This file is indexed.

/usr/include/sbml/compress/bzfstream.h is in libsbml5-dev 5.12.0+dfsg-3.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
/**
 * @file    bzfstream.h
 * @brief   C++ I/O streams interface to the bzlib bz* functions
 * @author  Akiya Jouraku
 * 
 * <!--------------------------------------------------------------------------
 * This file is part of libSBML.  Please visit http://sbml.org for more
 * information about SBML, and the latest version of libSBML.
 *
 * Copyright (C) 2013-2015 jointly by the following organizations:
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
 *     3. University of Heidelberg, Heidelberg, Germany
 *
 * Copyright (C) 2009-2013 jointly by the following organizations: 
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
 *  
 * Copyright (C) 2006-2008 by the California Institute of Technology,
 *     Pasadena, CA, USA 
 *  
 * Copyright (C) 2002-2005 jointly by the following organizations: 
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. Japan Science and Technology Agency, Japan
 * 
 * This library is free software; you can redistribute it and/or modify it
 * under the terms of the GNU Lesser General Public License as published by
 * the Free Software Foundation.  A copy of the license agreement is provided
 * in the file named "LICENSE.txt" included with this software distribution
 * and also available online as http://sbml.org/software/libsbml/license.html
 * ------------------------------------------------------------------------- -->
 *
 * Most of the code (except for bzip2 specific code) is based on zfstream.h 
 * implemented by Ludwig Schwardt <schwardt@sun.ac.za> 
 * original version by Kevin Ruland <kevin@rodin.wustl.edu>
 * zfstream.h is contained in the contributed samples in zlib version 1.2.3
 * (http://www.zlib.net).
 *
 * ---------------------------------------------------------------------- -->*/


#ifndef BZFSTREAM_H
#define BZFSTREAM_H

#include <istream>  // not iostream, since we don't need cin/cout
#include <ostream>
#include "bzlib.h"

/*****************************************************************************/

/**
 *  @brief  bzip2 file stream buffer class.
 *
 *  This class implements basic_filebuf for bzip2 files. It doesn't yet support
 *  seeking (allowed by zlib but slow/limited), putback and read/write access
 *  (tricky). Otherwise, it attempts to be a drop-in replacement for the standard
 *  file streambuf.
*/
class bzfilebuf : public std::streambuf
{
public:
  //  Default constructor.
  bzfilebuf();

  //  Destructor.
  virtual
  ~bzfilebuf();

  /**
   *  @brief  Check if file is open.
   *  @return  True if file is open.
  */
  bool
  is_open() const { return (file != NULL); }

  /**
   *  @brief  Open bzip2 file.
   *  @param  name  File name.
   *  @param  mode  Open mode flags.
   *  @return  @c this on success, NULL on failure.
  */
  bzfilebuf*
  open(const char* name,
       std::ios_base::openmode mode);

  /**
   *  @brief  Attach to already open bzip2 file.
   *  @param  fd  File descriptor.
   *  @param  mode  Open mode flags.
   *  @return  @c this on success, NULL on failure.
  */
  bzfilebuf*
  attach(int fd,
         std::ios_base::openmode mode);

  /**
   *  @brief  Close bzip2 file.
   *  @return  @c this on success, NULL on failure.
  */
  bzfilebuf*
  close();

protected:
  /**
   *  @brief  Convert ios open mode int to mode string used by zlib.
   *  @return  True if valid mode flag combination.
  */
  bool
  open_mode(std::ios_base::openmode mode,
            char* c_mode) const;

  /**
   *  @brief  Number of characters available in stream buffer.
   *  @return  Number of characters.
   *
   *  This indicates number of characters in get area of stream buffer.
   *  These characters can be read without accessing the bzip2 file.
  */
  virtual std::streamsize
  showmanyc();

  /**
   *  @brief  Fill get area from bzip2 file.
   *  @return  First character in get area on success, EOF on error.
   *
   *  This actually reads characters from bzip2 file to stream
   *  buffer. Always buffered.
  */
  virtual int_type
  underflow();

  /**
   *  @brief  Write put area to bzip2 file.
   *  @param  c  Extra character to add to buffer contents.
   *  @return  Non-EOF on success, EOF on error.
   *
   *  This actually writes characters in stream buffer to
   *  bzip2 file. With unbuffered output this is done one
   *  character at a time.
  */
  virtual int_type
  overflow(int_type c = std::streambuf::traits_type::eof());

