SeqAn-1.1/seqan/file/file_generated_forwards.h

   1  /*==========================================================================
   2                 SeqAn - The Library for Sequence Analysis
   3                           http://www.seqan.de
   4  ============================================================================
   5   Copyright (C) 2007
   6
   7   This library is free software; you can redistribute it and/or
   8   modify it under the terms of the GNU Lesser General Public
   9   License as published by the Free Software Foundation; either
  10   version 3 of the License, or (at your option) any later version.
  11
  12   This library is distributed in the hope that it will be useful,
  13   but WITHOUT ANY WARRANTY; without even the implied warranty of
  14   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  15   Lesser General Public License for more details.
  16
  17  ==========================================================================*/
  18
  19 #ifndef SEQAN_HEADER_FILE_GENERATED_FORWARDS_H
  20 #define SEQAN_HEADER_FILE_GENERATED_FORWARDS_H
  21
  22 //////////////////////////////////////////////////////////////////////////////
  23 // NOTE: This file is automatically generated by build_forwards.py
  24 //       Do not edit this file manually!
  25 //////////////////////////////////////////////////////////////////////////////
  26
  27
  28 //////////////////////////////////////////////////////////////////////////////
  29 // CLASSES
  30 //////////////////////////////////////////////////////////////////////////////
  31
  32 namespace SEQAN_NAMESPACE_MAIN {
  33
  34 //____________________________________________________________________________
  35 // Async
  36
  37 template <typename TSpec > struct Async;        // "projects/library/seqan/file/file_base.h"(58)
  38
  39 //____________________________________________________________________________
  40 // Chained
  41
  42 template <__int64 _FileSize , typename TFile > struct Chained;          // "projects/library/seqan/file/file_base.h"(90)
  43
  44 //____________________________________________________________________________
  45 // ChunkLength
  46
  47 template <typename T> struct ChunkLength;               // "projects/library/seqan/file/chunk_collector.h"(41)
  48
  49 //____________________________________________________________________________
  50 // DefaultOpenMode
  51
  52 template <typename T> struct DefaultOpenMode;           // "projects/library/seqan/file/file_base.h"(122)
  53
  54 //____________________________________________________________________________
  55 // DefaultOpenTempMode
  56
  57 template <typename T> struct DefaultOpenTempMode;               // "projects/library/seqan/file/file_base.h"(127)
  58
  59 //____________________________________________________________________________
  60 // Dynamic
  61
  62 template <typename TSpec > struct Dynamic;              // "projects/library/seqan/file/file_page.h"(185)
  63
  64 //____________________________________________________________________________
  65 // External
  66
  67 template <typename TConfig > struct External;           // "projects/library/seqan/file/string_external.h"(158)
  68
  69 //____________________________________________________________________________
  70 // ExternalConfig
  71
  72 template <typename _TFile , unsigned _PageSize , unsigned _Frames > struct ExternalConfig;              // "projects/library/seqan/file/string_external.h"(83)
  73
  74 //____________________________________________________________________________
  75 // ExternalConfigLarge
  76
  77 template <typename _TFile , unsigned _PageSize , unsigned _Frames > struct ExternalConfigLarge;         // "projects/library/seqan/file/string_external.h"(118)
  78
  79 //____________________________________________________________________________
  80 // ExternalConfigSize
  81
  82 template <typename TSize, typename _TFile , unsigned _PageSize , unsigned _Frames > struct ExternalConfigSize;          // "projects/library/seqan/file/string_external.h"(150)
  83
  84 //____________________________________________________________________________
  85 // File
  86
  87 template <typename TSpec > class File;          // "projects/library/seqan/file/file_base.h"(71)
  88
  89 //____________________________________________________________________________
  90 // FileFormat
  91
  92 template <typename TFile, typename TData, typename TMeta, typename TFormat > struct FileFormat;         // "projects/library/seqan/file/file_format.h"(60)
  93
  94 //____________________________________________________________________________
  95 // FileReader
  96
  97 template <typename TFormat, typename TFile , typename TSpec > struct FileReader;        // "projects/library/seqan/file/file_filereaderiterator.h"(30)
  98
  99 //____________________________________________________________________________
 100 // FileReaderIterator
 101
 102 struct FileReaderIterator;              // "projects/library/seqan/file/file_filereader.h"(402)
 103
 104 //____________________________________________________________________________
 105 // Fixed
 106
 107 template <unsigned _PageSize > struct Fixed;            // "projects/library/seqan/file/file_page.h"(228)
 108
 109 //____________________________________________________________________________
 110 // PageBucket
 111
 112 template <typename TValue > struct PageBucket;          // "projects/library/seqan/file/file_page.h"(159)
 113
 114 //____________________________________________________________________________
 115 // PageBucketExtended
 116
 117 template <typename TValue > struct PageBucketExtended;          // "projects/library/seqan/file/file_page.h"(165)
 118
 119 //____________________________________________________________________________
 120 // PageChain
 121
 122 template <typename TPageFrame > struct PageChain;               // "projects/library/seqan/file/file_page.h"(189)
 123 template <typename TPageFrame > struct PageChain;               // "projects/library/seqan/file/file_page.h"(509)
 124
 125 //____________________________________________________________________________
 126 // PageContainer
 127
 128 template <typename TPageFrame, unsigned _Frames, unsigned _PriorityLevels > struct PageContainer;               // "projects/library/seqan/file/file_page.h"(723)
 129
 130 //____________________________________________________________________________
 131 // PageFrame
 132
 133 template <typename TValue, typename TFile, typename TSpec > struct PageFrame;           // "projects/library/seqan/file/file_page.h"(178)
 134
 135 //____________________________________________________________________________
 136 // Row
 137
 138 template <typename T> struct Row;               // "projects/library/seqan/file/file_format_fasta_align.h"(33)
 139
 140 //____________________________________________________________________________
 141 // Rows
 142
 143 template <typename T> struct Rows;              // "projects/library/seqan/file/file_format_fasta_align.h"(36)
 144
 145 //____________________________________________________________________________
 146 // SimpleBuffer
 147
 148 template <typename TValue > struct SimpleBuffer;        // "projects/library/seqan/file/file_page.h"(35)
 149
 150 //____________________________________________________________________________
 151 // Striped
 152
 153 template <unsigned _FileCount , typename TFile > struct Striped;        // "projects/library/seqan/file/file_base.h"(107)
 154
 155 //____________________________________________________________________________
 156 // Sync
 157
 158 template <typename TSpec > struct Sync;         // "projects/library/seqan/file/file_base.h"(47)
 159
 160 //____________________________________________________________________________
 161 // TagCGViz_
 162
 163 struct TagCGViz_;               // "projects/library/seqan/file/file_format_cgviz.h"(36)
 164
 165 //____________________________________________________________________________
 166 // TagEmbl_
 167
 168 struct TagEmbl_;        // "projects/library/seqan/file/file_format_embl.h"(34)
 169
 170 //____________________________________________________________________________
 171 // TagFastaAlign_
 172
 173 struct TagFastaAlign_;          // "projects/library/seqan/file/file_format_fasta_align.h"(44)
 174
 175 //____________________________________________________________________________
 176 // TagFasta_
 177
 178 struct TagFasta_;               // "projects/library/seqan/file/file_format_fasta.h"(35)
 179
 180 //____________________________________________________________________________
 181 // TagGenbank_
 182
 183 struct TagGenbank_;             // "projects/library/seqan/file/file_format_genbank.h"(35)
 184
 185 //____________________________________________________________________________
 186 // TagRaw_
 187
 188 struct TagRaw_;         // "projects/library/seqan/file/file_format_raw.h"(37)
 189
 190 //____________________________________________________________________________
 191 // VectorConstIterator
 192
 193 template <typename _Vector > struct VectorConstIterator;        // "projects/library/seqan/file/string_external.h"(275)
 194
 195 //____________________________________________________________________________
 196 // VectorFwdConstIterator
 197
 198 template <typename _Vector > struct VectorFwdConstIterator;             // "projects/library/seqan/file/string_external.h"(641)
 199
 200 //____________________________________________________________________________
 201 // VectorFwdIterator
 202
 203 template <typename _Vector > struct VectorFwdIterator;          // "projects/library/seqan/file/string_external.h"(392)
 204
 205 //____________________________________________________________________________
 206 // VectorIterator
 207
 208 template <typename _Vector > struct VectorIterator;             // "projects/library/seqan/file/string_external.h"(165)
 209
 210 //____________________________________________________________________________
 211 // _Append_ChunkCollector_2_String
 212
 213 template <typename TExpand> struct _Append_ChunkCollector_2_String;             // "projects/library/seqan/file/chunk_collector.h"(334)
 214
 215 //____________________________________________________________________________
 216 // _Assign_ChunkCollector_2_String
 217
 218 template <typename TExpand> struct _Assign_ChunkCollector_2_String;             // "projects/library/seqan/file/chunk_collector.h"(264)
 219
 220 //____________________________________________________________________________
 221 // _Assign_Stream_2_ChunkCollector
 222
 223 struct _Assign_Stream_2_ChunkCollector;         // "projects/library/seqan/file/chunk_collector.h"(186)
 224
 225 //____________________________________________________________________________
 226 // _ChunkCollector
 227
 228 template <typename THost> class _ChunkCollector;        // "projects/library/seqan/file/chunk_collector.h"(51)
 229
 230 //____________________________________________________________________________
 231 // _FileReader_Types
 232
 233 template <typename T> struct _FileReader_Types;         // "projects/library/seqan/file/file_filereader.h"(410)
 234
 235 //____________________________________________________________________________
 236 // _IsTellSeekStream
 237
 238 template <typename T> struct _IsTellSeekStream;         // "projects/library/seqan/file/stream.h"(179)
 239 template <typename T> struct _IsTellSeekStream;         // "projects/library/seqan/file/cstream.h"(63)
 240
 241 //____________________________________________________________________________
 242 // _Read_Raw
 243
 244 template <typename TFile, typename TData, typename TTag> struct _Read_Raw;              // "projects/library/seqan/file/file_format_raw.h"(47)
 245
 246 //____________________________________________________________________________
 247 // _Replace_ChunkCollector_2_String
 248
 249 template <typename TExpand> struct _Replace_ChunkCollector_2_String;            // "projects/library/seqan/file/chunk_collector.h"(407)
 250
 251 //____________________________________________________________________________
 252 // aDummyRequest
 253
 254 struct aDummyRequest;           // "projects/library/seqan/file/file_base.h"(143)
 255
