SeqAn-1.1/seqan/find/find_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_FIND_GENERATED_FORWARDS_H
  20 #define SEQAN_HEADER_FIND_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 // AbndmAlgo
  36
  37 struct AbndmAlgo;               // "projects/library/seqan/find/find_abndm.h"(76)
  38
  39 //____________________________________________________________________________
  40 // AlignTextBanded
  41
  42 struct AlignTextBanded;         // "projects/library/seqan/find/find_myers_ukkonen.h"(46)
  43
  44 //____________________________________________________________________________
  45 // AlignTextGlobal
  46
  47 struct AlignTextGlobal;         // "projects/library/seqan/find/find_myers_ukkonen.h"(45)
  48
  49 //____________________________________________________________________________
  50 // AlignTextLocal
  51
  52 struct AlignTextLocal;          // "projects/library/seqan/find/find_myers_ukkonen.h"(44)
  53
  54 //____________________________________________________________________________
  55 // DPSearch
  56
  57 template <typename TScore> struct DPSearch;             // "projects/library/seqan/find/find_score.h"(32)
  58
  59 //____________________________________________________________________________
  60 // DefaultFinder
  61
  62 template <typename TObject > struct DefaultFinder;              // "projects/library/seqan/find/find_base.h"(41)
  63
  64 //____________________________________________________________________________
  65 // DefaultHash
  66
  67 class DefaultHash;              // "projects/library/seqan/find/find_wumanber.h"(63)
  68
  69 //____________________________________________________________________________
  70 // DefaultPattern
  71
  72 template <typename TObject > struct DefaultPattern;             // "projects/library/seqan/find/find_base.h"(54)
  73
  74 //____________________________________________________________________________
  75 // FileReader
  76
  77 template <typename TFormat, typename TFile, typename TSpec> struct FileReader;          // "projects/library/seqan/find/find_horspool.h"(308)
  78
  79 //____________________________________________________________________________
  80 // Finder
  81
  82 template <typename THaystack, typename TSpec > class Finder;            // "projects/library/seqan/find/find_base.h"(343)
  83
  84 //____________________________________________________________________________
  85 // Haystack
  86
  87 template <typename TFinder> struct Haystack;            // "projects/library/seqan/find/find_base.h"(69)
  88
  89 //____________________________________________________________________________
  90 // Hierarchical
  91
  92 struct Hierarchical;            // "projects/library/seqan/find/find_pex.h"(30)
  93
  94 //____________________________________________________________________________
  95 // Index
  96
  97 template <typename TObject, typename TSpec > class Index;               // "projects/library/seqan/find/find_swift.h"(34)
  98
  99 //____________________________________________________________________________
 100 // Needle
 101
 102 template <typename TPattern> struct Needle;             // "projects/library/seqan/find/find_base.h"(84)
 103
 104 //____________________________________________________________________________
 105 // NonHierarchical
 106
 107 struct NonHierarchical;         // "projects/library/seqan/find/find_pex.h"(31)
 108
 109 //____________________________________________________________________________
 110 // Pattern
 111
 112 template <typename TNeedle, typename TSpec > class Pattern;             // "projects/library/seqan/find/find_base.h"(114)
 113
 114 //____________________________________________________________________________
 115 // Pex
 116
 117 template <typename TVerification, typename TMultiFinder > struct Pex;           // "projects/library/seqan/find/find_pex.h"(34)
 118
 119 //____________________________________________________________________________
 120 // PexMultiFinder
 121