  /**
   *  @brief  Installs external stream buffer.
   *  @param  p  Pointer to char buffer.
   *  @param  n  Size of external buffer.
   *  @return  @c this on success, NULL on failure.
   *
   *  Call setbuf(0,0) to enable unbuffered output.
  */
  virtual std::streambuf*
  setbuf(char_type* p,
         std::streamsize n);

  /**
   *  @brief  Flush stream buffer to file.
   *  @return  0 on success, -1 on error.
   *
   *  This calls underflow(EOF) to do the job.
  */
  virtual int
  sync();

//
// Some future enhancements
//
//  virtual int_type uflow();
//  virtual int_type pbackfail(int_type c = traits_type::eof());
//  virtual pos_type
//  seekoff(off_type off,
//          std::ios_base::seekdir way,
//          std::ios_base::openmode mode = std::ios_base::in|std::ios_base::out);
//  virtual pos_type
//  seekpos(pos_type sp,
//          std::ios_base::openmode mode = std::ios_base::in|std::ios_base::out);

private:
  /**
   *  @brief  Allocate internal buffer.
   *
   *  This function is safe to call multiple times. It will ensure
   *  that a proper internal buffer exists if it is required. If the
   *  buffer already exists or is external, the buffer pointers will be
   *  reset to their original state.
  */
  void
  enable_buffer();

  /**
   *  @brief  Destroy internal buffer.
   *
   *  This function is safe to call multiple times. It will ensure
   *  that the internal buffer is deallocated if it exists. In any
   *  case, it will also reset the buffer pointers.
  */
  void
  disable_buffer();

  /**
   *  Underlying file pointer.
  */
  BZFILE* file;

  /**
   *  Mode in which file was opened.
  */
  std::ios_base::openmode io_mode;

  /**
   *  @brief  True if this object owns file descriptor.
   *
   *  This makes the class responsible for closing the file
   *  upon destruction.
  */
  bool own_fd;

  /**
   *  @brief  Stream buffer.
   *
   *  For simplicity this remains allocated on the free store for the
   *  entire life span of the bzfilebuf object, unless replaced by setbuf.
  */
  char_type* buffer;

  /**
   *  @brief  Stream buffer size.
   *
   *  Defaults to system default buffer size (typically 8192 bytes).
   *  Modified by setbuf.
  */
  std::streamsize buffer_size;

  /**
   *  @brief  True if this object owns stream buffer.
   *
   *  This makes the class responsible for deleting the buffer
   *  upon destruction.
  */
  bool own_buffer;
};

/*****************************************************************************/

/**
 *  @brief  bzip2 file input stream class.
 *
 *  This class implements ifstream for bzip2 files. Seeking and putback
 *  is not supported yet.
*/
class bzifstream : public std::istream
{
public:
  //  Default constructor
  bzifstream();

  /**
   *  @brief  Construct stream on bzip2 file to be opened.
   *  @param  name  File name.
   *  @param  mode  Open mode flags (forced to contain ios::in).
  */
  explicit
  bzifstream(const char* name,
             std::ios_base::openmode mode = std::ios_base::in);

  /**
   *  @brief  Construct stream on already open bzip2 file.
   *  @param  fd    File descriptor.
   *  @param  mode  Open mode flags (forced to contain ios::in).
  */
  explicit
  bzifstream(int fd,
             std::ios_base::openmode mode = std::ios_base::in);

  /**
   *  Obtain underlying stream buffer.
  */
  bzfilebuf*
  rdbuf() const
  { return const_cast<bzfilebuf*>(&sb); }

  /**
   *  @brief  Check if file is open.
   *  @return  True if file is open.
  */
  bool
  is_open() { return sb.is_open(); }

  /**
   *  @brief  Open bzip2 file.
   *  @param  name  File name.
   *  @param  mode  Open mode flags (forced to contain ios::in).
   *
   *  Stream will be in state good() if file opens successfully;
   *  otherwise in state fail(). This differs from the behavior of
   *  ifstream, which never sets the state to good() and therefore
   *  won't allow you to reuse the stream for a second file unless
   *  you manually clear() the state. The choice is a matter of
   *  convenience.
  */
  void
  open(const char* name,
       std::ios_base::openmode mode = std::ios_base::in);

