    return reader_.HasKey(spk);
-  } else {
-    return reader_.HasKey(utt);
-  }
-}
-
-template<class Holder>
-const typename Holder::T& RandomAccessTableReaderMapped<Holder>::Value(
-    const std::string &utt) {
-  if (token_reader_.IsOpen()) { // We need to map the key from utt to spk.
-    if (!token_reader_.HasKey(utt))
-      KALDI_ERR << "Attempting to read key " << utt << ", which is not present "
-                << "in utt2spk map or similar map being read from "
-                << PrintableRxfilename(utt2spk_rxfilename_);
-    const std::string &spk = token_reader_.Value(utt);
-    return reader_.Value(spk);
-  } else {
-    return reader_.Value(utt);
-  }
-}
-
-
-
-/// @}
-
-} // end namespace kaldi
-
-
-
-#endif
diff --git a/kaldi_io/src/kaldi/util/kaldi-table.h b/kaldi_io/src/kaldi/util/kaldi-table.h
deleted file mode 100644
index 6f6cb98..0000000
--- a/kaldi_io/src/kaldi/util/kaldi-table.h
+++ /dev/null
@@ -1,459 +0,0 @@
-// util/kaldi-table.h
-
-// Copyright 2009-2011    Microsoft Corporation
-//                2013    Johns Hopkins University (author: Daniel Povey)
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_UTIL_KALDI_TABLE_H_
-#define KALDI_UTIL_KALDI_TABLE_H_
-
-#include <string>
-#include <vector>
-#include <utility>
-
-#include "base/kaldi-common.h"
-#include "util/kaldi-holder.h"
-
-namespace kaldi {
-
-// Forward declarations
-template<class Holder> class RandomAccessTableReaderImplBase;
-template<class Holder>  class SequentialTableReaderImplBase;
-template<class Holder>  class TableWriterImplBase;
-
-/// \addtogroup table_group
-/// @{
-
-// This header defines the Table classes (RandomAccessTableReader,
-// SequentialTableReader and TableWriter) and explains what the Holder classes,
-// which the Table class requires as a template argument, are like.  It also
-// explains the "rspecifier" and "wspecifier" concepts (these are strings that
-// explain how to read/write objects via archives or scp files.  A table is
-// conceptually a collection of objects of a particular type T indexed by keys
-// of type std::string (these Keys additionally have an order within each table).
-// The Table classes are templated on a type (call it Holder) such that Holder::T
-// is a typedef equal to T.
-
-// see kaldi-holder.h for detail on the Holder classes.
-
-typedef std::vector<std::string> KeyList;
-
-// Documentation for "wspecifier"
-// "wspecifier" describes how we write a set of objects indexed by keys.
-// The basic, unadorned wspecifiers are as follows:
-//
-//  ark:wxfilename
-//  scp:rxfilename
-//  ark,scp:filename,wxfilename
-//  ark,scp:filename,wxfilename
-//
-//
-//  We also allow the following modifiers:
-//  t means text mode.
-//  b means binary mode.
-//  f means flush the stream after writing each entry.
-//   (nf means don't flush, and isn't very useful as the default is to flush).
-//  p means permissive mode, when writing to an "scp" file only: will ignore
-//     missing scp entries, i.e. won't write anything for those files but will
-//     return success status).
-//
-//  So the following are valid wspecifiers:
-//  ark,b,f:foo
-//  "ark,b,b:| gzip -c > foo"
-//  "ark,scp,t,nf:foo.ark,|gzip -c > foo.scp.gz"
-//  ark,b:-
-//
-//  The meanings of rxfilename and wxfilename are as described in
-//  kaldi-stream.h (they are filenames but include pipes, stdin/stdout
-//  and so on; filename is a regular filename.
-//
-
-//  The ark:wxfilename type of wspecifier instructs the class to
-//  write directly to an archive.  For small objects (e.g. lists of ints),
-//  the text archive format will generally be human readable with one line
-//  per entry in the archive.
-//
-//  The type "scp:xfilename" refers to an scp file which should
-//  already exist on disk, and tells us where to write the data for
-//  each key (usually an actual file); each line of the scp file
-//  would be:
-//   key xfilename
-//
-//  The type ark,scp:filename,wxfilename means
-//  we write both an archive and an scp file that specifies offsets into the
-//  archive, with lines like:
-//    key filename:12407
-//  where the number is the byte offset into the file.
-//  In this case we restrict the archive-filename to be an actual filename,
-//  as we can't see a situtation where an extended filename would make sense
-//  for this (we can't fseek() in pipes).
-
-enum WspecifierType  {
-  kNoWspecifier,
-  kArchiveWspecifier,
-  kScriptWspecifier,
-  kBothWspecifier
-};
-
-struct WspecifierOptions {
-  bool binary;
-  bool flush;
-  bool permissive; // will ignore absent scp entries.
-  WspecifierOptions(): binary(true), flush(false), permissive(false) { }
-};
-
-// ClassifyWspecifier returns the type of the wspecifier string,
-// and (if pointers are non-NULL) outputs the extra information
-// about the options, and the script and archive
-// filenames.
-WspecifierType ClassifyWspecifier(const std::string &wspecifier,
-                                  std::string *archive_wxfilename,
-                                  std::string *script_wxfilename,
-                                  WspecifierOptions *opts);
-
-// ReadScriptFile reads an .scp file in its entirety, and appends it
-// (in order as it was in the scp file) in script_out_, which contains
-// pairs of (key, xfilename).  The .scp
-// file format is: on each line, key xfilename
-// where xfilename means rxfilename or wxfilename, and may contain internal spaces
-// (we trim away any leading or trailing space).  The key is space-free.
-// ReadScriptFile returns true if the format was valid (empty files
-// are valid).
-// If 'print_warnings', it will print out warning messages that explain what kind
-// of error there was.
-bool ReadScriptFile(const std::string &rxfilename,
-                    bool print_warnings,
-                    std::vector<std::pair<std::string, std::string> > *script_out);
-
-// This version of ReadScriptFile works from an istream.
-bool ReadScriptFile(std::istream &is,
-                    bool print_warnings,
-                    std::vector<std::pair<std::string, std::string> > *script_out);
-
-// Writes, for each entry in script, the first element, then ' ', then the second
-// element then '\n'.  Checks that the keys (first elements of pairs) are valid
-// tokens (nonempty, no whitespace), and the values (second elements of pairs)
-// are newline-free and contain no leading or trailing space.  Returns true on
-// success.
-bool WriteScriptFile(const std::string &wxfilename,
-                     const std::vector<std::pair<std::string, std::string> > &script);
-
-// This version writes to an ostream.
-bool WriteScriptFile(std::ostream &os,
-                     const std::vector<std::pair<std::string, std::string> > &script);
-
-// Documentation for "rspecifier"
-// "rspecifier" describes how we read a set of objects indexed by keys.
-// The possibilities are:
-//
-// ark:rxfilename
-// scp:rxfilename
-//
-// We also allow various modifiers:
-//   o   means the program will only ask for each key once, which enables
-//       the reader to discard already-asked-for values.
-//   s   means the keys are sorted on input (means we don't have to read till
-//       eof if someone asked for a key that wasn't there).
-//   cs  means that it is called in sorted order (we are generally asserting this
-//       based on knowledge of how the program works).
-//   p   means "permissive", and causes it to skip over keys whose corresponding
-//       scp-file entries cannot be read. [and to ignore errors in archives and
-//       script files, and just consider the "good" entries].
-//       We allow the negation of the options above, as in no, ns, np,
-//       but these aren't currently very useful (just equivalent to omitting the
-//       corresponding option).
-//      [any of the above options can be prefixed by n to negate them, e.g. no, ns,
-//       ncs, np; but these aren't currently useful as you could just omit the option].