 122 template <typename T> struct PexMultiFinder;            // "projects/library/seqan/find/find_pex.h"(53)
 123
 124 //____________________________________________________________________________
 125 // Pipe
 126
 127 //template <typename TInput, typename TSpec > struct Pipe;              // "projects/library/seqan/find/find_swift.h"(179)
 128
 129 //____________________________________________________________________________
 130 // Swift
 131
 132 template <typename TSpec > struct Swift;        // "projects/library/seqan/find/find_swift.h"(44)
 133
 134 //____________________________________________________________________________
 135 // SwiftParameters
 136
 137 struct SwiftParameters;         // "projects/library/seqan/find/find_swift.h"(65)
 138
 139 //____________________________________________________________________________
 140 // WuManber
 141
 142 template <typename THash > class WuManber;              // "projects/library/seqan/find/find_wumanber.h"(238)
 143
 144 //____________________________________________________________________________
 145 // _AhoCorasick
 146
 147 struct _AhoCorasick;            // "projects/library/seqan/find/find_ahocorasick.h"(46)
 148
 149 //____________________________________________________________________________
 150 // _BndmAlgo
 151
 152 struct _BndmAlgo;               // "projects/library/seqan/find/find_bndm.h"(44)
 153
 154 //____________________________________________________________________________
 155 // _BomAlgo
 156
 157 struct _BomAlgo;        // "projects/library/seqan/find/find_bom.h"(44)
 158
 159 //____________________________________________________________________________
 160 // _Horspool
 161
 162 struct _Horspool;               // "projects/library/seqan/find/find_horspool.h"(43)
 163
 164 //____________________________________________________________________________
 165 // _MultipatternFinder
 166
 167 struct _MultipatternFinder;             // "projects/library/seqan/find/find_multi.h"(29)
 168
 169 //____________________________________________________________________________
 170 // _MultipleShiftAnd
 171
 172 struct _MultipleShiftAnd;               // "projects/library/seqan/find/find_multiple_shiftand.h"(44)
 173
 174 //____________________________________________________________________________
 175 // _MyersUkkonen
 176
 177 template <typename TSpec> struct _MyersUkkonen;         // "projects/library/seqan/find/find_myers_ukkonen.h"(49)
 178
 179 //____________________________________________________________________________
 180 // _MyersUkkonenHP0
 181
 182 template <typename T> struct _MyersUkkonenHP0;          // "projects/library/seqan/find/find_myers_ukkonen.h"(62)
 183
 184 //____________________________________________________________________________
 185 // _PexRange
 186
 187 template <typename TPosition,typename TScore,typename TVerifier,typename TNeedle> struct _PexRange;             // "projects/library/seqan/find/find_pex.h"(64)
 188
 189 //____________________________________________________________________________
 190 // _Quasar
 191
 192 struct _Quasar;         // "projects/library/seqan/find/find_quasar.h"(33)
 193
 194 //____________________________________________________________________________
 195 // _SetHorspool
 196
 197 struct _SetHorspool;            // "projects/library/seqan/find/find_set_horspool.h"(44)
 198
 199 //____________________________________________________________________________
 200 // _ShiftAnd
 201
 202 struct _ShiftAnd;               // "projects/library/seqan/find/find_shiftand.h"(44)
 203
 204 //____________________________________________________________________________
 205 // _ShiftOr
 206
 207 struct _ShiftOr;        // "projects/library/seqan/find/find_shiftor.h"(44)
 208
 209 //____________________________________________________________________________
 210 // _SwiftBucket
 211
 212 template <typename TSpec, typename TSize, typename TShortSize > struct _SwiftBucket;            // "projects/library/seqan/find/find_swift.h"(79)
 213
 214 //____________________________________________________________________________