 256 //____________________________________________________________________________
 257 // aRequest
 258
 259 template <typename T > struct aRequest;         // "projects/library/seqan/file/file_base.h"(156)
 260
 261 } //namespace SEQAN_NAMESPACE_MAIN
 262
 263
 264 //////////////////////////////////////////////////////////////////////////////
 265 // TYPEDEFS
 266 //////////////////////////////////////////////////////////////////////////////
 267
 268 namespace SEQAN_NAMESPACE_MAIN {
 269
 270 //____________________________________________________________________________
 271 // CGViz
 272
 273 typedef Tag<TagCGViz_> const CGViz;             // "projects/library/seqan/file/file_format_cgviz.h"(37)
 274
 275 //____________________________________________________________________________
 276 // Embl
 277
 278 typedef Tag<TagEmbl_> const Embl;               // "projects/library/seqan/file/file_format_embl.h"(35)
 279
 280 //____________________________________________________________________________
 281 // Fasta
 282
 283 typedef Tag<TagFasta_> const Fasta;             // "projects/library/seqan/file/file_format_fasta.h"(36)
 284
 285 //____________________________________________________________________________
 286 // FastaAlign
 287
 288 typedef Tag<TagFastaAlign_> const FastaAlign;           // "projects/library/seqan/file/file_format_fasta_align.h"(45)
 289
 290 //____________________________________________________________________________
 291 // Genbank
 292
 293 typedef Tag<TagGenbank_> const Genbank;         // "projects/library/seqan/file/file_format_genbank.h"(36)
 294
 295 //____________________________________________________________________________
 296 // Raw
 297
 298 typedef Tag<TagRaw_> const Raw;         // "projects/library/seqan/file/file_format_raw.h"(38)
 299
 300 } //namespace SEQAN_NAMESPACE_MAIN
 301
 302
 303 //////////////////////////////////////////////////////////////////////////////
 304 // FUNCTIONS
 305 //////////////////////////////////////////////////////////////////////////////
 306
 307 namespace SEQAN_NAMESPACE_MAIN {
 308
 309 //____________________________________________________________________________
 310 // _FileReaderString_construct
 311
 312 template <typename TValue, typename TFormat, typename TFile, typename TSpec> inline void _FileReaderString_construct(String<TValue, FileReader<TFormat, TFile, TSpec> > & me);          // "projects/library/seqan/file/file_filereader.h"(254)
 313
 314 //____________________________________________________________________________
 315 // _FileReaderString_findblock
 316
 317 template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TPosition> inline unsigned int _FileReaderString_findblock(String<TValue, FileReader<TFormat, TFile, TSpec> > & me, TPosition pos);               // "projects/library/seqan/file/file_filereader.h"(233)
 318
 319 //____________________________________________________________________________
 320 // _FileReaderString_isValidBlock
 321
 322 template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TUint> inline bool _FileReaderString_isValidBlock(String<TValue, FileReader<TFormat, TFile, TSpec> > & me, TUint block_number);           // "projects/library/seqan/file/file_filereader.h"(271)
 323
 324 //____________________________________________________________________________
 325 // _FileReaderString_loadComplete
 326
 327 template <typename TValue, typename TFormat, typename TFile, typename TSpec> inline void _FileReaderString_loadComplete(String<TValue, FileReader<TFormat, TFile, TSpec> > & me);               // "projects/library/seqan/file/file_filereader.h"(288)
 328
 329 //____________________________________________________________________________
 330 // _FileReaderString_loadblock
 331
 332 template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TPosition> inline void _FileReaderString_loadblock(String<TValue, FileReader<TFormat, TFile, TSpec> > & me, TPosition blocknum);          // "projects/library/seqan/file/file_filereader.h"(167)
 333
 334 //____________________________________________________________________________
 335 // _cancelFArray
 336
 337 template <typename TFileArray, typename TRequest > inline bool _cancelFArray(TFileArray &me, TRequest &request);        // "projects/library/seqan/file/file_array.h"(272)
 338
 339 //____________________________________________________________________________
 340 // _closeFArray
 341
 342 template <typename TFileArray > inline bool _closeFArray(TFileArray &me);               // "projects/library/seqan/file/file_array.h"(242)
 343
 344 //____________________________________________________________________________
 345 // _dataFile
 346
 347 template <typename TValue, typename TFormat, typename TFile, typename TSpec> inline TFile & _dataFile(String<TValue, FileReader<TFormat, TFile, TSpec> > & me);         // "projects/library/seqan/file/file_filereader.h"(156)
 348
 349 //____________________________________________________________________________
 350 // _fasta_align_scan_line
 351
 352 template <typename TFile, typename TSize> void _fasta_align_scan_line(TFile & file, TSize & count);             // "projects/library/seqan/file/file_format_fasta_align.h"(51)
 353
 354 //____________________________________________________________________________
 355 // _fasta_scan_line
 356
 357 template <typename TFile, typename TSize> inline typename Value<TFile>::Type _fasta_scan_line(TFile & file, TSize & count_valid, TSize & count_all);            // "projects/library/seqan/file/file_format_fasta.h"(145)
 358
 359 //____________________________________________________________________________
 360 // _flushFArray
 361
 362 template <typename TFileArray > inline bool _flushFArray(TFileArray &me);               // "projects/library/seqan/file/file_array.h"(264)
 363
 364 //____________________________________________________________________________
 365 // _getCStyleOpenMode
 366
 367 inline const char * _getCStyleOpenMode(int openMode);           // "projects/library/seqan/file/file_cstyle.h"(66)
 368
 369 //____________________________________________________________________________
 370 // _openTempFArray
 371
 372 template <typename TFileArray > inline bool _openTempFArray(TFileArray &me, int openMode);              // "projects/library/seqan/file/file_array.h"(221)
 373 template <typename TFileArray > inline bool _openTempFArray(TFileArray &me);            // "projects/library/seqan/file/file_array.h"(229)
 374
 375 //____________________________________________________________________________
 376 // _read_n_chars_from_file
 377
 378 template <typename TFile, typename TSize> inline void _read_n_chars_from_file(TFile & file, TSize count);               // "projects/library/seqan/file/file_format_fasta.h"(187)
 379
 380 //____________________________________________________________________________
 381 // _reopenFArray
 382
 383 template <typename TFileArray > inline bool _reopenFArray(TFileArray &me, int openMode);        // "projects/library/seqan/file/file_array.h"(234)
 384
 385 //____________________________________________________________________________
 386 // _sectorSizeFArray
 387
 388 template <typename TFileArray > inline unsigned _sectorSizeFArray(TFileArray &me, int openMode);        // "projects/library/seqan/file/file_array.h"(250)
 389
 390 //____________________________________________________________________________
 391 // _sizeFArray
 392
 393 template <typename TFileArray > inline typename Size<TFileArray>::Type _sizeFArray(TFileArray &me);             // "projects/library/seqan/file/file_array.h"(256)
 394
 395 //____________________________________________________________________________
 396 // _streamClose
 397
 398 inline void _streamClose(::std::FILE * & me);           // "projects/library/seqan/file/cstream.h"(93)
 399
 400 //____________________________________________________________________________
 401 // _streamEOF
 402
 403 template <typename TValue, typename TTraits> inline bool _streamEOF(::std::basic_ios<TValue, TTraits> const & me);              // "projects/library/seqan/file/stream.h"(209)
 404 inline bool _streamEOF(::std::FILE * me);               // "projects/library/seqan/file/cstream.h"(108)
 405
 406 //____________________________________________________________________________
 407 // _streamGet
 408
 409 template <typename TValue, typename TTraits> inline TValue _streamGet(::std::basic_istream<TValue, TTraits> & source);          // "projects/library/seqan/file/stream.h"(253)
 410 inline char _streamGet(::std::FILE * source);           // "projects/library/seqan/file/cstream.h"(133)
 411
 412 //____________________________________________________________________________
 413 // _streamOpen
 414
 415 inline bool _streamOpen(::std::FILE * & me, String<char> path, bool for_read );         // "projects/library/seqan/file/cstream.h"(75)
 416
 417 //____________________________________________________________________________
 418 // _streamPeek
 419
 420 template <typename TValue, typename TTraits> inline TValue _streamPeek(::std::basic_istream<TValue, TTraits> & source);         // "projects/library/seqan/file/stream.h"(273)
 421
 422 //____________________________________________________________________________
 423 // _streamPut
 424
 425 template <typename TValue, typename TTraits, typename TChar> inline void _streamPut(::std::basic_ostream<TValue, TTraits> & target, TChar character);           // "projects/library/seqan/file/stream.h"(313)
 426 inline void _streamPut(::std::FILE * target, char character);           // "projects/library/seqan/file/cstream.h"(145)
 427
 428 //____________________________________________________________________________
 429 // _streamPutFloat
 430
 431 template <typename TStream> inline void _streamPutFloat(TStream & target, float number, char const * format_string);            // "projects/library/seqan/file/stream_algorithms.h"(73)
 432 template <typename TStream> inline void _streamPutFloat(TStream & target, float number);        // "projects/library/seqan/file/stream_algorithms.h"(83)
 433
 434 //____________________________________________________________________________
 435 // _streamPutInt
 436
 437 template <typename TStream> inline void _streamPutInt(TStream & target, int number, char const * format_string);        // "projects/library/seqan/file/stream_algorithms.h"(44)
 438 template <typename TStream> inline void _streamPutInt(TStream & target, int number);            // "projects/library/seqan/file/stream_algorithms.h"(54)
 439
 440 //____________________________________________________________________________
 441 // _streamRead
 442
 443 template <typename TValue, typename TTraits> inline ::std::streamsize _streamRead(TValue * target, ::std::basic_istream<TValue, TTraits> & source, ::std::streamsize limit);            // "projects/library/seqan/file/stream.h"(232)
 444 template <typename TValue> inline size_t _streamRead(TValue * target, ::std::FILE * source, size_t limit);              // "projects/library/seqan/file/cstream.h"(122)
 445
 446 //____________________________________________________________________________
 447 // _streamSeek2G
 448
 449 template <typename TValue, typename TTraits> inline void _streamSeek2G(::std::basic_istream<TValue, TTraits> & me, int off);            // "projects/library/seqan/file/stream.h"(420)
 450 inline void _streamSeek2G(FILE * me, int off);          // "projects/library/seqan/file/cstream.h"(208)
 451
 452 //____________________________________________________________________________
 453 // _streamSeekG
 454
 455 template <typename TValue, typename TTraits> inline void _streamSeekG(::std::basic_istream<TValue, TTraits> & me, typename Position< ::std::basic_istream<TValue, TTraits> >::Type pos);        // "projects/library/seqan/file/stream.h"(373)
 456 inline void _streamSeekG(FILE * me, Position<FILE *>::Type pos);        // "projects/library/seqan/file/cstream.h"(184)
 457
 458 //____________________________________________________________________________
 459 // _streamSeekP
 460
 461 template <typename TValue, typename TTraits> inline void _streamSeekP(::std::basic_ostream<TValue, TTraits> & me, typename Position< ::std::basic_ostream<TValue, TTraits> >::Type pos);        // "projects/library/seqan/file/stream.h"(397)