-//
-//   b   is ignored [for scripting convenience]
-//   t   is ignored [for scripting convenience]
-//
-//
-//  So for instance the following would be a valid rspecifier:
-//
-//   "o, s, p, ark:gunzip -c foo.gz|"
-
-struct  RspecifierOptions {
-  // These options only make a difference for the RandomAccessTableReader class.
-  bool once;   // we assert that the program will only ask for each key once.
-  bool sorted;  // we assert that the keys are sorted.
-  bool called_sorted;  // we assert that the (HasKey(), Value() functions will
-  // also be called in sorted order.  [this implies "once" but not vice versa].
-  bool permissive;  // If "permissive", when reading from scp files it treats
-  // scp files that can't be read as if the corresponding key were not there.
-  // For archive files it will suppress errors getting thrown if the archive
-  
-  // is corrupted and can't be read to the end.
-
-  RspecifierOptions(): once(false), sorted(false),
-                       called_sorted(false), permissive(false) { }
-};
-
-enum RspecifierType  {
-  kNoRspecifier,
-  kArchiveRspecifier,
-  kScriptRspecifier
-};
-
-RspecifierType ClassifyRspecifier(const std::string &rspecifier, std::string *rxfilename,
-                                  RspecifierOptions *opts);
-
-// Class Table<Holder> is useful when you want the entire set of
-// objects in memory.  NOT IMPLEMENTED YET.
-// It is the least scalable way of accessing data in Tables.
-// The *TableReader and TableWriter classes are more scalable.
-
-
-/// Allows random access to a collection
-/// of objects in an archive or script file; see \ref io_sec_tables.
-template<class Holder>
-class RandomAccessTableReader {
- public:
-  typedef typename Holder::T T;
-
-  RandomAccessTableReader(): impl_(NULL) { }
-
-  // This constructor equivalent to default constructor + "open", but
-  // throws on error.
-  RandomAccessTableReader(const std::string &rspecifier);
-
-  // Opens the table.
-  bool Open(const std::string &rspecifier);
-
-  // Returns true if table is open.
-  bool IsOpen() const { return (impl_ != NULL); }
-
-  // Close() will close the table [throws if it was not open],
-  // and returns true on success (false if we were reading an
-  // archive and we discovered an error in the archive).
-  bool Close();
-
-  // Says if it has this key.
-  // If you are using the "permissive" (p) read option,
-  // it will return false for keys whose corresponding entry
-  // in the scp file cannot be read.
-
-  bool HasKey(const std::string &key);
-
-  // Value() may throw if you are reading an scp file, you
-  // do not have the "permissive" (p) option, and an entry
-  // in the scp file cannot be read.  Typically you won't
-  // want to catch this error.
-  const T &Value(const std::string &key);
-
-  ~RandomAccessTableReader();
-
-  // Allow copy-constructor only for non-opened readers (needed for inclusion in
-  // stl vector)
-  RandomAccessTableReader(const RandomAccessTableReader<Holder> &other):
-      impl_(NULL) { KALDI_ASSERT(other.impl_ == NULL); }
- private:
-  // Disallow assignment.
-  RandomAccessTableReader &operator=(const RandomAccessTableReader<Holder>&);
-  void CheckImpl() const; // Checks that impl_ is non-NULL; prints an error
-                          // message and dies (with KALDI_ERR) if NULL.
-  RandomAccessTableReaderImplBase<Holder> *impl_;
-};
-
-
-
-/// A templated class for reading objects sequentially from an archive or script
-/// file; see \ref io_sec_tables.
-template<class Holder>
-class SequentialTableReader {
- public:
-  typedef typename Holder::T T;
-
-  SequentialTableReader(): impl_(NULL) { }
-
-  // This constructor equivalent to default constructor + "open", but
-  // throws on error.
-  SequentialTableReader(const std::string &rspecifier);
-
-  // Opens the table.  Returns exit status; but does throw if previously
-  // open stream was in error state.  Call Close to stop this [anyway,
-  // calling Open more than once is not recommended.]
-  bool Open(const std::string &rspecifier);
-
-  // Returns true if we're done.  It will also return true if there's some kind
-  // of error and we can't read any more; in this case, you can detect the
-  // error by calling Close and checking the return status; otherwise
-  // the destructor will throw.
-  inline bool Done();
-
-  // Only valid to call Key() if Done() returned false.
-  inline std::string Key();
-
-  // FreeCurrent() is provided as an optimization to save memory, for large
-  // objects.  It instructs the class to deallocate the current value. The
-  // reference Value() will/ be invalidated by this.
-
-  void FreeCurrent();
-
-  // Return reference to the current value.
-  // The reference is valid till next call to this object.
-  // If will throw if you are reading an scp file, did not
-  // specify the "permissive" (p) option and the file cannot
-  // be read.  [The permissive option makes it behave as if that
-  // key does not even exist, if the corresponding file cannot be
-  // read.]  You probably wouldn't want to catch this exception;
-  // the user can just specify the p option in the rspecifier.
-  const T &Value();
-
-  // Next goes to the next key.  It will not throw; any error will
-  // result in Done() returning true, and then the destructor will
-  // throw unless you call Close().
-  void Next();
-
-  // Returns true if table is open for reading (does not imply
-  // stream is in good state).
-  bool IsOpen() const;
-
-  // Close() will return false (failure) if Done() became true
-  // because of an error/ condition rather than because we are
-  // really done [e.g. because of an error or early termination
-  // in the archive].
-  // If there is an error and you don't call Close(), the destructor
-  // will fail.
-  // Close()
-  bool Close();
-
-  // The destructor may throw.  This is the desired behaviour, as it's the way we
-  // signal the error to the user (to detect it, call Close().  The issue is that
-  // otherwise the user has no way to tell whether Done() returned true because
-  // we reached the end of the archive or script, or because there was an error
-  // that prevented further reading.
-  ~SequentialTableReader();
-
-  // Allow copy-constructor only for non-opened readers (needed for inclusion in
-  // stl vector)
-  SequentialTableReader(const SequentialTableReader<Holder> &other):
-      impl_(NULL) { KALDI_ASSERT(other.impl_ == NULL); }
- private:
-  // Disallow assignment.
-  SequentialTableReader &operator = (const SequentialTableReader<Holder>&); 
-  void CheckImpl() const; // Checks that impl_ is non-NULL; prints an error
-                          // message and dies (with KALDI_ERR) if NULL.
-  SequentialTableReaderImplBase<Holder> *impl_;
-};
-
-
-/// A templated class for writing objects to an
-/// archive or script file; see \ref io_sec_tables.
-template<class Holder>
-class TableWriter {
- public:
-  typedef typename Holder::T T;
-
-  TableWriter(): impl_(NULL) { }
-
-  // This constructor equivalent to default constructor
-  // + "open", but throws on error.  See docs for
-  // wspecifier above.
-  TableWriter(const std::string &wspecifier);
-
-  // Opens the table.  See docs for wspecifier above.
-  // If it returns true, it is open.
-  bool Open(const std::string &wspecifier);
-
-  // Returns true if open for writing.
-  bool IsOpen() const;
-
-  // Write the object.  Throws  std::runtime_error on error (via the
-  // KALDI_ERR macro)
-  inline void Write(const std::string &key, const T &value) const;
-
-
-  // Flush will flush any archive; it does not return error status
-  // or throw, any errors will be reported on the next Write or Close.
-  // Useful if we may be writing to a command in a pipe and want
-  // to ensure good CPU utilization.
-  void Flush();
-
-  // Close() is not necessary to call, as the destructor
-  // closes it; it's mainly useful if you want to handle
-  // error states because the destructor will throw on
-  // error if you do not call Close().