 215 // _SwiftBucketParams
 216
 217 template <typename TSpec, typename TSize, typename TShortSize > struct _SwiftBucketParams;              // "projects/library/seqan/find/find_swift.h"(98)
 218
 219 //____________________________________________________________________________
 220 // _SwiftHit
 221
 222 template <typename THstkPos> struct _SwiftHit;          // "projects/library/seqan/find/find_swift.h"(113)
 223
 224 //____________________________________________________________________________
 225 // _SwiftLocal
 226
 227 struct _SwiftLocal;             // "projects/library/seqan/find/find_swift.h"(36)
 228
 229 //____________________________________________________________________________
 230 // _SwiftSemiGlobal
 231
 232 struct _SwiftSemiGlobal;        // "projects/library/seqan/find/find_swift.h"(39)
 233
 234 //____________________________________________________________________________
 235 // _WildShiftAnd
 236
 237 struct _WildShiftAnd;           // "projects/library/seqan/find/find_wild_shiftand.h"(31)
 238
 239 } //namespace SEQAN_NAMESPACE_MAIN
 240
 241
 242 //////////////////////////////////////////////////////////////////////////////
 243 // TYPEDEFS
 244 //////////////////////////////////////////////////////////////////////////////
 245
 246 namespace SEQAN_NAMESPACE_MAIN {
 247
 248 //____________________________________________________________________________
 249 // AhoCorasick
 250
 251 typedef Tag<_AhoCorasick> AhoCorasick;          // "projects/library/seqan/find/find_ahocorasick.h"(47)
 252
 253 //____________________________________________________________________________
 254 // BndmAlgo
 255
 256 typedef Tag<_BndmAlgo> BndmAlgo;        // "projects/library/seqan/find/find_bndm.h"(45)
 257
 258 //____________________________________________________________________________
 259 // BomAlgo
 260
 261 typedef Tag<_BomAlgo> BomAlgo;          // "projects/library/seqan/find/find_bom.h"(45)
 262
 263 //____________________________________________________________________________
 264 // Horspool
 265
 266 typedef Tag<_Horspool> Horspool;        // "projects/library/seqan/find/find_horspool.h"(44)
 267
 268 //____________________________________________________________________________
 269 // MultipatternFinder
 270
 271 typedef Tag<_MultipatternFinder> MultipatternFinder;            // "projects/library/seqan/find/find_multi.h"(30)
 272
 273 //____________________________________________________________________________
 274 // MultipleShiftAnd
 275
 276 typedef Tag<_MultipleShiftAnd> MultipleShiftAnd;        // "projects/library/seqan/find/find_multiple_shiftand.h"(45)
 277
 278 //____________________________________________________________________________
 279 // MyersUkkonen
 280
 281 typedef Tag<_MyersUkkonen<AlignTextLocal> >  MyersUkkonen;              // "projects/library/seqan/find/find_myers_ukkonen.h"(51)
 282
 283 //____________________________________________________________________________
 284 // MyersUkkonenBanded
 285
 286 typedef Tag<_MyersUkkonen<AlignTextBanded> > MyersUkkonenBanded;        // "projects/library/seqan/find/find_myers_ukkonen.h"(53)
 287
 288 //____________________________________________________________________________
 289 // MyersUkkonenGlobal
 290
 291 typedef Tag<_MyersUkkonen<AlignTextGlobal> > MyersUkkonenGlobal;        // "projects/library/seqan/find/find_myers_ukkonen.h"(52)
 292
 293 //____________________________________________________________________________
 294 // PexHierarchical
 295
 296 typedef Pex<Hierarchical,AhoCorasick>   PexHierarchical;        // "projects/library/seqan/find/find_pex.h"(36)
 297
 298 //____________________________________________________________________________
 299 // PexNonHierarchical
 300
 301 typedef Pex<NonHierarchical,AhoCorasick>  PexNonHierarchical;           // "projects/library/seqan/find/find_pex.h"(37)
 302
 303 //____________________________________________________________________________
 304 // Quasar
 305