  /**
   *  @brief  Attach to already open bzip2 file.
   *  @param  fd  File descriptor.
   *  @param  mode  Open mode flags (forced to contain ios::in).
   *
   *  Stream will be in state good() if attach succeeded; otherwise
   *  in state fail().
  */
  void
  attach(int fd,
         std::ios_base::openmode mode = std::ios_base::in);

  /**
   *  @brief  Close bzip2 file.
   *
   *  Stream will be in state fail() if close failed.
  */
  void
  close();

private:
  /**
   *  Underlying stream buffer.
  */
  bzfilebuf sb;
};

/*****************************************************************************/

/**
 *  @brief  Gzipped file output stream class.
 *
 *  This class implements ofstream for bzip2 files. Seeking and putback
 *  is not supported yet.
*/
class bzofstream : public std::ostream
{
public:
  //  Default constructor
  bzofstream();

  /**
   *  @brief  Construct stream on bzip2 file to be opened.
   *  @param  name  File name.
   *  @param  mode  Open mode flags (forced to contain ios::out).
  */
  explicit
  bzofstream(const char* name,
             std::ios_base::openmode mode = std::ios_base::out);

  /**
   *  @brief  Construct stream on already open bzip2 file.
   *  @param  fd    File descriptor.
   *  @param  mode  Open mode flags (forced to contain ios::out).
  */
  explicit
  bzofstream(int fd,
             std::ios_base::openmode mode = std::ios_base::out);

  /**
   *  Obtain underlying stream buffer.
  */
  bzfilebuf*
  rdbuf() const
  { return const_cast<bzfilebuf*>(&sb); }

  /**
   *  @brief  Check if file is open.
   *  @return  True if file is open.
  */
  bool
  is_open() { return sb.is_open(); }

  /**
   *  @brief  Open bzip2 file.
   *  @param  name  File name.
   *  @param  mode  Open mode flags (forced to contain ios::out).
   *
   *  Stream will be in state good() if file opens successfully;
   *  otherwise in state fail(). This differs from the behavior of
   *  ofstream, which never sets the state to good() and therefore
   *  won't allow you to reuse the stream for a second file unless
   *  you manually clear() the state. The choice is a matter of
   *  convenience.
  */
  void
  open(const char* name,
       std::ios_base::openmode mode = std::ios_base::out);

  /**
   *  @brief  Attach to already open bzip2 file.
   *  @param  fd  File descriptor.
   *  @param  mode  Open mode flags (forced to contain ios::out).
   *
   *  Stream will be in state good() if attach succeeded; otherwise
   *  in state fail().
  */
  void
  attach(int fd,
         std::ios_base::openmode mode = std::ios_base::out);

  /**
   *  @brief  Close bzip2 file.
   *
   *  Stream will be in state fail() if close failed.
  */
  void
  close();

private:
  /**
   *  Underlying stream buffer.
  */
  bzfilebuf sb;
};

/*****************************************************************************/

/**
 *  @brief  Gzipped file output stream manipulator class.
 *
 *  This class defines a two-argument manipulator for bzofstream. It is used
 *  as base for the setcompression(int,int) manipulator.
*/
template<typename T1, typename T2>
  class bzomanip2
  {
  public:
    // Allows insertor to peek at internals
    template <typename Ta, typename Tb>
      friend bzofstream&
      operator<<(bzofstream&,
                 const bzomanip2<Ta,Tb>&);

    // Constructor
    bzomanip2(bzofstream& (*f)(bzofstream&, T1, T2),
              T1 v1,
              T2 v2);
  private:
    // Underlying manipulator function
    bzofstream&
    (*func)(bzofstream&, T1, T2);

    // Arguments for manipulator function
    T1 val1;
    T2 val2;
  };

/*****************************************************************************/


// Manipulator constructor stores arguments
template<typename T1, typename T2>
  inline
  bzomanip2<T1,T2>::bzomanip2(bzofstream &(*f)(bzofstream &, T1, T2),
                              T1 v1,
                              T2 v2)
  : func(f), val1(v1), val2(v2)
  { }

// Insertor applies underlying manipulator function to stream
template<typename T1, typename T2>
  inline bzofstream&
  operator<<(bzofstream& s, const bzomanip2<T1,T2>& m)
  { return (*m.func)(s, m.val1, m.val2); }


#endif // BZFSTREAM_H