 462 inline void _streamSeekP(FILE * me, Position<FILE *>::Type pos);        // "projects/library/seqan/file/cstream.h"(196)
 463
 464 //____________________________________________________________________________
 465 // _streamTellG
 466
 467 template <typename TValue, typename TTraits> inline typename Position< ::std::basic_istream<TValue, TTraits> >::Type _streamTellG(::std::basic_istream<TValue, TTraits> & me);          // "projects/library/seqan/file/stream.h"(332)
 468 inline Position<FILE *>::Type _streamTellG(FILE * me);          // "projects/library/seqan/file/cstream.h"(161)
 469
 470 //____________________________________________________________________________
 471 // _streamTellP
 472
 473 template <typename TValue, typename TTraits> inline typename Position< ::std::basic_ostream<TValue, TTraits> >::Type _streamTellP(::std::basic_ostream<TValue, TTraits> & me);          // "projects/library/seqan/file/stream.h"(351)
 474 inline Position<FILE *>::Type _streamTellP(FILE * me);          // "projects/library/seqan/file/cstream.h"(172)
 475
 476 //____________________________________________________________________________
 477 // _streamUnget
 478
 479 template <typename TValue, typename TTraits> inline void _streamUnget(::std::basic_istream<TValue, TTraits> & source);          // "projects/library/seqan/file/stream.h"(292)
 480 inline void _streamUnget(::std::FILE * stream);         // "projects/library/seqan/file/cstream.h"(219)
 481
 482 //____________________________________________________________________________
 483 // _streamWrite
 484
 485 template <typename TTarget, typename T1, typename T2, typename TCompression> inline void _streamWrite(TTarget & target, Pair<T1, T2, TCompression> const & source);             // "projects/library/seqan/file/stream_algorithms.h"(94)
 486 template <typename TTarget, typename T1, typename T2, typename T3, typename TCompression> inline void _streamWrite(TTarget & target, Triple<T1, T2, T3, TCompression> const & source);          // "projects/library/seqan/file/stream_algorithms.h"(104)
 487 template <typename TTarget, typename TSource> inline void _streamWrite(TTarget & target, TSource const & source);               // "projects/library/seqan/file/stream_algorithms.h"(128)
 488
 489 //____________________________________________________________________________
 490 // _streamWriteRange
 491
 492 template <typename TTarget, typename TIterator> inline void _streamWriteRange(TTarget & target, TIterator begin_, TIterator end_);              // "projects/library/seqan/file/stream_algorithms.h"(193)
 493
 494 //____________________________________________________________________________
 495 // _streamWriteSeq
 496
 497 template <typename TTarget, typename TSource> inline void _streamWriteSeq(TTarget & target, TSource const & source, False const);               // "projects/library/seqan/file/stream_algorithms.h"(140)
 498 template <typename TTarget, typename TSource> inline void _streamWriteSeq(TTarget & target, TSource const & source, True const);        // "projects/library/seqan/file/stream_algorithms.h"(151)
 499 template <typename TTarget, typename TSourceValue> inline void _streamWriteSeq(TTarget & target, TSourceValue const * source, True const);              // "projects/library/seqan/file/stream_algorithms.h"(168)
 500
 501 //____________________________________________________________________________
 502 // _stream_appendLine
 503
 504 template <typename TFile, typename TString, typename TChar> inline void _stream_appendLine(TFile & file, TString & str, TChar & c);             // "projects/library/seqan/file/file_format.h"(432)
 505
 506 //____________________________________________________________________________
 507 // _stream_countLine
 508
 509 template <typename TFile, typename TChar> inline void _stream_countLine(TFile & file, TChar & c);               // "projects/library/seqan/file/file_format.h"(464)
 510
 511 //____________________________________________________________________________
 512 // _stream_isLetter
 513
 514 template <typename TChar> inline bool _stream_isLetter(TChar const c);          // "projects/library/seqan/file/file_format.h"(564)
 515
 516 //____________________________________________________________________________
 517 // _stream_readWord
 518
 519 template <typename TFile, typename TChar> inline String<char> _stream_readWord(TFile & file, TChar& c);         // "projects/library/seqan/file/file_format.h"(548)
 520
 521 //____________________________________________________________________________
 522 // _stream_skipLine
 523
 524 template <typename TFile, typename TChar> inline typename Size<TFile>::Type _stream_skipLine(TFile & file, TChar & c);          // "projects/library/seqan/file/file_format.h"(495)
 525
 526 //____________________________________________________________________________
 527 // _stream_skipWhitespace
 528
 529 template <typename TFile, typename TChar> inline void _stream_skipWhitespace(TFile& file, TChar& c);            // "projects/library/seqan/file/file_format.h"(534)
 530
 531 //____________________________________________________________________________
 532 // _string_appendLine
 533
 534 template <typename TString1, typename TString2, typename TIter> inline void _string_appendLine(TString1 & str, TString2 & a_str, TIter & it);           // "projects/library/seqan/file/file_format.h"(624)
 535
 536 //____________________________________________________________________________
 537 // _string_readNumber
 538
 539 template <typename TString, typename TIter> inline int _string_readNumber(TString & str, TIter& it);            // "projects/library/seqan/file/file_format.h"(668)
 540
 541 //____________________________________________________________________________
 542 // _string_skipLine
 543
 544 template <typename TString, typename TIter> inline typename Size<TString>::Type _string_skipLine(TString & str, TIter & it);            // "projects/library/seqan/file/file_format.h"(588)
 545
 546 //____________________________________________________________________________
 547 // _string_skipWhitespace
 548
 549 template <typename TString, typename TIter> inline void _string_skipWhitespace(TString& str, TIter& it);        // "projects/library/seqan/file/file_format.h"(655)
 550
 551 //____________________________________________________________________________
 552 // _write_impl
 553
 554 template <typename TFile, typename TStringContainer, typename TSource, typename TSpec> void _write_impl(TFile& target, Align<TSource, TSpec>& align, TStringContainer& ids, CGViz);             // "projects/library/seqan/file/file_format_cgviz.h"(62)
 555 template <typename TFile, typename TString, typename TData> void _write_impl(TFile & file, TData & data, TString & id, Fasta);          // "projects/library/seqan/file/file_format_fasta.h"(434)
 556 template <typename TFile, typename TStringContainer, typename TSource, typename TSpec> void _write_impl(TFile& file, Align<TSource, TSpec>& align, TStringContainer& ids, FastaAlign);          // "projects/library/seqan/file/file_format_fasta_align.h"(246)
 557
 558 //____________________________________________________________________________
 559 // alignSize
 560
 561 template <typename T1, typename T2> inline T1 alignSize(T1 _size, T2 _aligning);        // "projects/library/seqan/file/file_base.h"(688)
 562
 563 //____________________________________________________________________________
 564 // allocPage
 565
 566 template <typename TValue, typename TSize, typename T > inline void allocPage(SimpleBuffer<TValue> &pf, TSize size, T const & me);              // "projects/library/seqan/file/file_page.h"(119)
 567 template <typename TValue, typename TFile, typename TSpec, typename T > inline void allocPage(PageFrame<TValue, TFile, TSpec> &pf, T const & me);               // "projects/library/seqan/file/file_page.h"(334)
 568
 569 //____________________________________________________________________________
 570 // allocate
 571
 572 template <__int64 _FileSize, typename TFile, typename TValue, typename TSize > inline void allocate(File< Chained<_FileSize, TFile> > const &me, TValue* &data, TSize count);           // "projects/library/seqan/file/file_array.h"(340)
 573 template <unsigned _FileCount, typename TFile, typename TValue, typename TSize > inline void allocate(File< Striped<_FileCount, TFile> > const &me, TValue* &data, TSize count);        // "projects/library/seqan/file/file_array.h"(350)
 574
 575 //____________________________________________________________________________
 576 // append
 577
 578 template <typename TValue, typename TConfig, typename TString, typename TExpand > inline void append(String<TValue, External<TConfig> > &me, TString const &string, Tag<TExpand> const expand);         // "projects/library/seqan/file/string_external.h"(1895)
 579 template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand> inline void append(String<TTargetValue, TTargetSpec> & target, _ChunkCollector<TSourceHost> const & source, Tag<TExpand> const );        // "projects/library/seqan/file/chunk_collector.h"(390)
 580 template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand> inline void append(String<TTargetValue, TTargetSpec> & target, _ChunkCollector<TSourceHost> const & source, typename Size< String<TTargetValue, TTargetSpec> >::Type limit, Tag<TExpand> const );        // "projects/library/seqan/file/chunk_collector.h"(399)
 581
 582 //____________________________________________________________________________
 583 // appendValue
 584
 585 template <typename TValue, typename TConfig, typename TExpand > inline void appendValue(String<TValue, External<TConfig> > &me, TValue const &_Val, Tag<TExpand> const);        // "projects/library/seqan/file/string_external.h"(1886)
 586
 587 //____________________________________________________________________________
 588 // areadAt
 589
 590 template <typename File, typename TValue, typename TSize, typename TPos, typename aRequest > inline bool areadAt(File & me, TValue *memPtr, TSize const count, TPos const fileOfs, aRequest &request);          // "projects/library/seqan/file/file_base.h"(588)
 591 template <__int64 _FileSize, typename TFile, typename TValue, typename TSize, typename TOffset, typename TRequest > inline bool areadAt(File< Chained<_FileSize, TFile> > &me, TValue *memPtr, TSize count, TOffset offset, TRequest &req);             // "projects/library/seqan/file/file_array.h"(392)
 592
 593 //____________________________________________________________________________
 594 // assign
 595
 596 template <typename TValue, typename TConfig, typename TSource, typename TExpand > inline void assign( String<TValue, External<TConfig> > &target, TSource const &source, Tag<TExpand> const);           // "projects/library/seqan/file/string_external.h"(1937)
 597 template <typename THost, typename TSource> inline void assign(_ChunkCollector<THost> & target, TSource & source);              // "projects/library/seqan/file/chunk_collector.h"(231)
 598 template <typename THost, typename TSource> inline void assign(_ChunkCollector<THost> & target, TSource const & source);        // "projects/library/seqan/file/chunk_collector.h"(238)
 599 template <typename THost, typename TSource, typename TSize> inline void assign(_ChunkCollector<THost> & target, TSource & source, TSize limit);         // "projects/library/seqan/file/chunk_collector.h"(247)
 600 template <typename THost, typename TSource, typename TSize> inline void assign(_ChunkCollector<THost> & target, TSource const & source, TSize limit);           // "projects/library/seqan/file/chunk_collector.h"(255)
 601 template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand> inline void assign(String<TTargetValue, TTargetSpec> & target, _ChunkCollector<TSourceHost> const & source, Tag<TExpand> const tag);             // "projects/library/seqan/file/chunk_collector.h"(316)
 602 template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand> inline void assign(String<TTargetValue, TTargetSpec> & target, _ChunkCollector<TSourceHost> const & source, typename Size< String<TTargetValue, TTargetSpec> >::Type limit, Tag<TExpand> const tag);             // "projects/library/seqan/file/chunk_collector.h"(325)
 603