 306 typedef Tag<_Quasar> Quasar;            // "projects/library/seqan/find/find_quasar.h"(34)
 307
 308 //____________________________________________________________________________
 309 // SetHorspool
 310
 311 typedef Tag<_SetHorspool> SetHorspool;          // "projects/library/seqan/find/find_set_horspool.h"(45)
 312
 313 //____________________________________________________________________________
 314 // ShiftAnd
 315
 316 typedef Tag<_ShiftAnd> ShiftAnd;        // "projects/library/seqan/find/find_shiftand.h"(45)
 317
 318 //____________________________________________________________________________
 319 // ShiftOr
 320
 321 typedef Tag<_ShiftOr> ShiftOr;          // "projects/library/seqan/find/find_shiftor.h"(45)
 322
 323 //____________________________________________________________________________
 324 // SwiftLocal
 325
 326 typedef Tag<_SwiftLocal> SwiftLocal;            // "projects/library/seqan/find/find_swift.h"(37)
 327
 328 //____________________________________________________________________________
 329 // SwiftSemiGlobal
 330
 331 typedef Tag<_SwiftSemiGlobal> SwiftSemiGlobal;          // "projects/library/seqan/find/find_swift.h"(40)
 332
 333 //____________________________________________________________________________
 334 // WildShiftAnd
 335
 336 typedef Tag<_WildShiftAnd> WildShiftAnd;        // "projects/library/seqan/find/find_wild_shiftand.h"(32)
 337
 338 } //namespace SEQAN_NAMESPACE_MAIN
 339
 340
 341 //////////////////////////////////////////////////////////////////////////////
 342 // FUNCTIONS
 343 //////////////////////////////////////////////////////////////////////////////
 344
 345 namespace SEQAN_NAMESPACE_MAIN {
 346
 347 //____________________________________________________________________________
 348 // _createAcTrie
 349
 350 template <typename TNeedle> inline void _createAcTrie(Pattern<TNeedle, AhoCorasick> & me);              // "projects/library/seqan/find/find_ahocorasick.h"(120)
 351
 352 //____________________________________________________________________________
 353 // _createTree
 354
 355 template <typename TNeedle, typename TMultiFinder> void _createTree(Pattern<TNeedle, Pex<Hierarchical, TMultiFinder > > &me, unsigned start, unsigned end, unsigned k, unsigned parent, unsigned direction ,unsigned idx, unsigned plen);               // "projects/library/seqan/find/find_pex.h"(424)
 356
 357 //____________________________________________________________________________
 358 // _dataHost
 359
 360 template <typename TNeedle, typename TSpec> inline Holder<TNeedle> & _dataHost(Pattern<TNeedle, TSpec> & me);           // "projects/library/seqan/find/find_base.h"(143)
 361 template <typename TNeedle, typename TSpec> inline Holder<TNeedle> & _dataHost(Pattern<TNeedle, TSpec> const & me);             // "projects/library/seqan/find/find_base.h"(149)
 362
 363 //____________________________________________________________________________
 364 // _findAbndm_LargeNeedle
 365
 366 template <typename TFinder, typename TNeedle> inline bool _findAbndm_LargeNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo> & me);           // "projects/library/seqan/find/find_abndm.h"(371)
 367
 368 //____________________________________________________________________________
 369 // _findAbndm_SmallNeedle
 370
 371 template <typename TFinder, typename TNeedle> inline bool _findAbndm_SmallNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo> & me);           // "projects/library/seqan/find/find_abndm.h"(237)
 372
 373 //____________________________________________________________________________
 374 // _findBndm_LargeNeedle
 375
 376 template <typename TFinder, typename TNeedle> inline bool _findBndm_LargeNeedle(TFinder & finder, Pattern<TNeedle, BndmAlgo> & me);             // "projects/library/seqan/find/find_bndm.h"(184)
 377
 378 //____________________________________________________________________________
 379 // _findBndm_SmallNeedle
 380