-  bool Close();
-
-  ~TableWriter();
-  
-  // Allow copy-constructor only for non-opened writers (needed for inclusion in
-  // stl vector)
-  TableWriter(const TableWriter &other): impl_(NULL) {
-    KALDI_ASSERT(other.impl_ == NULL);
-  }
- private:
-  TableWriter &operator = (const TableWriter&); // Disallow assignment.
-  void CheckImpl() const; // Checks that impl_ is non-NULL; prints an error
-                          // message and dies (with KALDI_ERR) if NULL.
-  TableWriterImplBase<Holder> *impl_;
-};
-
-
-/// This class is for when you are reading something in random access, but
-/// it may actually be stored per-speaker (or something similar) but the 
-/// keys you're using are per utterance.  So you also provide an "rxfilename"
-/// for a file containing lines like
-/// utt1 spk1
-/// utt2 spk1
-/// utt3 spk1
-/// and so on.  Note: this is optional; if it is an empty string, we just won't
-/// do the mapping.  Also, "table_rxfilename" may be the empty string (as for
-/// a regular table), in which case the table just won't be opened.
-/// We provide only the most frequently used of the functions of RandomAccessTableReader.
-
-template<class Holder>
-class RandomAccessTableReaderMapped {
- public:
-  typedef typename Holder::T T;
-  /// Note: "utt2spk_rxfilename" will in the normal case be an rxfilename
-  /// for an utterance to speaker map, but this code is general; it accepts
-  /// a generic map.
-  RandomAccessTableReaderMapped(const std::string &table_rxfilename,
-                                const std::string &utt2spk_rxfilename);
-
-  RandomAccessTableReaderMapped() {};
-
-  /// Note: when calling Open, utt2spk_rxfilename may be empty.
-  bool Open(const std::string &table_rxfilename,
-            const std::string &utt2spk_rxfilename);
-
-  bool HasKey(const std::string &key);
-  const T &Value(const std::string &key);
-  inline bool IsOpen() const { return reader_.IsOpen(); }
-  inline bool Close() { return reader_.Close(); }
-  
-
-
-  // The default copy-constructor will do what we want: it will crash
-  // for already-opened readers, by calling the member-variable copy-constructors.
- private:
-  // Disallow assignment.
-  RandomAccessTableReaderMapped &operator=(const RandomAccessTableReaderMapped<Holder>&);
-  RandomAccessTableReader<Holder> reader_;
-  RandomAccessTableReader<TokenHolder> token_reader_;
-  std::string utt2spk_rxfilename_; // Used only in diagnostic messages.
-};
-
-
-/// @} end "addtogroup table_group"
-} // end namespace kaldi
-
-#include "kaldi-table-inl.h"
-
-#endif  // KALDI_UTIL_KALDI_TABLE_H_
diff --git a/kaldi_io/src/kaldi/util/parse-options.h b/kaldi_io/src/kaldi/util/parse-options.h
deleted file mode 100644
index f563b54..0000000
--- a/kaldi_io/src/kaldi/util/parse-options.h
+++ /dev/null
@@ -1,264 +0,0 @@
-// util/parse-options.h
-
-// Copyright 2009-2011  Karel Vesely;  Microsoft Corporation;
-//                      Saarland University (Author: Arnab Ghoshal);
-// Copyright 2012-2013  Frantisek Skala;  Arnab Ghoshal
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_UTIL_PARSE_OPTIONS_H_
-#define KALDI_UTIL_PARSE_OPTIONS_H_
-
-#include <map>
-#include <string>
-#include <vector>
-
-#include "base/kaldi-common.h"
-#include "itf/options-itf.h"
-
-namespace kaldi {
-
-/// The class ParseOptions is for parsing command-line options; see
-/// \ref parse_options for more documentation.
-class ParseOptions : public OptionsItf {
- public:
-  explicit ParseOptions(const char *usage) :
-    print_args_(true), help_(false), usage_(usage), argc_(0), argv_(NULL),
-    prefix_(""), other_parser_(NULL) {
-#ifndef _MSC_VER  // This is just a convenient place to set the stderr to line
-    setlinebuf(stderr);  // buffering mode, since it's called at program start.
-#endif  // This helps ensure different programs' output is not mixed up.
-    RegisterStandard("config", &config_, "Configuration file to read (this "
-                     "option may be repeated)");
-    RegisterStandard("print-args", &print_args_,
-                     "Print the command line arguments (to stderr)");
-    RegisterStandard("help", &help_, "Print out usage message");
-    RegisterStandard("verbose", &g_kaldi_verbose_level,
-                     "Verbose level (higher->more logging)");
-  }
-
-  /**
-    This is a constructor for the special case where some options are
-    registered with a prefix to avoid conflicts.  The object thus created will
-    only be used temporarily to register an options class with the original
-    options parser (which is passed as the *other pointer) using the given
-    prefix.  It should not be used for any other purpose, and the prefix must
-    not be the empty string.  It seems to be the least bad way of implementing
-    options with prefixes at this point.
-    Example of usage is:
-     ParseOptions po;  // original ParseOptions object
-     ParseOptions po_mfcc("mfcc", &po); // object with prefix.
-     MfccOptions mfcc_opts;
-     mfcc_opts.Register(&po_mfcc);
-    The options will now get registered as, e.g., --mfcc.frame-shift=10.0
-    instead of just --frame-shift=10.0
-   */
-  ParseOptions(const std::string &prefix, OptionsItf *other);
-
-  ~ParseOptions() {}
-
-  // Methods from the interface
-  void Register(const std::string &name,
-                bool *ptr, const std::string &doc); 
-  void Register(const std::string &name,
-                int32 *ptr, const std::string &doc); 
-  void Register(const std::string &name,
-                uint32 *ptr, const std::string &doc); 
-  void Register(const std::string &name,
-                float *ptr, const std::string &doc); 
-  void Register(const std::string &name,
-                double *ptr, const std::string &doc); 
-  void Register(const std::string &name,
-                std::string *ptr, const std::string &doc);
-
-  /// If called after registering an option and before calling
-  /// Read(), disables that option from being used.  Will crash
-  /// at runtime if that option had not been registered.
-  void DisableOption(const std::string &name);
-
-  /// This one is used for registering standard parameters of all the programs
-  template<typename T>
-  void RegisterStandard(const std::string &name,
-                        T *ptr, const std::string &doc);
-
-  /**
-    Parses the command line options and fills the ParseOptions-registered
-    variables. This must be called after all the variables were registered!!!
-   
-    Initially the variables have implicit values,
-    then the config file values are set-up,
-    finally the command line vaues given.
-    Returns the first position in argv that was not used.
-    [typically not useful: use NumParams() and GetParam(). ]
-   */
-  int Read(int argc, const char *const *argv);
-
-  /// Prints the usage documentation [provided in the constructor].
-  void PrintUsage(bool print_command_line = false);
-  /// Prints the actual configuration of all the registered variables
-  void PrintConfig(std::ostream &os);
-
-  /// Reads the options values from a config file.  Must be called after
-  /// registering all options.  This is usually used internally after the
-  /// standard --config option is used, but it may also be called from a
-  /// program.
-  void ReadConfigFile(const std::string &filename);
-
-  /// Number of positional parameters (c.f. argc-1).
-  int NumArgs() const;
-
-  /// Returns one of the positional parameters; 1-based indexing for argc/argv
-  /// compatibility. Will crash if param is not >=1 and <=NumArgs().
-  std::string GetArg(int param) const;
-
-  std::string GetOptArg(int param) const {
-    return (param <= NumArgs() ? GetArg(param) : "");
-  }
-
-  /// The following function will return a possibly quoted and escaped
-  /// version of "str", according to the current shell.  Currently
-  /// this is just hardwired to bash.  It's useful for debug output.