 604 //____________________________________________________________________________
 605 // atBegin
 606
 607 template <typename TContainer> inline bool atBegin(Iter<TContainer, FileReaderIterator> & it);          // "projects/library/seqan/file/file_filereader.h"(760)
 608 template <typename TContainer> inline bool atBegin(Iter<TContainer, FileReaderIterator> const & it);            // "projects/library/seqan/file/file_filereader.h"(766)
 609 template <typename TExtString> inline bool atBegin(VectorIterator<TExtString> &it);             // "projects/library/seqan/file/string_external.h"(1650)
 610 template <typename TExtString> inline bool atBegin(VectorIterator<TExtString> const &it);               // "projects/library/seqan/file/string_external.h"(1652)
 611 template <typename TExtString> inline bool atBegin(VectorConstIterator<TExtString> &it);        // "projects/library/seqan/file/string_external.h"(1655)
 612 template <typename TExtString> inline bool atBegin(VectorConstIterator<TExtString> const &it);          // "projects/library/seqan/file/string_external.h"(1657)
 613 template <typename TExtString> inline bool atBegin(VectorFwdIterator<TExtString> &it);          // "projects/library/seqan/file/string_external.h"(1660)
 614 template <typename TExtString> inline bool atBegin(VectorFwdIterator<TExtString> const &it);            // "projects/library/seqan/file/string_external.h"(1664)
 615 template <typename TExtString> inline bool atBegin(VectorFwdConstIterator<TExtString> &it);             // "projects/library/seqan/file/string_external.h"(1669)
 616 template <typename TExtString> inline bool atBegin(VectorFwdConstIterator<TExtString> const &it);               // "projects/library/seqan/file/string_external.h"(1673)
 617
 618 //____________________________________________________________________________
 619 // atEnd
 620
 621 template <typename TContainer> inline bool atEnd(Iter<TContainer, FileReaderIterator> & it);            // "projects/library/seqan/file/file_filereader.h"(745)
 622 template <typename TContainer> inline bool atEnd(Iter<TContainer, FileReaderIterator> const & it);              // "projects/library/seqan/file/file_filereader.h"(751)
 623 template <typename TExtString> inline bool atEnd(VectorIterator<TExtString> &it);               // "projects/library/seqan/file/string_external.h"(1679)
 624 template <typename TExtString> inline bool atEnd(VectorIterator<TExtString> const &it);         // "projects/library/seqan/file/string_external.h"(1681)
 625 template <typename TExtString> inline bool atEnd(VectorConstIterator<TExtString> &it);          // "projects/library/seqan/file/string_external.h"(1684)
 626 template <typename TExtString> inline bool atEnd(VectorConstIterator<TExtString> const &it);            // "projects/library/seqan/file/string_external.h"(1686)
 627 template <typename TExtString> inline bool atEnd(VectorFwdIterator<TExtString> &it);            // "projects/library/seqan/file/string_external.h"(1689)
 628 template <typename TExtString> inline bool atEnd(VectorFwdIterator<TExtString> const &it);              // "projects/library/seqan/file/string_external.h"(1693)
 629 template <typename TExtString> inline bool atEnd(VectorFwdConstIterator<TExtString> &it);               // "projects/library/seqan/file/string_external.h"(1698)
 630 template <typename TExtString> inline bool atEnd(VectorFwdConstIterator<TExtString> const &it);         // "projects/library/seqan/file/string_external.h"(1702)
 631 template <typename TFile, typename TFormat, typename TFile2, typename TSpec> inline bool atEnd(Iter<TFile, FileReader<TFormat, TFile2, TSpec> > & it);          // "projects/library/seqan/file/file_filereaderiterator.h"(127)
 632
 633 //____________________________________________________________________________
 634 // awriteAt
 635
 636 template <typename File, typename TValue, typename TSize, typename TPos, typename aRequest > inline bool awriteAt(File & me, TValue const *memPtr, TSize const count, TPos const fileOfs, aRequest &request);           // "projects/library/seqan/file/file_base.h"(612)
 637 template <__int64 _FileSize, typename TFile, typename TValue, typename TSize, typename TOffset, typename TRequest > inline bool awriteAt(File< Chained<_FileSize, TFile> > &me, TValue const *memPtr, TSize count, TOffset offset, TRequest &req);              // "projects/library/seqan/file/file_array.h"(409)
 638
 639 //____________________________________________________________________________
 640 // begin
 641
 642 template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TIteratorSpec> inline typename Iterator< String<TValue, FileReader<TFormat, TFile, TSpec> >, TIteratorSpec >::Type begin(String<TValue, FileReader<TFormat, TFile, TSpec> > & me, Tag<TIteratorSpec> const);              // "projects/library/seqan/file/file_filereader.h"(340)
 643 template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TIteratorSpec> inline typename Iterator< String<TValue, FileReader<TFormat, TFile, TSpec> > const, TIteratorSpec >::Type begin(String<TValue, FileReader<TFormat, TFile, TSpec> > const & me, Tag<TIteratorSpec> const);          // "projects/library/seqan/file/file_filereader.h"(348)
 644 template <typename TValue, typename TConfig, typename TSpec > inline typename Iterator<String<TValue, External<TConfig> >, Tag<TSpec> const>::Type begin(String<TValue, External<TConfig> > &me, Tag<TSpec> const);             // "projects/library/seqan/file/string_external.h"(1834)
 645 template <typename TValue, typename TConfig, typename TSpec > inline typename Iterator<String<TValue, External<TConfig> > const, Tag<TSpec> const>::Type begin(String<TValue, External<TConfig> > const &me, Tag<TSpec> const);         // "projects/library/seqan/file/string_external.h"(1840)
 646 template <typename TValue > inline TValue* begin(SimpleBuffer<TValue> &pf, Standard);           // "projects/library/seqan/file/file_page.h"(134)
 647 template <typename TValue > inline TValue const * begin(SimpleBuffer<TValue> const &pf, Standard);              // "projects/library/seqan/file/file_page.h"(139)
 648
 649 //____________________________________________________________________________
 650 // cancel
 651
 652 template <typename TSpec, typename aRequest > inline bool cancel(File<TSpec> &, aRequest &);            // "projects/library/seqan/file/file_base.h"(675)
 653 template <typename TValue, typename TFile, typename TSpec > inline bool cancel(PageFrame<TValue, TFile, TSpec> &pf, TFile &file);               // "projects/library/seqan/file/file_page.h"(427)
 654
 655 //____________________________________________________________________________
 656 // clear
 657
 658 template <typename TValue, typename TConfig > inline void clear(String<TValue, External<TConfig> > &me);        // "projects/library/seqan/file/string_external.h"(1710)
 659
 660 //____________________________________________________________________________
 661 // close
 662
 663 inline bool close(FILE* me);            // "projects/library/seqan/file/file_cstyle.h"(103)
 664 template <typename TValue, typename TConfig > inline bool close(String<TValue, External<TConfig> > &me);        // "projects/library/seqan/file/string_external.h"(1795)
 665 template <typename TSpec > inline bool close(File<TSpec> & me);         // "projects/library/seqan/file/file_base.h"(261)
 666 template <__int64 _FileSize, typename TFile > inline bool close(File< Chained<_FileSize, TFile> > &me);         // "projects/library/seqan/file/file_array.h"(315)
 667 template <unsigned _FileCount, typename TFile > inline bool close(File< Striped<_FileCount, TFile> > &me);              // "projects/library/seqan/file/file_array.h"(322)
 668
 669 //____________________________________________________________________________
 670 // container
 671
 672 template <typename TContainer> inline TContainer & container(Iter<TContainer, FileReaderIterator> & it);        // "projects/library/seqan/file/file_filereader.h"(573)
 673 template <typename TContainer> inline TContainer & container(Iter<TContainer, FileReaderIterator> const & it);          // "projects/library/seqan/file/file_filereader.h"(579)
 674 template <typename TExtString> inline TExtString & container(VectorIterator<TExtString> &it);           // "projects/library/seqan/file/string_external.h"(1629)
 675 template <typename TExtString> inline TExtString & container(VectorIterator<TExtString> const &it);             // "projects/library/seqan/file/string_external.h"(1631)
 676 template <typename TExtString> inline TExtString & container(VectorConstIterator<TExtString> &it);              // "projects/library/seqan/file/string_external.h"(1634)
 677 template <typename TExtString> inline TExtString & container(VectorConstIterator<TExtString> const &it);        // "projects/library/seqan/file/string_external.h"(1636)
 678 template <typename TExtString> inline TExtString & container(VectorFwdIterator<TExtString> &it);        // "projects/library/seqan/file/string_external.h"(1639)
 679 template <typename TExtString> inline TExtString & container(VectorFwdIterator<TExtString> const &it);          // "projects/library/seqan/file/string_external.h"(1641)
 680 template <typename TExtString> inline TExtString & container(VectorFwdConstIterator<TExtString> &it);           // "projects/library/seqan/file/string_external.h"(1644)
 681 template <typename TExtString> inline TExtString & container(VectorFwdConstIterator<TExtString> const &it);             // "projects/library/seqan/file/string_external.h"(1646)
 682
 683 //____________________________________________________________________________
 684 // deallocate
 685
 686 template <__int64 _FileSize, typename TFile, typename TValue, typename TSize > inline void deallocate(File< Chained<_FileSize, TFile> > const &me, TValue* &data, TSize count);         // "projects/library/seqan/file/file_array.h"(345)
 687 template <unsigned _FileCount, typename TFile, typename TValue, typename TSize > inline void deallocate(File< Striped<_FileCount, TFile> > const &me, TValue* &data, TSize count);              // "projects/library/seqan/file/file_array.h"(355)
 688
 689 //____________________________________________________________________________
 690 // enclosingBlocks
 691
 692 template <typename T1, typename T2> inline T1 enclosingBlocks(T1 _size, T2 _blockSize);         // "projects/library/seqan/file/file_base.h"(683)
 693
 694 //____________________________________________________________________________
 695 // end
 696
 697 template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TIteratorSpec> inline typename Iterator< String<TValue, FileReader<TFormat, TFile, TSpec> >, TIteratorSpec >::Type end(String<TValue, FileReader<TFormat, TFile, TSpec> > & me, Tag<TIteratorSpec> const);        // "projects/library/seqan/file/file_filereader.h"(360)
 698 template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TIteratorSpec> inline typename Iterator< String<TValue, FileReader<TFormat, TFile, TSpec> > const, TIteratorSpec >::Type end(String<TValue, FileReader<TFormat, TFile, TSpec> > const & me, Tag<TIteratorSpec> const);            // "projects/library/seqan/file/file_filereader.h"(368)
 699 template <typename TValue, typename TConfig, typename TSpec > inline typename Iterator<String<TValue, External<TConfig> >, Tag<TSpec> const>::Type end(String<TValue, External<TConfig> > &me, Tag<TSpec> const);               // "projects/library/seqan/file/string_external.h"(1846)
 700 template <typename TValue, typename TConfig, typename TSpec > inline typename Iterator<String<TValue, External<TConfig> > const, Tag<TSpec> const>::Type end(String<TValue, External<TConfig> > const &me, Tag<TSpec> const);           // "projects/library/seqan/file/string_external.h"(1853)
 701 template <typename TValue > inline TValue * end(SimpleBuffer<TValue> &pf, Standard);            // "projects/library/seqan/file/file_page.h"(144)
 702 template <typename TValue > inline TValue const * end(SimpleBuffer<TValue> const &pf, Standard);        // "projects/library/seqan/file/file_page.h"(149)
 703
 704 //____________________________________________________________________________
 705 // equiDistantAlignedDistribution
 706