 381 template <typename TFinder, typename TNeedle> inline bool _findBndm_SmallNeedle(TFinder & finder, Pattern<TNeedle, BndmAlgo> & me);             // "projects/library/seqan/find/find_bndm.h"(160)
 382
 383 //____________________________________________________________________________
 384 // _findMyersLargePatterns
 385
 386 template <typename TFinder, typename TNeedle, typename TSpec> inline bool _findMyersLargePatterns (TFinder & finder, Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > & me);               // "projects/library/seqan/find/find_myers_ukkonen.h"(362)
 387 template <typename TFinder, typename TNeedle, typename TSpec> inline bool _findMyersLargePatterns( TFinder & finder, Pattern<TNeedle, Tag<_MyersUkkonen<AlignTextBanded> > > & me);             // "projects/library/seqan/find/find_myers_ukkonen.h"(505)
 388
 389 //____________________________________________________________________________
 390 // _findMyersSmallPatterns
 391
 392 template <typename TFinder, typename TNeedle, typename TSpec> inline bool _findMyersSmallPatterns (TFinder & finder, Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > & me);               // "projects/library/seqan/find/find_myers_ukkonen.h"(457)
 393 template <typename TFinder, typename TNeedle> inline bool _findMyersSmallPatterns( TFinder & finder, Pattern<TNeedle, Tag<_MyersUkkonen<AlignTextBanded> > > & me);             // "projects/library/seqan/find/find_myers_ukkonen.h"(775)
 394
 395 //____________________________________________________________________________
 396 // _findShiftAnd_LargeNeedle
 397
 398 template <typename TFinder, typename TNeedle> inline bool _findShiftAnd_LargeNeedle(TFinder & finder, Pattern<TNeedle, ShiftAnd> & me);         // "projects/library/seqan/find/find_shiftand.h"(180)
 399 template <typename TFinder, typename TNeedle> bool _findShiftAnd_LargeNeedle(TFinder & finder, Pattern<TNeedle, MultipleShiftAnd> & me);        // "projects/library/seqan/find/find_multiple_shiftand.h"(313)
 400 template <typename TFinder, typename TNeedle> inline bool _findShiftAnd_LargeNeedle(TFinder & finder, Pattern<TNeedle, WildShiftAnd> & me);             // "projects/library/seqan/find/find_wild_shiftand.h"(590)
 401
 402 //____________________________________________________________________________
 403 // _findShiftAnd_SmallNeedle
 404
 405 template <typename TFinder, typename TNeedle> inline bool _findShiftAnd_SmallNeedle(TFinder & finder, Pattern<TNeedle, ShiftAnd> & me);         // "projects/library/seqan/find/find_shiftand.h"(160)
 406 template <typename TFinder, typename TNeedle> bool _findShiftAnd_SmallNeedle(TFinder & finder, Pattern<TNeedle, MultipleShiftAnd> & me);        // "projects/library/seqan/find/find_multiple_shiftand.h"(261)
 407 template <typename TFinder, typename TNeedle> inline bool _findShiftAnd_SmallNeedle(TFinder & finder, Pattern<TNeedle, WildShiftAnd> & me);             // "projects/library/seqan/find/find_wild_shiftand.h"(567)
 408
 409 //____________________________________________________________________________
 410 // _findShiftOr_LargeNeedle
 411
 412 template <typename TFinder, typename TNeedle> bool _findShiftOr_LargeNeedle(TFinder & finder, Pattern<TNeedle, ShiftOr> & me);          // "projects/library/seqan/find/find_shiftor.h"(212)
 413
 414 //____________________________________________________________________________
 415 // _findShiftOr_SmallNeedle
 416
 417 template <typename TFinder, typename TNeedle> bool _findShiftOr_SmallNeedle(TFinder & finder, Pattern<TNeedle, ShiftOr> & me);          // "projects/library/seqan/find/find_shiftor.h"(178)
 418
 419 //____________________________________________________________________________
 420 // _find_score_simple_proportional
 421
 422 template <typename TFinder, typename TNeedle, typename TScore> bool _find_score_simple_proportional(TFinder & finder, Pattern<TNeedle, DPSearch<TScore> > & me);        // "projects/library/seqan/find/find_score.h"(350)
 423
 424 //____________________________________________________________________________
 425 // _finderSetNonEmpty
 426