-  static std::string Escape(const std::string &str);
-
- private:
-  /// Template to register various variable types,
-  /// used for program-specific parameters
-  template<typename T>
-  void RegisterTmpl(const std::string &name, T *ptr, const std::string &doc);
-
-  // Following functions do just the datatype-specific part of the job
-  /// Register boolean variable
-  void RegisterSpecific(const std::string &name, const std::string &idx,
-                        bool *b, const std::string &doc, bool is_standard);
-  /// Register int32 variable
-  void RegisterSpecific(const std::string &name, const std::string &idx,
-                        int32 *i, const std::string &doc, bool is_standard);
-  /// Register unsinged  int32 variable
-  void RegisterSpecific(const std::string &name, const std::string &idx,
-                        uint32 *u,
-                        const std::string &doc, bool is_standard);
-  /// Register float variable
-  void RegisterSpecific(const std::string &name, const std::string &idx,
-                        float *f, const std::string &doc, bool is_standard);
-  /// Register double variable [useful as we change BaseFloat type].
-  void RegisterSpecific(const std::string &name, const std::string &idx,
-                        double *f, const std::string &doc, bool is_standard);
-  /// Register string variable
-  void RegisterSpecific(const std::string &name, const std::string &idx,
-                        std::string *s, const std::string &doc,
-                        bool is_standard);
-
-  /// Does the actual job for both kinds of parameters
-  /// Does the common part of the job for all datatypes,
-  /// then calls RegisterSpecific
-  template<typename T>
-  void RegisterCommon(const std::string &name,
-                      T *ptr, const std::string &doc, bool is_standard);
-
-  /// SplitLongArg parses an argument of the form --a=b, --a=, or --a,
-  /// and sets "has_equal_sign" to true if an equals-sign was parsed..
-  /// this is needed in order to correctly allow --x for a boolean option
-  /// x, and --y= for a string option y, and to disallow --x= and --y.
-  void SplitLongArg(std::string in, std::string *key, std::string *value,
-                    bool *has_equal_sign);
-  
-  void NormalizeArgName(std::string *str);
-
-  /// Set option with name "key" to "value"; will crash if can't do it.
-  /// "has_equal_sign" is used to allow --x for a boolean option x,
-  /// and --y=, for a string option y.
-  bool SetOption(const std::string &key, const std::string &value,
-                 bool has_equal_sign);
-
-  bool ToBool(std::string str);
-  int32 ToInt(std::string str);
-  uint32 ToUInt(std::string str);
-  float ToFloat(std::string str);
-  double ToDouble(std::string str);
-
-  // maps for option variables
-  std::map<std::string, bool*> bool_map_;
-  std::map<std::string, int32*> int_map_;
-  std::map<std::string, uint32*> uint_map_;
-  std::map<std::string, float*> float_map_;
-  std::map<std::string, double*> double_map_;
-  std::map<std::string, std::string*> string_map_;
-
-  /**
-     Structure for options' documentation
-   */
-  struct DocInfo {
-    DocInfo() {}
-    DocInfo(const std::string &name, const std::string &usemsg)
-      : name_(name), use_msg_(usemsg), is_standard_(false) {}
-    DocInfo(const std::string &name, const std::string &usemsg,
-            bool is_standard)
-      : name_(name), use_msg_(usemsg),  is_standard_(is_standard) {}
-
-    std::string name_;
-    std::string use_msg_;
-    bool is_standard_;
-  };
-  typedef std::map<std::string, DocInfo> DocMapType;
-  DocMapType doc_map_;  ///< map for the documentation
-
-  bool print_args_;     ///< variable for the implicit --print-args parameter
-  bool help_;           ///< variable for the implicit --help parameter
-  std::string config_;  ///< variable for the implicit --config parameter
-  std::vector<std::string> positional_args_;
-  const char *usage_;
-  int argc_;
-  const char *const *argv_;
-
-  /// These members are not normally used. They are only used when the object
-  /// is constructed with a prefix
-  std::string prefix_;
-  OptionsItf *other_parser_;
-};
-
-/// This template is provided for convenience in reading config classes from
-/// files; this is not the standard way to read configuration options, but may
-/// occasionally be needed.  This function assumes the config has a function
-/// "void Register(OptionsItf *po)" which it can call to register the
-/// ParseOptions object.
-template<class C> void ReadConfigFromFile(const std::string config_filename,
-                                          C *c) {
-  std::ostringstream usage_str;
-  usage_str << "Parsing config from "
-            << "from '" << config_filename << "'";
-  ParseOptions po(usage_str.str().c_str());
-  c->Register(&po);
-  po.ReadConfigFile(config_filename);
-}
-
-/// This variant of the template ReadConfigFromFile is for if you need to read
-/// two config classes from the same file.
-template<class C1, class C2> void ReadConfigsFromFile(const std::string config_filename,
-                                                      C1 *c1, C2 *c2) {
-  std::ostringstream usage_str;
-  usage_str << "Parsing config from "
-            << "from '" << config_filename << "'";
-  ParseOptions po(usage_str.str().c_str());
-  c1->Register(&po);
-  c2->Register(&po);
-  po.ReadConfigFile(config_filename);
-}
-
-
-
-}  // namespace kaldi
-
-#endif  // KALDI_UTIL_PARSE_OPTIONS_H_
diff --git a/kaldi_io/src/kaldi/util/simple-io-funcs.h b/kaldi_io/src/kaldi/util/simple-io-funcs.h
deleted file mode 100644
index 56573e4..0000000
--- a/kaldi_io/src/kaldi/util/simple-io-funcs.h
+++ /dev/null
@@ -1,56 +0,0 @@
-// util/simple-io-funcs.h
-
-// Copyright 2009-2011  Microsoft Corporation;  Jan Silovsky
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-
-//  http://www.apache.org/licenses/LICENSE-2.0
-
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-#ifndef KALDI_UTIL_SIMPLE_IO_FUNCS_H_
-#define KALDI_UTIL_SIMPLE_IO_FUNCS_H_
-
-#include "kaldi-io.h"
-
-// This header contains some utilities for reading some common, simple text formats:
-// integers in files, one per line, and integers in files, possibly multiple per line.
-// these are not really fully native Kaldi formats; they are mostly for small files that
-// might be generated by scripts, and can be read all at one time.
-// for longer files of this type, we would probably use the Table code.
-
-namespace kaldi {
-
-/// WriteToList attempts to write this list of integers, one per line,
-/// to the given file, in text format.
-/// returns true if succeeded.
-bool WriteIntegerVectorSimple(std::string wxfilename, const std::vector<int32> &v);
-
-/// ReadFromList attempts to read this list of integers, one per line,
-/// from the given file, in text format.
-/// returns true if succeeded.
-bool ReadIntegerVectorSimple(std::string rxfilename, std::vector<int32> *v);
-
-// This is a file format like:
-// 1 2
-// 3
-//
-// 4 5 6
-// etc.
-bool WriteIntegerVectorVectorSimple(std::string wxfilename, const std::vector<std::vector<int32> > &v);
-
-bool ReadIntegerVectorVectorSimple(std::string rxfilename, std::vector<std::vector<int32> > *v);
-
-
-}  // end namespace kaldi.
-
-
-#endif
diff --git a/kaldi_io/src/kaldi/util/simple-options.h b/kaldi_io/src/kaldi/util/simple-options.h
deleted file mode 100644
index 58816af..0000000
--- a/kaldi_io/src/kaldi/util/simple-options.h
+++ /dev/null
@@ -1,112 +0,0 @@
-// util/simple-options.hh
-
-// Copyright 2013  Tanel Alumae, Tallinn University of Technology
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_UTIL_SIMPLE_OPTIONS_H_
-#define KALDI_UTIL_SIMPLE_OPTIONS_H_
-
-#include <map>
-#include <string>
-#include <vector>
-
-#include "base/kaldi-common.h"
-#include "itf/options-itf.h"
-
-namespace kaldi {
-
-
-/// The class SimpleOptions is an implementation of OptionsItf that allows
-/// setting and getting option values programmatically, i.e., via getter
-/// and setter methods. It doesn't provide any command line parsing functionality.