 707 template <typename TValue, typename TSize, typename T, class Function > inline unsigned equiDistantAlignedDistribution( SimpleBuffer<TValue> &_clusterBuffer, unsigned aligning, unsigned _bufferSize, T const &me, TSize _size, unsigned _pageSize, Function const &_Func);            // "projects/library/seqan/file/file_page.h"(934)
 708
 709 //____________________________________________________________________________
 710 // equiDistantDistribution
 711
 712 template <typename TValue, typename TSize, typename T, class Function > inline bool equiDistantDistribution( SimpleBuffer<TValue> &_clusterBuffer, unsigned _bufferSize, T const &me, TSize _size, unsigned _pageSize, Function const &_Func);          // "projects/library/seqan/file/file_page.h"(872)
 713
 714 //____________________________________________________________________________
 715 // flush
 716
 717 inline bool flush(FILE*);               // "projects/library/seqan/file/file_cstyle.h"(182)
 718 template <typename TValue, typename TConfig > inline void flush(String<TValue, External<TConfig> > &me);        // "projects/library/seqan/file/string_external.h"(1722)
 719 template <typename TSpec > inline void flush(File<TSpec> &);            // "projects/library/seqan/file/file_base.h"(631)
 720
 721 //____________________________________________________________________________
 722 // formatID
 723
 724 template <typename TFile, typename TData, typename TMeta, typename TFormat> inline void * formatID(FileFormat<TFile, TData, TMeta, TFormat> const & file_format);               // "projects/library/seqan/file/file_format.h"(171)
 725
 726 //____________________________________________________________________________
 727 // freePage
 728
 729 template <typename TValue, typename T > inline void freePage(SimpleBuffer<TValue> &pf, T const & me);           // "projects/library/seqan/file/file_page.h"(126)
 730 template <typename TValue, typename TFile, typename TSpec, typename T > inline void freePage(PageFrame<TValue, TFile, TSpec> &pf, T const & me);        // "projects/library/seqan/file/file_page.h"(344)
 731
 732 //____________________________________________________________________________
 733 // getValue
 734
 735 template <typename TContainer> inline typename GetValue<Iter<TContainer, FileReaderIterator> >::Type getValue(Iter<TContainer, FileReaderIterator> & it);               // "projects/library/seqan/file/file_filereader.h"(533)
 736 template <typename TContainer> inline typename GetValue<Iter<TContainer, FileReaderIterator> >::Type getValue(Iter<TContainer, FileReaderIterator> const & it);         // "projects/library/seqan/file/file_filereader.h"(544)
 737 template <typename TFile, typename TFormat, typename TFile2, typename TSpec> inline typename GetValue<Iter<TFile, FileReader<TFormat, TFile2, TSpec> > >::Type getValue(Iter<TFile, FileReader<TFormat, TFile2, TSpec> > & it);         // "projects/library/seqan/file/file_filereaderiterator.h"(120)
 738
 739 //____________________________________________________________________________
 740 // goBegin
 741
 742 template <typename TContainer> inline void goBegin(Iter<TContainer, FileReaderIterator> & it);          // "projects/library/seqan/file/file_filereader.h"(711)
 743 template <typename TFile, typename TFile2, typename TSpec> inline void goBegin(Iter<TFile, FileReader<Fasta, TFile2, TSpec> > & it, bool skip_meta);            // "projects/library/seqan/file/file_format_fasta.h"(45)
 744 template <typename TFile, typename TFile2, typename TSpec> inline void goBegin(Iter<TFile, FileReader<Fasta, TFile2, TSpec> > & it);            // "projects/library/seqan/file/file_format_fasta.h"(82)
 745 template <typename TFile, typename TFile2, typename TSpec> inline void goBegin(Iter<TFile, FileReader<Genbank, TFile2, TSpec> > & it, bool skip_meta );         // "projects/library/seqan/file/file_format_genbank.h"(46)
 746 template <typename TFile, typename TFile2, typename TSpec> inline void goBegin(Iter<TFile, FileReader<Embl, TFile2, TSpec> > & it, bool skip_meta );            // "projects/library/seqan/file/file_format_embl.h"(47)
 747
 748 //____________________________________________________________________________
 749 // goEnd
 750
 751 template <typename TContainer> inline void goEnd(Iter<TContainer, FileReaderIterator> & it);            // "projects/library/seqan/file/file_filereader.h"(733)
 752
 753 //____________________________________________________________________________
 754 // goNext
 755
 756 template <typename TFile> void goNext(TFile & file, CGViz);             // "projects/library/seqan/file/file_format_cgviz.h"(48)
 757 template <typename TFile> void goNext(TFile & file, Raw);               // "projects/library/seqan/file/file_format_raw.h"(247)
 758 template <typename TContainer> inline void goNext(Iter<TContainer, FileReaderIterator> & it);           // "projects/library/seqan/file/file_filereader.h"(645)
 759 template <typename TFile, typename TFile2, typename TSpec> inline void goNext(Iter<TFile, FileReader<Fasta, TFile2, TSpec> > & it);             // "projects/library/seqan/file/file_format_fasta.h"(90)
 760 template <typename TFile> void goNext(TFile & file, Fasta);             // "projects/library/seqan/file/file_format_fasta.h"(390)
 761 template <typename TFile, typename TFile2, typename TSpec> inline void goNext(Iter<TFile, FileReader<Genbank, TFile2, TSpec> > & it);           // "projects/library/seqan/file/file_format_genbank.h"(124)
 762 template <typename TFile> inline void goNext(TFile & file, Genbank);            // "projects/library/seqan/file/file_format_genbank.h"(254)
 763 template <typename TFile> void goNext(TFile & file, FastaAlign);        // "projects/library/seqan/file/file_format_fasta_align.h"(233)
 764 template <typename TFile, typename TData, typename TMeta, typename TFormat> inline void goNext(TFile & file, FileFormat<TFile, TData, TMeta, TFormat> const & file_format);             // "projects/library/seqan/file/file_format.h"(251)
 765 template <typename TFile, typename TFile2, typename TSpec> inline void goNext(Iter<TFile, FileReader<Embl, TFile2, TSpec> > & it);              // "projects/library/seqan/file/file_format_embl.h"(108)
 766 template <typename TFile> inline void goNext(TFile & file, Embl);               // "projects/library/seqan/file/file_format_embl.h"(427)
 767
 768 //____________________________________________________________________________
 769 // goPrevious
 770
 771 template <typename TContainer> inline void goPrevious(Iter<TContainer, FileReaderIterator> & it);               // "projects/library/seqan/file/file_filereader.h"(677)
 772
 773 //____________________________________________________________________________
 774 // guessFileFormat
 775
 776 template <typename TFile, typename TData, typename TMeta> inline FileFormat<TFile, TData, TMeta, void> & guessFileFormat(TFile & file, TData & data);           // "projects/library/seqan/file/file_format_guess.h"(52)
 777
 778 //____________________________________________________________________________
 779 // host
 780
 781 template <typename TFile, typename TFormat, typename TFile2, typename TSpec> inline TFile & host(Iter<TFile, FileReader<TFormat, TFile2, TSpec> > & it);        // "projects/library/seqan/file/file_filereaderiterator.h"(105)
 782
 783 //____________________________________________________________________________
 784 // id
 785
 786 template <typename TValue, typename TFormat, typename TFile, typename TSpec> inline void const * id(String<TValue, FileReader<TFormat, TFile, TSpec> > const & me);             // "projects/library/seqan/file/file_filereader.h"(301)
 787 template <typename TValue, typename TConfig > inline void const * id(String<TValue, External<TConfig> > const &me);             // "projects/library/seqan/file/string_external.h"(1958)
 788
 789 //____________________________________________________________________________
 790 // iterator
 791
 792 template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TPosition, typename TIteratorSpec> inline typename Iterator< String<TValue, FileReader<TFormat, TFile, TSpec> >, TIteratorSpec >::Type iterator(String<TValue, FileReader<TFormat, TFile, TSpec> > & me, TPosition pos, Tag<TIteratorSpec> const);        // "projects/library/seqan/file/file_filereader.h"(381)
 793 template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TPosition, typename TIteratorSpec> inline typename Iterator< String<TValue, FileReader<TFormat, TFile, TSpec> > const, TIteratorSpec >::Type iterator(String<TValue, FileReader<TFormat, TFile, TSpec> > const & me, TPosition pos, Tag<TIteratorSpec> const);            // "projects/library/seqan/file/file_filereader.h"(390)
 794
 795 //____________________________________________________________________________
 796 // length
 797
 798 template <typename TValue, typename TFormat, typename TFile, typename TSpec> inline typename Size< String<TValue, FileReader<TFormat, TFile, TSpec> > >::Type length(String<TValue, FileReader<TFormat, TFile, TSpec> > & me);          // "projects/library/seqan/file/file_filereader.h"(328)
 799 template <typename TValue, typename TConfig > inline typename Size< String<TValue, External<TConfig> > >::Type length(String<TValue, External<TConfig> > const &me);            // "projects/library/seqan/file/string_external.h"(1803)
 800 template <typename TValue > inline typename Size<SimpleBuffer<TValue> >::Type length(SimpleBuffer<TValue> const &me);           // "projects/library/seqan/file/file_page.h"(109)
 801 template <typename TValue, typename TFile, unsigned _PageSize > inline typename Size<PageFrame<TValue, TFile, Fixed<_PageSize> > >::Type length(PageFrame<TValue, TFile, Fixed<_PageSize> > const & );          // "projects/library/seqan/file/file_page.h"(286)
 802 template <__int64 _FileSize, typename TFile > inline unsigned length(File< Chained<_FileSize, TFile> > const &me);              // "projects/library/seqan/file/file_array.h"(284)
 803 template <unsigned _FileCount, typename TFile > inline unsigned length(File< Striped<_FileCount, TFile> > const &me);           // "projects/library/seqan/file/file_array.h"(289)
 804 template <typename TFile, typename TData, typename TMeta, typename TFormat> inline void length(TFile & file, FileFormat<TFile, TData, TMeta, TFormat> const & file_format);             // "projects/library/seqan/file/file_format.h"(267)
 805
 806 //____________________________________________________________________________
 807 // open
 808
 809 inline bool open(FILE* &me, const char *fileName, int openMode);        // "projects/library/seqan/file/file_cstyle.h"(89)
 810 inline bool open(FILE* &me, const char *fileName);              // "projects/library/seqan/file/file_cstyle.h"(94)
 811 template <typename TValue, typename TConfig > inline bool open(String<TValue, External<TConfig> > &me, const char *fileName, int openMode);             // "projects/library/seqan/file/string_external.h"(1734)
 812 template <typename TValue, typename TConfig > inline bool open(String<TValue, External<TConfig> > &me, const char *fileName);           // "projects/library/seqan/file/string_external.h"(1740)
 813 template <typename TValue, typename TConfig > inline bool open(String<TValue, External<TConfig> > &me, typename TConfig::TFile file);           // "projects/library/seqan/file/string_external.h"(1746)
 814 template <typename TSpec > inline bool open(File<TSpec> &me, const char *fileName, int openMode);               // "projects/library/seqan/file/file_base.h"(215)
 815 template <typename TSpec > inline bool open(File<TSpec> &me, const char *fileName);             // "projects/library/seqan/file/file_base.h"(220)
 816 template <__int64 _FileSize, typename TFile > inline bool open(File< Chained<_FileSize, TFile> > &me, const char *fileName, int openMode);              // "projects/library/seqan/file/file_array.h"(294)
 817
 818 //____________________________________________________________________________
 819 // openTemp
 820
 821 inline bool openTemp(FILE* &me);        // "projects/library/seqan/file/file_cstyle.h"(98)
 822 template <typename TValue, typename TConfig > inline bool openTemp(String<TValue, External<TConfig> > &me);             // "projects/library/seqan/file/string_external.h"(1758)
 823 template <typename TSpec > inline bool openTemp(File<TSpec> &me);               // "projects/library/seqan/file/file_base.h"(237)
 824 template <typename TSpec > inline bool openTemp(File<TSpec> &me, int openMode);         // "projects/library/seqan/file/file_base.h"(242)
 825 template <__int64 _FileSize, typename TFile > inline bool openTemp(File< Chained<_FileSize, TFile> > &me, int openMode);        // "projects/library/seqan/file/file_array.h"(303)
 826 template <unsigned _FileCount, typename TFile > inline bool openTemp(File< Striped<_FileCount, TFile> > &me, int openMode);             // "projects/library/seqan/file/file_array.h"(310)
 827
 828 //____________________________________________________________________________
 829 // operator!=
 830
 831 template <typename TContainer> inline bool operator!= (Iter<TContainer, FileReaderIterator> const & left, Iter<TContainer, FileReaderIterator> const & right);          // "projects/library/seqan/file/file_filereader.h"(791)
 832 template <typename TFileLeft, typename TDataLeft, typename TMetaLeft, typename TFormatLeft, typename TFileRight, typename TDataRight, typename TMetaRight, typename TFormatRight> inline bool operator!= (FileFormat<TFileLeft, TDataLeft, TMetaLeft, TFormatLeft> const & left, FileFormat<TFileRight, TDataRight, TMetaRight, TFormatRight> const & right);           // "projects/library/seqan/file/file_format.h"(348)
 833 template <typename TFile, typename TData, typename TMeta, typename TFormat, typename TFormat2> inline bool operator!= (FileFormat<TFile, TData, TMeta, TFormat> const & left, Tag<TFormat2> const);             // "projects/library/seqan/file/file_format.h"(357)
 834 template <typename TFile, typename TData, typename TMeta, typename TFormat, typename TFormat2> inline bool operator!= (Tag<TFormat2> const, FileFormat<TFile, TData, TMeta, TFormat> const & right);            // "projects/library/seqan/file/file_format.h"(366)
 835
 836 //____________________________________________________________________________
 837 // operator+
 838
 839 template <typename TContainer, typename TIntegral> inline Iter<TContainer, FileReaderIterator> operator+ (Iter<TContainer, FileReaderIterator> const & left, TIntegral right);          // "projects/library/seqan/file/file_filereader.h"(848)
 840 template <typename TContainer, typename TIntegral> inline Iter<TContainer, FileReaderIterator> operator+ (TIntegral left, Iter<TContainer, FileReaderIterator> const & right);          // "projects/library/seqan/file/file_filereader.h"(856)
 841
 842 //____________________________________________________________________________
 843 // operator+=
 844
 845 template <typename TContainer, typename TIntegral> inline Iter<TContainer, FileReaderIterator> & operator+= (Iter<TContainer, FileReaderIterator> & left, TIntegral right);             // "projects/library/seqan/file/file_filereader.h"(869)
 846
 847 //____________________________________________________________________________
 848 // operator-
 849
 850 template <typename TContainer, typename TIntegral> inline Iter<TContainer, FileReaderIterator> operator- (Iter<TContainer, FileReaderIterator> const & left, TIntegral right);          // "projects/library/seqan/file/file_filereader.h"(887)
 851 template <typename TContainer> inline typename Difference<Iter<TContainer, FileReaderIterator> >::Type operator- (Iter<TContainer, FileReaderIterator> const & left, Iter<TContainer, FileReaderIterator> const & right);               // "projects/library/seqan/file/file_filereader.h"(898)
 852
 853 //____________________________________________________________________________
 854 // operator-=
 855
 856 template <typename TContainer, typename TIntegral> inline Iter<TContainer, FileReaderIterator> & operator-= (Iter<TContainer, FileReaderIterator> & left, TIntegral right);             // "projects/library/seqan/file/file_filereader.h"(911)
 857
 858 //____________________________________________________________________________
 859 // operator<
 860
 861 template <typename TContainer> inline bool operator< (Iter<TContainer, FileReaderIterator> const & left, Iter<TContainer, FileReaderIterator> const & right);           // "projects/library/seqan/file/file_filereader.h"(804)
 862
 863 //____________________________________________________________________________
 864 // operator<<
 865
 866 template <typename TValue > ::std::ostream& operator<<(::std::ostream &out, const PageBucketExtended<TValue> &pb);              // "projects/library/seqan/file/file_page.h"(170)
 867 template <typename TValue, typename TFile, typename TSpec > ::std::ostream& operator<<(::std::ostream &out, const PageFrame<TValue, TFile, TSpec > &pf);        // "projects/library/seqan/file/file_page.h"(304)
 868
 869 //____________________________________________________________________________
 870 // operator<=
 871
 872 template <typename TContainer> inline bool operator<= (Iter<TContainer, FileReaderIterator> const & left, Iter<TContainer, FileReaderIterator> const & right);          // "projects/library/seqan/file/file_filereader.h"(826)
 873
 874 //____________________________________________________________________________
 875 // operator==
 876
 877 template <typename TContainer> inline bool operator== (Iter<TContainer, FileReaderIterator> const & left, Iter<TContainer, FileReaderIterator> const & right);          // "projects/library/seqan/file/file_filereader.h"(778)
 878 template <typename TFileLeft, typename TDataLeft, typename TMetaLeft, typename TFormatLeft, typename TFileRight, typename TDataRight, typename TMetaRight, typename TFormatRight> inline bool operator== (FileFormat<TFileLeft, TDataLeft, TMetaLeft, TFormatLeft> const & left, FileFormat<TFileRight, TDataRight, TMetaRight, TFormatRight> const & right);           // "projects/library/seqan/file/file_format.h"(319)
 879 template <typename TFile, typename TData, typename TMeta, typename TFormat, typename TFormat2> inline bool operator== (FileFormat<TFile, TData, TMeta, TFormat> const & left, Tag<TFormat2> const);             // "projects/library/seqan/file/file_format.h"(328)
 880 template <typename TFile, typename TData, typename TMeta, typename TFormat, typename TFormat2> inline bool operator== (Tag<TFormat2> const, FileFormat<TFile, TData, TMeta, TFormat> const & right);            // "projects/library/seqan/file/file_format.h"(337)
 881
 882 //____________________________________________________________________________
 883 // operator>
 884
 885 template <typename TContainer> inline bool operator> (Iter<TContainer, FileReaderIterator> const & left, Iter<TContainer, FileReaderIterator> const & right);           // "projects/library/seqan/file/file_filereader.h"(813)
 886
 887 //____________________________________________________________________________
 888 // operator>=
 889
 890 template <typename TContainer> inline bool operator>= (Iter<TContainer, FileReaderIterator> const & left, Iter<TContainer, FileReaderIterator> const & right);          // "projects/library/seqan/file/file_filereader.h"(835)
 891
 892 //____________________________________________________________________________
 893 // pageSize
 894
 895 template <typename TValue > inline typename Size<SimpleBuffer<TValue> >::Type pageSize(SimpleBuffer<TValue> &me);               // "projects/library/seqan/file/file_page.h"(92)
 896 template <typename TValue, typename TFile, unsigned _PageSize > inline typename Size<PageFrame<TValue, TFile, Fixed<_PageSize> > >::Type pageSize(PageFrame<TValue, TFile, Fixed<_PageSize> > & );              // "projects/library/seqan/file/file_page.h"(292)
 897
 898 //____________________________________________________________________________
 899 // position
 900
 901 template <typename TContainer> inline typename Position<Iter<TContainer, FileReaderIterator> >::Type position(Iter<TContainer, FileReaderIterator> const & it);         // "projects/library/seqan/file/file_filereader.h"(588)
 902
 903 //____________________________________________________________________________
 904 // push_back
 905
 906 template <typename TValue, typename TConfig > inline void push_back(String<TValue, External<TConfig> > &me, TValue const &_Val);        // "projects/library/seqan/file/string_external.h"(1877)
 907
 908 //____________________________________________________________________________
 909 // read
 910
 911 template <typename TFile, typename TData> void read(TFile & file, TData & data, Raw);           // "projects/library/seqan/file/file_format_raw.h"(191)
 912 template <typename TFile, typename TData, typename TSize> void read(TFile & file, TData & data, TSize limit, Raw);              // "projects/library/seqan/file/file_format_raw.h"(204)
 913 template <typename TFile, typename TData> void read(TFile & file, TData & data);        // "projects/library/seqan/file/file_format_raw.h"(307)
 914 template <typename TFile, typename TData, typename TSize> void read(TFile & file, TData & data, TSize limit);           // "projects/library/seqan/file/file_format_raw.h"(316)
 915 template <typename TValue, typename TSize > inline bool read(FILE* me, TValue *memPtr, TSize const count);              // "projects/library/seqan/file/file_cstyle.h"(127)
 916 template <typename TFile, typename TData, typename TSize> void read(TFile & file, TData & data, TSize limit, Fasta);            // "projects/library/seqan/file/file_format_fasta.h"(206)
 917 template <typename TFile, typename TData> void read(TFile & file, TData & data, Fasta tag);             // "projects/library/seqan/file/file_format_fasta.h"(306)
 918 template <typename TSpec, typename TValue, typename TSize > inline bool read(File<TSpec> & me, TValue *memPtr, TSize const count);              // "projects/library/seqan/file/file_base.h"(288)
 919 template <typename TFile, typename TData> inline void read(TFile & file, TData & data, Genbank);        // "projects/library/seqan/file/file_format_genbank.h"(170)
 920 template <typename TFile, typename TData, typename TSize> inline void read(TFile & file, TData & data, TSize limit, Genbank);           // "projects/library/seqan/file/file_format_genbank.h"(188)
 921 template <typename TFile, typename TSource, typename TSpec> void read(TFile & file, Align<TSource, TSpec> & align, FastaAlign);         // "projects/library/seqan/file/file_format_fasta_align.h"(72)
 922 template <typename TFile, typename TData, typename TMeta, typename TFormat> inline void read(TFile & file, TData & data, FileFormat<TFile, TData, TMeta, TFormat> const & file_format);         // "projects/library/seqan/file/file_format.h"(200)
 923 template <typename TFile, typename TData, typename TMeta, typename TFormat, typename TSize> inline void read(TFile & file, TData & data, TSize limit, FileFormat<TFile, TData, TMeta, TFormat> const & file_format);            // "projects/library/seqan/file/file_format.h"(211)
 924 template <typename TFile, typename TData> inline void read(TFile & file, TData & data, Embl);           // "projects/library/seqan/file/file_format_embl.h"(153)
 925 template <typename TFile, typename TData, typename TSize> inline void read(TFile & file, TData & data, TSize limit, Embl);              // "projects/library/seqan/file/file_format_embl.h"(171)
 926
 927 //____________________________________________________________________________
 928 // readAt
 929
 930 template <typename TValue, typename TSize, typename TPos > inline bool readAt(FILE* me, TValue *memPtr, TSize const count, TPos const fileOfs);         // "projects/library/seqan/file/file_cstyle.h"(145)
 931 template <typename TFile, typename TValue, typename TSize, typename TPos > inline bool readAt(TFile & me, TValue *memPtr, TSize const count, TPos const fileOfs);               // "projects/library/seqan/file/file_base.h"(324)
 932 template <__int64 _FileSize, typename TFile, typename TValue, typename TSize, typename TOffset > inline bool readAt(File< Chained<_FileSize, TFile> > &me, TValue *memPtr, TSize count, TOffset offset);        // "projects/library/seqan/file/file_array.h"(364)
 933
 934 //____________________________________________________________________________
 935 // readBucket
 936
 937 template <typename TValue, unsigned _FileCount, typename TFile > inline unsigned readBucket( PageBucket<TValue> &b, int pageNo, unsigned pageSize, unsigned dataSize, File< Striped<_FileCount, TFile> > &file);        // "projects/library/seqan/file/file_page_raid0.h"(134)