-/// The class ParseOptions should be used for command-line options.
-class SimpleOptions : public OptionsItf {
- public:
-  SimpleOptions() {
-  }
-
-  virtual ~SimpleOptions() {
-  }
-
-  // Methods from the interface
-  void Register(const std::string &name, bool *ptr, const std::string &doc);
-  void Register(const std::string &name, int32 *ptr, const std::string &doc);
-  void Register(const std::string &name, uint32 *ptr, const std::string &doc);
-  void Register(const std::string &name, float *ptr, const std::string &doc);
-  void Register(const std::string &name, double *ptr, const std::string &doc);
-  void Register(const std::string &name, std::string *ptr,
-                const std::string &doc);
-
-  // set option with the specified key, return true if successful
-  bool SetOption(const std::string &key, const bool &value);
-  bool SetOption(const std::string &key, const int32 &value);
-  bool SetOption(const std::string &key, const uint32 &value);
-  bool SetOption(const std::string &key, const float &value);
-  bool SetOption(const std::string &key, const double &value);
-  bool SetOption(const std::string &key, const std::string &value);
-  bool SetOption(const std::string &key, const char* value);
-
-  // get option with the specified key and put to 'value',
-  // return true if successful
-  bool GetOption(const std::string &key, bool *value);
-  bool GetOption(const std::string &key, int32 *value);
-  bool GetOption(const std::string &key, uint32 *value);
-  bool GetOption(const std::string &key, float *value);
-  bool GetOption(const std::string &key, double *value);
-  bool GetOption(const std::string &key, std::string *value);
-
-  enum OptionType {
-    kBool,
-    kInt32,
-    kUint32,
-    kFloat,
-    kDouble,
-    kString
-  };
-
-  struct OptionInfo {
-    OptionInfo(const std::string &doc, OptionType type) :
-      doc(doc), type(type) {
-    }
-    std::string doc;
-    OptionType type;
-  };
-
-  std::vector<std::pair<std::string, OptionInfo> > GetOptionInfoList();
-
-  /*
-   * Puts the type of the option with name 'key' in the argument 'type'.
-   * Return true if such option is found, false otherwise.
-   */
-  bool GetOptionType(const std::string &key, OptionType *type);
-
- private:
-
-  std::vector<std::pair<std::string, OptionInfo> > option_info_list_;
-
-  // maps for option variables
-  std::map<std::string, bool*> bool_map_;
-  std::map<std::string, int32*> int_map_;
-  std::map<std::string, uint32*> uint_map_;
-  std::map<std::string, float*> float_map_;
-  std::map<std::string, double*> double_map_;
-  std::map<std::string, std::string*> string_map_;
-};
-
-}  // namespace kaldi
-
-#endif  // KALDI_UTIL_SIMPLE_OPTIONS_H_
diff --git a/kaldi_io/src/kaldi/util/stl-utils.h b/kaldi_io/src/kaldi/util/stl-utils.h
deleted file mode 100644
index 12526ff..0000000
--- a/kaldi_io/src/kaldi/util/stl-utils.h
+++ /dev/null
@@ -1,327 +0,0 @@
-// util/stl-utils.h
-
-// Copyright 2009-2011  Microsoft Corporation;  Saarland University
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_UTIL_STL_UTILS_H_
-#define KALDI_UTIL_STL_UTILS_H_
-
-#include <algorithm>
-#include <map>
-#include <set>
-#include <string>
-#include <vector>
-#include "base/kaldi-common.h"
-
-#ifdef _MSC_VER
-#include <unordered_map>
-#include <unordered_set>
-using std::unordered_map;
-using std::unordered_set;
-#elif __cplusplus > 199711L || defined(__GXX_EXPERIMENTAL_CXX0X__)
-#include <unordered_map>
-#include <unordered_set>
-using std::unordered_map;
-using std::unordered_set;
-#else
-#include <tr1/unordered_map>
-#include <tr1/unordered_set>
-using std::tr1::unordered_map;
-using std::tr1::unordered_set;
-#endif
-
-
-namespace kaldi {
-
-/// Sorts and uniq's (removes duplicates) from a vector.
-template<typename T>
-inline void SortAndUniq(std::vector<T> *vec) {
-  std::sort(vec->begin(), vec->end());
-  vec->erase(std::unique(vec->begin(), vec->end()), vec->end());
-}
-
-
-/// Returns true if the vector is sorted.
-template<typename T>
-inline bool IsSorted(const std::vector<T> &vec) {
-  typename std::vector<T>::const_iterator iter = vec.begin(), end = vec.end();
-  if (iter == end) return true;
-  while (1) {
-    typename std::vector<T>::const_iterator next_iter = iter;
-    ++next_iter;
-    if (next_iter == end) return true;  // end of loop and nothing out of order
-    if (*next_iter < *iter) return false;
-    iter = next_iter;
-  }
-}
-
-
-/// Returns true if the vector is sorted and contains each element
-/// only once.
-template<typename T>
-inline bool IsSortedAndUniq(const std::vector<T> &vec) {
-  typename std::vector<T>::const_iterator iter = vec.begin(), end = vec.end();
-  if (iter == end) return true;
-  while (1) {
-    typename std::vector<T>::const_iterator next_iter = iter;
-    ++next_iter;
-    if (next_iter == end) return true;  // end of loop and nothing out of order
-    if (*next_iter <= *iter) return false;
-    iter = next_iter;
-  }
-}
-
-
-/// Removes duplicate elements from a sorted list.
-template<typename T>
-inline void Uniq(std::vector<T> *vec) {  // must be already sorted.
-  KALDI_PARANOID_ASSERT(IsSorted(*vec));
-  KALDI_ASSERT(vec);
-  vec->erase(std::unique(vec->begin(), vec->end()), vec->end());
-}
-
-/// Copies the elements of a set to a vector.
-template<class T>
-void CopySetToVector(const std::set<T> &s, std::vector<T> *v) {
-  // adds members of s to v, in sorted order from lowest to highest
-  // (because the set was in sorted order).
-  KALDI_ASSERT(v != NULL);
-  v->resize(s.size());
-  typename std::set<T>::const_iterator siter = s.begin(), send = s.end();
-  typename std::vector<T>::iterator viter = v->begin();
-  for (; siter != send; ++siter, ++viter) {
-    *viter = *siter;
-  }
-}
-
-template<class T>
-void CopySetToVector(const unordered_set<T> &s, std::vector<T> *v) {
-  // adds members of s to v, in sorted order from lowest to highest
-  // (because the set was in sorted order).
-  KALDI_ASSERT(v != NULL);
-  v->resize(s.size());
-  typename unordered_set<T>::const_iterator siter = s.begin(), send = s.end();
-  typename std::vector<T>::iterator viter = v->begin();
-  for (; siter != send; ++siter, ++viter) {
-    *viter = *siter;
-  }
-}
-
-
-/// Copies the (key, value) pairs in a map to a vector of pairs.
-template<class A, class B>
-void CopyMapToVector(const std::map<A, B> &m,
-                     std::vector<std::pair<A, B> > *v) {
-  KALDI_ASSERT(v != NULL);
-  v->resize(m.size());
-  typename std::map<A, B>::const_iterator miter = m.begin(), mend = m.end();
-  typename std::vector<std::pair<A, B> >::iterator viter = v->begin();
-  for (; miter != mend; ++miter, ++viter) {
-    *viter = std::make_pair(miter->first, miter->second);
-    // do it like this because of const casting.