 938 template <typename TValue, typename TFile > inline unsigned readBucket(PageBucket<TValue> &b, int pageNo, unsigned pageSize, unsigned dataSize, TFile &file);           // "projects/library/seqan/file/file_page.h"(456)
 939
 940 //____________________________________________________________________________
 941 // readFeature
 942
 943 template <typename TData, typename TKey, typename TString> inline typename Position<TString>::Type readFeature(TString & str, typename Position<TString>::Type start_pos, TData & data, TKey key, Embl);        // "projects/library/seqan/file/file_format_embl.h"(372)
 944
 945 //____________________________________________________________________________
 946 // readID
 947
 948 template <typename TFile, typename TString> void readID(TFile & , TString & id, Raw);           // "projects/library/seqan/file/file_format_raw.h"(219)
 949 template <typename TFile, typename TString> void readID(TFile & file, TString & id, Fasta);             // "projects/library/seqan/file/file_format_fasta.h"(324)
 950
 951 //____________________________________________________________________________
 952 // readIDs
 953
 954 template <typename TFile, typename TStringContainer> void readIDs(TFile& file, TStringContainer& ids, FastaAlign);              // "projects/library/seqan/file/file_format_fasta_align.h"(178)
 955
 956 //____________________________________________________________________________
 957 // readLastPage
 958
 959 template <typename TValue, unsigned _FileCount, typename TFile, typename TSpec, typename TSize > inline bool readLastPage( int pageNo, PageFrame<TValue, File< Striped<_FileCount, TFile> >, TSpec> &pf, File< Striped<_FileCount, TFile> > &file, TSize size);         // "projects/library/seqan/file/file_page_raid0.h"(84)
 960 template <typename TValue, typename TFile, typename TSpec, typename TSize> inline bool readLastPage(int pageNo, PageFrame<TValue, TFile, TSpec> &pf, TFile &file, TSize size);          // "projects/library/seqan/file/file_page.h"(381)
 961
 962 //____________________________________________________________________________
 963 // readLineType
 964
 965 template <typename TFile, typename TData, typename TKey> inline void readLineType(TFile & file, TData & data, TKey key, Embl);          // "projects/library/seqan/file/file_format_embl.h"(248)
 966 template <typename TData, typename TValue, typename TSpec, typename TKey> inline void readLineType(String<TValue,TSpec> & meta, TData & data, TKey key, Embl);          // "projects/library/seqan/file/file_format_embl.h"(305)
 967
 968 //____________________________________________________________________________
 969 // readMeta
 970
 971 template <typename TFile, typename TMeta> void readMeta(TFile & file, TMeta & meta, Raw);               // "projects/library/seqan/file/file_format_raw.h"(233)
 972 template <typename TFile, typename TMeta> void readMeta(TFile & file, TMeta & meta, Fasta);             // "projects/library/seqan/file/file_format_fasta.h"(376)
 973 template <typename TFile, typename TMeta> inline void readMeta(TFile & file, TMeta & meta, Genbank);            // "projects/library/seqan/file/file_format_genbank.h"(212)
 974 template <typename TFile, typename TMeta> void readMeta(TFile & file, TMeta & meta, FastaAlign);        // "projects/library/seqan/file/file_format_fasta_align.h"(223)
 975 template <typename TFile, typename TData, typename TMeta, typename TFormat> inline void readMeta(TFile & file, TMeta & meta, FileFormat<TFile, TData, TMeta, TFormat> const & file_format);             // "projects/library/seqan/file/file_format.h"(235)
 976 template <typename TFile, typename TMeta> inline void readMeta(TFile & file, TMeta & meta, Embl);               // "projects/library/seqan/file/file_format_embl.h"(194)
 977
 978 //____________________________________________________________________________
 979 // readPage
 980
 981 template <typename TValue, unsigned _FileCount, typename TFile, typename TSpec > inline bool readPage( int pageNo, PageFrame<TValue, File< Striped<_FileCount, TFile> >, TSpec> &pf, File< Striped<_FileCount, TFile> > &file);         // "projects/library/seqan/file/file_page_raid0.h"(40)
 982 template <typename TValue, typename TFile, typename TSpec > inline bool readPage(int pageNo, PageFrame<TValue, TFile, TSpec> &pf, TFile &file);         // "projects/library/seqan/file/file_page.h"(356)
 983 template <typename TValue, typename TFile, typename TSpec > inline bool readPage(PageFrame<TValue, TFile, Dynamic<TSpec> > &pf, TFile &file);           // "projects/library/seqan/file/file_page.h"(440)
 984
 985 //____________________________________________________________________________
 986 // release
 987
 988 template <typename aRequest > inline void release(FILE*, aRequest &);           // "projects/library/seqan/file/file_cstyle.h"(187)
 989 template <typename TSpec, typename aRequest > inline void release(File<TSpec> &, aRequest &);           // "projects/library/seqan/file/file_base.h"(659)
 990
 991 //____________________________________________________________________________
 992 // reopen
 993
 994 template <typename File > inline void reopen(File &, int);              // "projects/library/seqan/file/file_base.h"(247)
 995
 996 //____________________________________________________________________________
 997 // replace
 998
 999 template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand> inline void replace(String<TTargetValue, TTargetSpec> & target, typename Size< String<TTargetValue, TTargetSpec> >::Type pos_begin, typename Size< String<TTargetValue, TTargetSpec> >::Type pos_end, _ChunkCollector<TSourceHost> const & source, Tag<TExpand> const tag);              // "projects/library/seqan/file/chunk_collector.h"(465)
1000 template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand> inline void replace(String<TTargetValue, TTargetSpec> & target, typename Size< String<TTargetValue, TTargetSpec> >::Type pos_begin, typename Size< String<TTargetValue, TTargetSpec> >::Type pos_end, _ChunkCollector<TSourceHost> const & source, typename Size< String<TTargetValue, TTargetSpec> >::Type limit, Tag<TExpand> const tag);              // "projects/library/seqan/file/chunk_collector.h"(477)
1001 template <typename TTargetValue, typename TSourceHost, typename TExpand> inline void replace(TTargetValue * target, size_t pos_begin, size_t pos_end, _ChunkCollector<TSourceHost> const & source, Tag<TExpand> const tag);             // "projects/library/seqan/file/chunk_collector.h"(490)
1002 template <typename TTargetValue, typename TSourceHost, typename TExpand> inline void replace(TTargetValue * target, size_t pos_begin, size_t pos_end, _ChunkCollector<TSourceHost> const & source, size_t limit, Tag<TExpand> const tag);               // "projects/library/seqan/file/chunk_collector.h"(502)
1003
1004 //____________________________________________________________________________
1005 // reserve
1006
1007 template <typename TValue, typename TConfig, typename TSize, typename TExpand > inline typename Size< String<TValue, External<TConfig> > >::Type reserve( String<TValue, External<TConfig> > &me, TSize new_capacity, Tag<TExpand> const);              // "projects/library/seqan/file/string_external.h"(1826)
1008
1009 //____________________________________________________________________________
1010 // resize
1011
1012 template <typename TSize > inline void resize(FILE* me, TSize new_length);              // "projects/library/seqan/file/file_cstyle.h"(176)
1013 template <typename TValue, typename TConfig, typename TSize, typename TExpand > inline typename Size< String<TValue, External<TConfig> > >::Type resize( String<TValue, External<TConfig> > &me, TSize new_length, Tag<TExpand> const);         // "projects/library/seqan/file/string_external.h"(1814)
1014 template <typename TSpec, typename TSize > inline void resize(File<TSpec> &me, TSize new_length);               // "projects/library/seqan/file/file_base.h"(443)
1015 template <typename TValue, typename TSize > inline void resize(SimpleBuffer<TValue> &me, TSize size);           // "projects/library/seqan/file/file_page.h"(114)
1016 template <typename TValue, typename TFile, typename TSpec, typename TSize > inline void resize(PageFrame<TValue, TFile, Dynamic<TSpec> > &me, TSize size);              // "projects/library/seqan/file/file_page.h"(274)
1017 template <typename TValue, typename TFile, unsigned _PageSize, typename TSize > inline void resize(PageFrame<TValue, TFile, Fixed<_PageSize> > & , TSize );             // "projects/library/seqan/file/file_page.h"(297)
1018 template <__int64 _FileSize, typename TFile, typename TSize > inline void resize(File< Chained<_FileSize, TFile> > &me, TSize new_length);              // "projects/library/seqan/file/file_array.h"(335)
1019
1020 //____________________________________________________________________________
1021 // rewind
1022
1023 template <typename File > inline void rewind(File &me);         // "projects/library/seqan/file/file_base.h"(411)
1024
1025 //____________________________________________________________________________
1026 // save
1027
1028 template <typename TValue, typename TConfig > inline bool save(String<TValue, External<TConfig> > const &me, const char *fileName, int openMode);               // "projects/library/seqan/file/string_external.h"(1765)
1029 template <typename TValue, typename TConfig > inline bool save(String<TValue, External<TConfig> > const &me, const char *fileName);             // "projects/library/seqan/file/string_external.h"(1773)
1030 template <typename TValue, typename TConfig > inline bool save(String<TValue, External<TConfig> > const &me, typename TConfig::TFile file);             // "projects/library/seqan/file/string_external.h"(1781)
1031
1032 //____________________________________________________________________________
1033 // sectorSize
1034
1035 inline unsigned sectorSize(FILE* const &);              // "projects/library/seqan/file/file_cstyle.h"(108)
1036 template <typename TSpec > inline unsigned sectorSize(File<TSpec> const & );            // "projects/library/seqan/file/file_base.h"(266)
1037
1038 //____________________________________________________________________________
1039 // seek
1040
1041 template <typename TPos > inline Size<FILE*>::Type seek(FILE* me, TPos const fileOfs, int origin);              // "projects/library/seqan/file/file_cstyle.h"(113)
1042 template <typename TPos > inline Size<FILE*>::Type seek(FILE* me, TPos const fileOfs);          // "projects/library/seqan/file/file_cstyle.h"(118)
1043 template <typename TSpec, typename TPos > inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const fileOfs, int origin);          // "projects/library/seqan/file/file_base.h"(370)
1044 template <typename TSpec, typename TPos > inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const fileOfs);              // "projects/library/seqan/file/file_base.h"(382)
1045
1046 //____________________________________________________________________________
1047 // setEOF
1048
1049 template <typename TSpec > inline bool setEOF(File<TSpec> & );          // "projects/library/seqan/file/file_base.h"(460)
1050
1051 //____________________________________________________________________________
1052 // setPageSize
1053
1054 template <typename TValue, typename TSize > inline void setPageSize(SimpleBuffer<TValue> &me, TSize size);              // "projects/library/seqan/file/file_page.h"(97)
1055
1056 //____________________________________________________________________________
1057 // setPosition
1058
1059 template <typename TContainer, typename TPos> inline void setPosition(Iter<TContainer, FileReaderIterator> & it, TPos pos);             // "projects/library/seqan/file/file_filereader.h"(613)
1060
1061 //____________________________________________________________________________
1062 // size
1063
1064 inline Size<FILE*>::Type size(FILE* me);        // "projects/library/seqan/file/file_cstyle.h"(166)
1065 template <typename TSpec > inline typename Size<File<TSpec> >::Type size(File<TSpec> &me);              // "projects/library/seqan/file/file_base.h"(426)
1066 template <typename TValue > inline typename Size<SimpleBuffer<TValue> >::Type size(SimpleBuffer<TValue> const &me);             // "projects/library/seqan/file/file_page.h"(103)