-  }
-}
-
-/// Copies the keys in a map to a vector.
-template<class A, class B>
-void CopyMapKeysToVector(const std::map<A, B> &m, std::vector<A> *v) {
-  KALDI_ASSERT(v != NULL);
-  v->resize(m.size());
-  typename std::map<A, B>::const_iterator miter = m.begin(), mend = m.end();
-  typename std::vector<A>::iterator viter = v->begin();
-  for (; miter != mend; ++miter, ++viter) {
-    *viter = miter->first;
-  }
-}
-
-/// Copies the values in a map to a vector.
-template<class A, class B>
-void CopyMapValuesToVector(const std::map<A, B> &m, std::vector<B> *v) {
-  KALDI_ASSERT(v != NULL);
-  v->resize(m.size());
-  typename std::map<A, B>::const_iterator miter = m.begin(), mend = m.end();
-  typename std::vector<B>::iterator viter = v->begin();
-  for (; miter != mend; ++miter, ++viter) {
-    *viter = miter->second;
-  }
-}
-
-/// Copies the keys in a map to a set.
-template<class A, class B>
-void CopyMapKeysToSet(const std::map<A, B> &m, std::set<A> *s) {
-  KALDI_ASSERT(s != NULL);
-  s->clear();
-  typename std::map<A, B>::const_iterator miter = m.begin(), mend = m.end();
-  for (; miter != mend; ++miter) {
-    s->insert(s->end(), miter->first);
-  }
-}
-
-/// Copies the values in a map to a set.
-template<class A, class B>
-void CopyMapValuesToSet(const std::map<A, B> &m, std::set<B> *s) {
-  KALDI_ASSERT(s != NULL);
-  s->clear();
-  typename std::map<A, B>::const_iterator miter = m.begin(), mend = m.end();
-  for (; miter != mend; ++miter)
-    s->insert(s->end(), miter->second);
-}
-
-
-/// Copies the contents of a vector to a set.
-template<class A>
-void CopyVectorToSet(const std::vector<A> &v, std::set<A> *s) {
-  KALDI_ASSERT(s != NULL);
-  s->clear();
-  typename std::vector<A>::const_iterator iter = v.begin(), end = v.end();
-  for (; iter != end; ++iter)
-    s->insert(s->end(), *iter);
-  // s->end() is a hint in case v was sorted.  will work regardless.
-}
-
-/// Deletes any non-NULL pointers in the vector v, and sets
-/// the corresponding entries of v to NULL
-template<class A>
-void DeletePointers(std::vector<A*> *v) {
-  KALDI_ASSERT(v != NULL);
-  typename std::vector<A*>::iterator iter = v->begin(), end = v->end();
-  for (; iter != end; ++iter) {
-    if (*iter != NULL) {
-      delete *iter;
-      *iter = NULL;  // set to NULL for extra safety.
-    }
-  }
-}
-
-/// Returns true if the vector of pointers contains NULL pointers.
-template<class A>
-bool ContainsNullPointers(const std::vector<A*> &v) {
-  typename std::vector<A*>::const_iterator iter = v.begin(), end = v.end();
-  for (; iter != end; ++iter)
-    if (*iter == static_cast<A*> (NULL)) return true;
-  return false;
-}
-
-/// Copies the contents a vector of one type to a vector
-/// of another type.
-template<typename A, typename B>
-void CopyVectorToVector(const std::vector<A> &vec_in, std::vector<B> *vec_out) {
-  KALDI_ASSERT(vec_out != NULL);
-  vec_out->resize(vec_in.size());
-  for (size_t i = 0; i < vec_in.size(); i++)
-    (*vec_out)[i] = static_cast<B> (vec_in[i]);
-}
-
-/// A hashing function-object for vectors.
-template<typename Int>
-struct VectorHasher {  // hashing function for vector<Int>.
-  size_t operator()(const std::vector<Int> &x) const {
-    size_t ans = 0;
-    typename std::vector<Int>::const_iterator iter = x.begin(), end = x.end();
-    for (; iter != end; ++iter) {
-      ans *= kPrime;
-      ans += *iter;
-    }
-    return ans;
-  }
-  VectorHasher() {  // Check we're instantiated with an integer type.
-    KALDI_ASSERT_IS_INTEGER_TYPE(Int);
-  }
- private:
-  static const int kPrime = 7853;
-};
-
-/// A hashing function-object for pairs of ints
-template<typename Int>
-struct PairHasher { // hashing function for pair<int>
-  size_t operator()(const std::pair<Int,Int> &x) const {
-    return x.first + x.second * kPrime;
-  }
-  PairHasher() {  // Check we're instantiated with an integer type.
-    KALDI_ASSERT_IS_INTEGER_TYPE(Int);
-  }
- private:
-  static const int kPrime = 7853;
-};
-
-
-/// A hashing function object for strings.
-struct StringHasher {  // hashing function for std::string
-  size_t operator()(const std::string &str) const {
-    size_t ans = 0, len = str.length();
-    const char *c = str.c_str(), *end = c + len;
-    for (; c != end; c++) {
-      ans *= kPrime;
-      ans += *c;
-    }
-    return ans;
-  }
- private:
-  static const int kPrime = 7853;
-};
-
-/// Reverses the contents of a vector.
-template<typename T>
-inline void ReverseVector(std::vector<T> *vec) {
-  KALDI_ASSERT(vec != NULL);
-  size_t sz = vec->size();
-  for (size_t i = 0; i < sz/2; i++)
-    std::swap( (*vec)[i], (*vec)[sz-1-i]);
-}
-
-
-/// Comparator object for pairs that compares only the first pair.
-template<class A, class B>
-struct CompareFirstMemberOfPair {
-  inline bool operator() (const std::pair<A, B> &p1,
-                          const std::pair<A, B> &p2) {
-    return p1.first < p2.first;
-  }
-};
-
-/// For a vector of pair<I, F> where I is an integer and F a floating-point or
-/// integer type, this function sorts a vector of type vector<pair<I, F> > on
-/// the I value and then merges elements with equal I values, summing these over
-/// the F component and then removing any F component with zero value.  This
-/// is for where the vector of pairs represents a map from the integer to float
-/// component, with an "adding" type of semantics for combining the elements.
-template<typename I, typename F>
-inline void MergePairVectorSumming(std::vector<std::pair<I, F> > *vec) {
-  KALDI_ASSERT_IS_INTEGER_TYPE(I);
-  CompareFirstMemberOfPair<I, F> c;
-  std::sort(vec->begin(), vec->end(), c); // sort on 1st element. 
-  typename std::vector<std::pair<I, F> >::iterator out = vec->begin(),
-      in = vec->begin(), end = vec->end();
-  while (in < end) {
-    // We reach this point only at the first element of
-    // each stretch of identical .first elements.
-    *out = *in;
-    ++in;
-    while (in < end && in->first == out->first) {
-      out->second += in->second; // this is the merge operation.
-      ++in;
-    }
-    if (out->second != static_cast<F>(0)) // Don't keep zero elements.
-      out++;
-  }
-  vec->erase(out, end);
-}
-
-}  // namespace kaldi
-
-#endif  // KALDI_UTIL_STL_UTILS_H_
-
diff --git a/kaldi_io/src/kaldi/util/table-types.h b/kaldi_io/src/kaldi/util/table-types.h
deleted file mode 100644
index 313d1aa..0000000
--- a/kaldi_io/src/kaldi/util/table-types.h
+++ /dev/null
@@ -1,137 +0,0 @@
-// util/table-types.h
-
-// Copyright 2009-2011     Microsoft Corporation
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-
-#ifndef KALDI_UTIL_TABLE_TYPES_H_
-#define KALDI_UTIL_TABLE_TYPES_H_
-#include "base/kaldi-common.h"
-#include "util/kaldi-table.h"
-#include "util/kaldi-holder.h"
-#include "matrix/matrix-lib.h"
-
-namespace kaldi {
-
-// This header defines typedefs that are specific instantiations of
-// the Table types.