1067 template <typename TValue, typename TFile, unsigned _PageSize > inline typename Size<PageFrame<TValue, TFile, Fixed<_PageSize> > >::Type size(PageFrame<TValue, TFile, Fixed<_PageSize> > & );          // "projects/library/seqan/file/file_page.h"(280)
1068 template <__int64 _FileSize, typename TFile > __int64 size(File< Chained<_FileSize, TFile> > &me);              // "projects/library/seqan/file/file_array.h"(325)
1069 template <unsigned _FileCount, typename TFile > __int64 size(File< Striped<_FileCount, TFile> > &me);           // "projects/library/seqan/file/file_array.h"(330)
1070
1071 //____________________________________________________________________________
1072 // tell
1073
1074 inline Size<FILE*>::Type tell(FILE* me);        // "projects/library/seqan/file/file_cstyle.h"(122)
1075 template <typename TSpec > inline typename Position< File<TSpec> >::Type tell(File<TSpec> &me);         // "projects/library/seqan/file/file_base.h"(396)
1076
1077 //____________________________________________________________________________
1078 // value
1079
1080 template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TPos> inline TValue value(String<TValue, FileReader<TFormat, TFile, TSpec> > & me, TPos pos);             // "projects/library/seqan/file/file_filereader.h"(312)
1081 template <typename TContainer> inline typename Reference<Iter<TContainer, FileReaderIterator> >::Type value(Iter<TContainer, FileReaderIterator> & it);         // "projects/library/seqan/file/file_filereader.h"(558)
1082 template <typename TContainer> inline typename Reference<Iter<TContainer, FileReaderIterator> >::Type value(Iter<TContainer, FileReaderIterator> const & it);           // "projects/library/seqan/file/file_filereader.h"(564)
1083 template <typename TValue, typename TConfig, typename TPos > inline typename Reference<String<TValue, External<TConfig> > >::Type value(String<TValue, External<TConfig> > &me, TPos pos);              // "projects/library/seqan/file/string_external.h"(1861)
1084 template <typename TValue, typename TConfig, typename TPos > inline typename Reference<String<TValue, External<TConfig> > const>::Type value(String<TValue, External<TConfig> > const &me, TPos pos);           // "projects/library/seqan/file/string_external.h"(1868)
1085 template <typename TFile, typename TFormat, typename TFile2, typename TSpec> inline typename Reference<Iter<TFile, FileReader<TFormat, TFile2, TSpec> > >::Type value(Iter<TFile, FileReader<TFormat, TFile2, TSpec> > & it);           // "projects/library/seqan/file/file_filereaderiterator.h"(113)
1086
1087 //____________________________________________________________________________
1088 // waitFor
1089
1090 inline bool waitFor(aDummyRequest &);           // "projects/library/seqan/file/file_base.h"(648)
1091 template <typename TTime > inline bool waitFor(aDummyRequest &, TTime);         // "projects/library/seqan/file/file_base.h"(653)
1092 template <typename TValue, typename TFile, typename TSpec > inline bool waitFor(PageFrame<TValue, TFile, TSpec> &pf);           // "projects/library/seqan/file/file_page.h"(407)
1093 template <typename TValue, typename TFile, typename TSpec, typename TTime > inline bool waitFor(PageFrame<TValue, TFile, TSpec> &pf, TTime timeOut);            // "projects/library/seqan/file/file_page.h"(417)
1094
1095 //____________________________________________________________________________
1096 // write
1097
1098 template <typename TFile, typename TSource, typename TSpec> void write(TFile & file, Align<TSource, TSpec>& align, CGViz);              // "projects/library/seqan/file/file_format_cgviz.h"(190)
1099 template <typename TFile, typename TStringContainer, typename TSource, typename TSpec> void write(TFile & file, Align<TSource, TSpec> & align, TStringContainer& ids, CGViz);           // "projects/library/seqan/file/file_format_cgviz.h"(198)
1100 template <typename TFile, typename TStringContainer, typename TSource, typename TSpec> void write(TFile & file, Align<TSource, TSpec>* align, TStringContainer & ids, CGViz);           // "projects/library/seqan/file/file_format_cgviz.h"(206)
1101 template <typename TFile, typename TStringContainer, typename TSource, typename TSpec, typename TMeta> void write(TFile & file, Align<TSource, TSpec> & align, TStringContainer& ids, TMeta &, CGViz);          // "projects/library/seqan/file/file_format_cgviz.h"(214)
1102 template <typename TFile, typename TString, typename TData> void write(TFile & file, TData const & data, Raw);          // "projects/library/seqan/file/file_format_raw.h"(266)
1103 template <typename TFile, typename TData, typename TString> void write(TFile & file, TData const & data, TString const &, Raw);         // "projects/library/seqan/file/file_format_raw.h"(279)
1104 template <typename TFile, typename TString, typename TData, typename TMeta> void write(TFile & file, TData const & data, TString const &, TMeta const &, Raw);          // "projects/library/seqan/file/file_format_raw.h"(293)
1105 template <typename TFile, typename TData> void write(TFile & file, TData & data);               // "projects/library/seqan/file/file_format_raw.h"(327)
1106 template <typename TFile, typename TData> void write(TFile & file, TData const & data);         // "projects/library/seqan/file/file_format_raw.h"(335)
1107 template <typename TValue, typename TSize > inline bool write(FILE* me, TValue const *memPtr, TSize const count);               // "projects/library/seqan/file/file_cstyle.h"(136)
1108 template <typename TFile, typename TString, typename TData, typename TMeta> void write(TFile & file, TData & data, Fasta);              // "projects/library/seqan/file/file_format_fasta.h"(468)
1109 template <typename TFile, typename TString, typename TData> void write(TFile & file, TData & data, TString & id, Fasta);        // "projects/library/seqan/file/file_format_fasta.h"(481)
1110 template <typename TFile, typename TString, typename TDataValue> void write(TFile & file, TDataValue * data, TString & id, Fasta);              // "projects/library/seqan/file/file_format_fasta.h"(494)
1111 template <typename TFile, typename TString, typename TData, typename TMeta> void write(TFile & file, TData & data, TString & id, TMeta &, Fasta);               // "projects/library/seqan/file/file_format_fasta.h"(509)
1112 template <typename TSpec, typename TValue, typename TSize > inline bool write(File<TSpec> & me, TValue const *memPtr, TSize const count);               // "projects/library/seqan/file/file_base.h"(306)
1113 template <typename TFile, typename TData> inline void write(TFile & file, TData & data, Genbank);               // "projects/library/seqan/file/file_format_genbank.h"(292)
1114 template <typename TFile, typename TData, typename TMeta> inline void write(TFile & file, TData & data, TMeta & meta, Genbank);         // "projects/library/seqan/file/file_format_genbank.h"(348)
1115 template <typename TFile, typename TSource, typename TSpec> void write(TFile & file, Align<TSource, TSpec>& align, FastaAlign);         // "projects/library/seqan/file/file_format_fasta_align.h"(284)
1116 template <typename TFile, typename TStringContainer, typename TSource, typename TSpec> void write(TFile & file, Align<TSource, TSpec> & align, TStringContainer& ids, FastaAlign);              // "projects/library/seqan/file/file_format_fasta_align.h"(292)
1117 template <typename TFile, typename TStringContainer, typename TSource, typename TSpec> void write(TFile & file, Align<TSource, TSpec>* align, TStringContainer & ids, FastaAlign);              // "projects/library/seqan/file/file_format_fasta_align.h"(300)
1118 template <typename TFile, typename TStringContainer, typename TSource, typename TSpec, typename TMeta> void write(TFile & file, Align<TSource, TSpec> & align, TStringContainer& ids, TMeta &, FastaAlign);             // "projects/library/seqan/file/file_format_fasta_align.h"(308)
1119 template <typename TFile, typename TData, typename TMeta, typename TFormat> inline void write(TFile & file, TData & data, FileFormat<TFile, TData, TMeta, TFormat> const & file_format);        // "projects/library/seqan/file/file_format.h"(293)
1120 template <typename TFile, typename TData, typename TMeta, typename TFormat> inline void write(TFile & file, TData & data, TMeta & meta, FileFormat<TFile, TData, TMeta, TFormat> const & file_format);          // "projects/library/seqan/file/file_format.h"(303)
1121 template <typename TFile, typename TData> inline void write(TFile & file, TData & data, Embl);          // "projects/library/seqan/file/file_format_embl.h"(465)
1122 template <typename TFile, typename TData, typename TMeta> inline void write(TFile & file, TData & data, TMeta & meta, Embl);            // "projects/library/seqan/file/file_format_embl.h"(531)
1123
1124 //____________________________________________________________________________
1125 // writeAt
1126
1127 template <typename TValue, typename TSize, typename TPos > inline bool writeAt(FILE* me, TValue const *memPtr, TSize const count, TPos const fileOfs);          // "projects/library/seqan/file/file_cstyle.h"(156)
1128 template <typename TFile, typename TValue, typename TSize, typename TPos > inline bool writeAt(TFile & me, TValue const *memPtr, TSize const count, TPos const fileOfs);        // "projects/library/seqan/file/file_base.h"(344)
1129 template <__int64 _FileSize, typename TFile, typename TValue, typename TSize, typename TOffset > inline bool writeAt(File< Chained<_FileSize, TFile> > &me, TValue const *memPtr, TSize count, TOffset offset);         // "projects/library/seqan/file/file_array.h"(378)
1130
1131 //____________________________________________________________________________
1132 // writeBucket
1133
1134 template <typename TValue, unsigned _FileCount, typename TFile > inline bool writeBucket( PageBucket<TValue> &b, int pageNo, unsigned pageSize, File< Striped<_FileCount, TFile> > &file);              // "projects/library/seqan/file/file_page_raid0.h"(158)
1135 template <typename TValue, unsigned _FileCount, typename TFile, typename TSpec > inline bool writeBucket( PageFrame<TValue, File< Striped<_FileCount, TFile> >, Dynamic<TSpec> > &pf, unsigned &pageOfs, File< Striped<_FileCount, TFile> > &file);             // "projects/library/seqan/file/file_page_raid0.h"(179)
1136 template <typename TValue, typename TFile > inline bool writeBucket(PageBucket<TValue> &b, int pageNo, unsigned pageSize, TFile &file);         // "projects/library/seqan/file/file_page.h"(474)
1137 template <typename TValue, typename TFile, typename TSpec > inline bool writeBucket(PageFrame<TValue, TFile, Dynamic<TSpec> > &pf, unsigned &pageOfs, TFile &file);             // "projects/library/seqan/file/file_page.h"(490)
1138
1139 //____________________________________________________________________________
1140 // writeLastPage
1141
1142 template <typename TValue, unsigned _FileCount, typename TFile, typename TSpec, typename TSize > inline bool writeLastPage( PageFrame<TValue, File< Striped<_FileCount, TFile> >, TSpec> &pf, int pageNo, File< Striped<_FileCount, TFile> > &file, TSize size);        // "projects/library/seqan/file/file_page_raid0.h"(106)
1143 template <typename TValue, typename TFile, typename TSpec, typename TSize > inline bool writeLastPage(PageFrame<TValue, TFile, TSpec> &pf, int pageNo, TFile &file, TSize size);        // "projects/library/seqan/file/file_page.h"(394)
1144
1145 //____________________________________________________________________________
1146 // writePage
1147
1148 template <typename TValue, unsigned _FileCount, typename TFile, typename TSpec > inline bool writePage( PageFrame<TValue, File< Striped<_FileCount, TFile> >, TSpec> &pf, int pageNo, File< Striped<_FileCount, TFile> > &file);        // "projects/library/seqan/file/file_page_raid0.h"(62)
1149 template <typename TValue, typename TFile, typename TSpec > inline bool writePage(PageFrame<TValue, TFile, TSpec> &pf, int pageNo, TFile &file);        // "projects/library/seqan/file/file_page.h"(369)
1150 template <typename TValue, typename TFile, typename TSpec > inline bool writePage(PageFrame<TValue, TFile, Dynamic<TSpec> > &pf, TFile &file);          // "projects/library/seqan/file/file_page.h"(448)
1151
1152 } //namespace SEQAN_NAMESPACE_MAIN
1153
1154 #endif
1155