-
-/// \addtogroup table_types
-/// @{
-
-typedef TableWriter<KaldiObjectHolder<Matrix<BaseFloat> > >  BaseFloatMatrixWriter;
-typedef SequentialTableReader<KaldiObjectHolder<Matrix<BaseFloat> > >  SequentialBaseFloatMatrixReader;
-typedef RandomAccessTableReader<KaldiObjectHolder<Matrix<BaseFloat> > >  RandomAccessBaseFloatMatrixReader;
-typedef RandomAccessTableReaderMapped<KaldiObjectHolder<Matrix<BaseFloat> > >  RandomAccessBaseFloatMatrixReaderMapped;
-
-typedef TableWriter<KaldiObjectHolder<Matrix<double> > >  DoubleMatrixWriter;
-typedef SequentialTableReader<KaldiObjectHolder<Matrix<double> > >  SequentialDoubleMatrixReader;
-typedef RandomAccessTableReader<KaldiObjectHolder<Matrix<double> > >  RandomAccessDoubleMatrixReader;
-typedef RandomAccessTableReaderMapped<KaldiObjectHolder<Matrix<double> > >  RandomAccessDoubleMatrixReaderMapped;
-
-typedef TableWriter<KaldiObjectHolder<CompressedMatrix> >  CompressedMatrixWriter;
-
-typedef TableWriter<KaldiObjectHolder<Vector<BaseFloat> > >  BaseFloatVectorWriter;
-typedef SequentialTableReader<KaldiObjectHolder<Vector<BaseFloat> > >  SequentialBaseFloatVectorReader;
-typedef RandomAccessTableReader<KaldiObjectHolder<Vector<BaseFloat> > >  RandomAccessBaseFloatVectorReader;
-typedef RandomAccessTableReaderMapped<KaldiObjectHolder<Vector<BaseFloat> > >  RandomAccessBaseFloatVectorReaderMapped;
-
-typedef TableWriter<KaldiObjectHolder<Vector<double> > >  DoubleVectorWriter;
-typedef SequentialTableReader<KaldiObjectHolder<Vector<double> > >  SequentialDoubleVectorReader;
-typedef RandomAccessTableReader<KaldiObjectHolder<Vector<double> > >  RandomAccessDoubleVectorReader;
-
-typedef TableWriter<KaldiObjectHolder<CuMatrix<BaseFloat> > >  BaseFloatCuMatrixWriter;
-typedef SequentialTableReader<KaldiObjectHolder<CuMatrix<BaseFloat> > >  SequentialBaseFloatCuMatrixReader;
-typedef RandomAccessTableReader<KaldiObjectHolder<CuMatrix<BaseFloat> > >  RandomAccessBaseFloatCuMatrixReader;
-typedef RandomAccessTableReaderMapped<KaldiObjectHolder<CuMatrix<BaseFloat> > >  RandomAccessBaseFloatCuMatrixReaderMapped;
-
-typedef TableWriter<KaldiObjectHolder<CuMatrix<double> > >  DoubleCuMatrixWriter;
-typedef SequentialTableReader<KaldiObjectHolder<CuMatrix<double> > >  SequentialDoubleCuMatrixReader;
-typedef RandomAccessTableReader<KaldiObjectHolder<CuMatrix<double> > >  RandomAccessDoubleCuMatrixReader;
-typedef RandomAccessTableReaderMapped<KaldiObjectHolder<CuMatrix<double> > >  RandomAccessDoubleCuMatrixReaderMapped;
-
-typedef TableWriter<KaldiObjectHolder<CuVector<BaseFloat> > >  BaseFloatCuVectorWriter;
-typedef SequentialTableReader<KaldiObjectHolder<CuVector<BaseFloat> > >  SequentialBaseFloatCuVectorReader;
-typedef RandomAccessTableReader<KaldiObjectHolder<CuVector<BaseFloat> > >  RandomAccessBaseFloatCuVectorReader;
-typedef RandomAccessTableReaderMapped<KaldiObjectHolder<CuVector<BaseFloat> > >  RandomAccessBaseFloatCuVectorReaderMapped;
-
-typedef TableWriter<KaldiObjectHolder<CuVector<double> > >  DoubleCuVectorWriter;
-typedef SequentialTableReader<KaldiObjectHolder<CuVector<double> > >  SequentialDoubleCuVectorReader;
-typedef RandomAccessTableReader<KaldiObjectHolder<CuVector<double> > >  RandomAccessDoubleCuVectorReader;
-
-
-typedef TableWriter<BasicHolder<int32> >  Int32Writer;
-typedef SequentialTableReader<BasicHolder<int32> >  SequentialInt32Reader;
-typedef RandomAccessTableReader<BasicHolder<int32> >  RandomAccessInt32Reader;
-
-typedef TableWriter<BasicVectorHolder<int32> >  Int32VectorWriter;
-typedef SequentialTableReader<BasicVectorHolder<int32> >  SequentialInt32VectorReader;
-typedef RandomAccessTableReader<BasicVectorHolder<int32> >  RandomAccessInt32VectorReader;
-
-typedef TableWriter<BasicVectorVectorHolder<int32> >  Int32VectorVectorWriter;
-typedef SequentialTableReader<BasicVectorVectorHolder<int32> >  SequentialInt32VectorVectorReader;
-typedef RandomAccessTableReader<BasicVectorVectorHolder<int32> >  RandomAccessInt32VectorVectorReader;
-
-typedef TableWriter<BasicPairVectorHolder<int32> >  Int32PairVectorWriter;
-typedef SequentialTableReader<BasicPairVectorHolder<int32> >  SequentialInt32PairVectorReader;
-typedef RandomAccessTableReader<BasicPairVectorHolder<int32> >  RandomAccessInt32PairVectorReader;
-
-typedef TableWriter<BasicPairVectorHolder<BaseFloat> >  BaseFloatPairVectorWriter;
-typedef SequentialTableReader<BasicPairVectorHolder<BaseFloat> >  SequentialBaseFloatPairVectorReader;
-typedef RandomAccessTableReader<BasicPairVectorHolder<BaseFloat> >  RandomAccessBaseFloatPairVectorReader;
-
-typedef TableWriter<BasicHolder<BaseFloat> >  BaseFloatWriter;
-typedef SequentialTableReader<BasicHolder<BaseFloat> >  SequentialBaseFloatReader;
-typedef RandomAccessTableReader<BasicHolder<BaseFloat> >  RandomAccessBaseFloatReader;
-typedef RandomAccessTableReaderMapped<BasicHolder<BaseFloat> >  RandomAccessBaseFloatReaderMapped;
-
-typedef TableWriter<BasicHolder<double> >  DoubleWriter;
-typedef SequentialTableReader<BasicHolder<double> >  SequentialDoubleReader;
-typedef RandomAccessTableReader<BasicHolder<double> >  RandomAccessDoubleReader;
-
-typedef TableWriter<BasicHolder<bool> >  BoolWriter;
-typedef SequentialTableReader<BasicHolder<bool> >  SequentialBoolReader;
-typedef RandomAccessTableReader<BasicHolder<bool> >  RandomAccessBoolReader;
-
-
-
-/// TokenWriter is a writer specialized for std::string where the strings
-/// are nonempty and whitespace-free.   T == std::string
-typedef TableWriter<TokenHolder> TokenWriter;
-typedef SequentialTableReader<TokenHolder> SequentialTokenReader;
-typedef RandomAccessTableReader<TokenHolder> RandomAccessTokenReader;
-
-
-/// TokenVectorWriter is a writer specialized for sequences of
-/// std::string where the strings are nonempty and whitespace-free.
-/// T == std::vector<std::string>
-typedef TableWriter<TokenVectorHolder> TokenVectorWriter;
-// Ditto for SequentialTokenVectorReader.
-typedef SequentialTableReader<TokenVectorHolder> SequentialTokenVectorReader;
-typedef RandomAccessTableReader<TokenVectorHolder> RandomAccessTokenVectorReader;
-
-
-/// @}
-
-// Note: for FST reader/writer, see ../fstext/fstext-utils.h
-// [not done yet].
-
-} // end namespace kaldi
-
-
-
-#endif
diff --git a/kaldi_io/src/kaldi/util/text-utils.h b/kaldi_io/src/kaldi/util/text-utils.h
deleted file mode 100644
index 1d85c47..0000000
--- a/kaldi_io/src/kaldi/util/text-utils.h
+++ /dev/null
@@ -1,169 +0,0 @@
-// util/text-utils.h
-
-// Copyright 2009-2011  Saarland University;  Microsoft Corporation
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//  http://www.apache.org/licenses/LICENSE-2.0
-//
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-#ifndef KALDI_UTIL_TEXT_UTILS_H_
-#define KALDI_UTIL_TEXT_UTILS_H_
-
-#include <algorithm>
-#include <map>
-#include <set>
-#include <string>
-#include <vector>
-#include <errno.h>
-
-#include "base/kaldi-common.h"
-
-namespace kaldi {
-
-/// Split a string using any of the single character delimiters.
-/// If omit_empty_strings == true, the output will contain any
-/// nonempty strings after splitting on any of the
-/// characters in the delimiter.  If omit_empty_strings == false,
-/// the output will contain n+1 strings if there are n characters
-/// in the set "delim" within the input string.  In this case
-/// the empty string is split to a single empty string.
-void SplitStringToVector(const std::string &full, const char *delim,
-                         bool omit_empty_strings,
-                         std::vector<std::string> *out);
-
-/// Joins the elements of a vector of strings into a single string using
-/// "delim" as the delimiter. If omit_empty_strings == true, any empty strings
-/// in the vector are skipped. A vector of empty strings results in an empty
-/// string on the output.
-void JoinVectorToString(const std::vector<std::string> &vec_in,
-                        const char *delim, bool omit_empty_strings,
-                        std::string *str_out);
-
-
-/// Split a string (e.g. 1:2:3) into a vector of integers.
-/// The delimiting char may be any character in "delim".
-/// returns true on success, false on failure.
-/// If omit_empty_strings == true, 1::2:3: will become
-/// { 1, 2, 3 }.  Otherwise it would be rejected.
-/// Regardless of the value of omit_empty_strings,
-/// the empty string is successfully parsed as an empty
-/// vector of integers
-template<class I>
-bool SplitStringToIntegers(const std::string &full,
-                           const char *delim,
-                           bool omit_empty_strings,  // typically false [but
-                                                     // should probably be true
-                                                     // if "delim" is spaces].
-                           std::vector<I> *out) {
-  KALDI_ASSERT(out != NULL);
-  KALDI_ASSERT_IS_INTEGER_TYPE(I);
-  if ( *(full.c_str()) == '\0') {
-    out->clear();
-    return true;
-  }
-  std::vector<std::string> split;
-  SplitStringToVector(full, delim, omit_empty_strings, &split);
-  out->resize(split.size());
-  for (size_t i = 0; i < split.size(); i++) {
-    const char *this_str = split[i].c_str();
-    char *end = NULL;
-    long long int j = 0;
-    j = KALDI_STRTOLL(this_str, &end);
-    if (end == this_str || *end != '\0') {
-      out->clear();
-      return false;
-    } else {
-      I jI = static_cast<I>(j);
-      if (static_cast<long long int>(jI) != j) {
-        // output type cannot fit this integer.
-        out->clear();
-        return false;
-      }
-      (*out)[i] = jI;
-    }
-  }
-  return true;
-}
-
-// This is defined for F = float and double.
-template<class F>
-bool SplitStringToFloats(const std::string &full,
-                         const char *delim,
-                         bool omit_empty_strings, // typically false
-                         std::vector<F> *out);
-
-
-/// Converts a string into an integer via strtoll and returns false if there was
-/// any kind of problem (i.e. the string was not an integer or contained extra
-/// non-whitespace junk, or the integer was too large to fit into the type it is
-/// being converted into).  Only sets *out if everything was OK and it returns
-/// true.
-template<class Int>
-bool ConvertStringToInteger(const std::string &str,
-                            Int *out) {
-  KALDI_ASSERT_IS_INTEGER_TYPE(Int);
-  const char *this_str = str.c_str();
-  char *end = NULL;
-  errno = 0;
-  long long int i = KALDI_STRTOLL(this_str, &end);
-  if (end != this_str)
-    while (isspace(*end)) end++;
-  if (end == this_str || *end != '\0' || errno != 0)
-    return false;
-  Int iInt = static_cast<Int>(i);
-  if (static_cast<long long int>(iInt) != i || (i<0 && !std::numeric_limits<Int>::is_signed)) {
-    return false;
-  }
-  *out = iInt;
-  return true;
-}
-
-
-/// ConvertStringToReal converts a string into either float or double via strtod,
-/// and returns false if there was any kind of problem (i.e. the string was not a
-/// floating point number or contained extra non-whitespace junk.
-/// Be careful- this function will successfully read inf's or nan's.
-bool ConvertStringToReal(const std::string &str,
-                         double *out);
-bool ConvertStringToReal(const std::string &str,
-                         float *out);
-
-
-/// Removes the beginning and trailing whitespaces from a string
-void Trim(std::string *str);
-
-
-/// Removes leading and trailing white space from the string, then splits on the
-/// first section of whitespace found (if present), putting the part before the
-/// whitespace in "first" and the rest in "rest".  If there is no such space,
-/// everything that remains after removing leading and trailing whitespace goes
-/// in "first".
-void SplitStringOnFirstSpace(const std::string &line,
-                             std::string *first,
-                             std::string *rest);
-
-
-/// Returns true if "token" is nonempty, and all characters are
-/// printable and whitespace-free.
-bool IsToken(const std::string &token);
-
-
-/// Returns true if "line" is free of \n characters and unprintable
-/// characters, and does not contain leading or trailing whitespace.
-bool IsLine(const std::string &line);
-
-
-}  // namespace kaldi
-
-#endif  // KALDI_UTIL_TEXT_UTILS_H_
diff --git a/kaldi_io/src/kaldi/util/timer.h b/kaldi_io/src/kaldi/util/timer.h
deleted file mode 100644
index e3ee8d5..0000000
--- a/kaldi_io/src/kaldi/util/timer.h
+++ /dev/null
@@ -1,27 +0,0 @@
-// util/timer.h
-
-// Copyright 2014  Johns Hopkins University (author: Daniel Povey)
-
-// See ../../COPYING for clarification regarding multiple authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-
-//  http://www.apache.org/licenses/LICENSE-2.0
-
-// THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-// KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED
-// WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,
-// MERCHANTABLITY OR NON-INFRINGEMENT.
-// See the Apache 2 License for the specific language governing permissions and
-// limitations under the License.
-
-// We are temporarily leaving this file to forward #includes to
-// base-timer.h.  Its use is deprecated; you should directrly
-// #include base/timer.h
-#ifndef KALDI_UTIL_TIMER_H_
-#define KALDI_UTIL_TIMER_H_
-#pragma message warning: please do not include util/timer.h, include base/timer.h (it has been moved)
-#include "base/timer.h"
-#endif