 427 template <typename T> inline void _finderSetNonEmpty(T & me);           // "projects/library/seqan/find/find_base.h"(494)
 428 template <typename THaystack, typename TSpec> inline void _finderSetNonEmpty(Finder<THaystack, TSpec> & me);            // "projects/library/seqan/find/find_base.h"(503)
 429
 430 //____________________________________________________________________________
 431 // _getCharacterClass
 432
 433 template <typename TValue,typename TNeedle2> String <unsigned> _getCharacterClass(TNeedle2 const & host,unsigned start,unsigned end);           // "projects/library/seqan/find/find_wild_shiftand.h"(261)
 434
 435 //____________________________________________________________________________
 436 // _getRoot
 437
 438 template <typename TNeedle, typename TMultiFinder> int _getRoot(Pattern<TNeedle, Pex<NonHierarchical, TMultiFinder > > & me);           // "projects/library/seqan/find/find_pex.h"(213)
 439 template <typename TNeedle, typename TMultiFinder> int _getRoot(Pattern<TNeedle, Pex<Hierarchical, TMultiFinder > > &);         // "projects/library/seqan/find/find_pex.h"(220)
 440
 441 //____________________________________________________________________________
 442 // _isInt
 443
 444 inline bool _isInt(String<char> const & number);        // "projects/library/seqan/find/find_wild_shiftand.h"(99)
 445
 446 //____________________________________________________________________________
 447 // _length_wo_wild
 448
 449 template <typename TNeedle> unsigned _length_wo_wild(TNeedle const & needle);           // "projects/library/seqan/find/find_wild_shiftand.h"(189)
 450
 451 //____________________________________________________________________________
 452 // _myersCoreSmall
 453
 454 template <typename TWord, typename TAlignSpec> inline int _myersCoreSmall(TWord &VP, TWord &VN, TWord const &bitmap, int scoreBit, Tag<_MyersUkkonen<TAlignSpec> >);            // "projects/library/seqan/find/find_myers_ukkonen.h"(743)
 455
 456 //____________________________________________________________________________
 457 // _myersCoreSmallDiag
 458
 459 template <typename TWord, typename TAlignSpec> inline int _myersCoreSmallDiag(TWord &VP, TWord &VN, TWord const &bitmap, int scoreBit, Tag<_MyersUkkonen<TAlignSpec> >);        // "projects/library/seqan/find/find_myers_ukkonen.h"(758)
 460
 461 //____________________________________________________________________________
 462 // _patternFirstInit
 463
 464 template <typename TNeedle, typename TSpec, typename TNeedle2> inline void _patternFirstInit(Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > & me, TNeedle2 & needle);            // "projects/library/seqan/find/find_myers_ukkonen.h"(174)
 465 template <typename TNeedle, typename TNeedle2> inline void _patternFirstInit(Pattern<TNeedle, Tag<_MyersUkkonen<AlignTextBanded> > > & me, TNeedle2 & ndl);             // "projects/library/seqan/find/find_myers_ukkonen.h"(199)
 466
 467 //____________________________________________________________________________
 468 // _patternInit
 469
 470 template <typename TNeedle, typename TSpec, typename TFinder> void _patternInit(Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > &me, TFinder &);          // "projects/library/seqan/find/find_myers_ukkonen.h"(284)
 471 template <typename TNeedle, typename TFinder> void _patternInit(Pattern<TNeedle, Tag<_MyersUkkonen<AlignTextBanded> > > &me, TFinder &finder);          // "projects/library/seqan/find/find_myers_ukkonen.h"(312)
 472 template <typename TIndex, typename TFloat, typename _TSize, typename TSpec> inline void _patternInit(Pattern<TIndex, Swift<TSpec> > &pattern, TFloat errorRate, _TSize minLengthForAll);               // "projects/library/seqan/find/find_swift.h"(333)
 473 template <typename TNeedle> inline void _patternInit (Pattern<TNeedle, Quasar> & me);           // "projects/library/seqan/find/find_quasar.h"(109)
 474 template <typename TNeedle, typename TFinder, typename TMultiFinder> void _patternInit(Pattern<TNeedle, Pex<NonHierarchical, TMultiFinder > > &me, TFinder &);          // "projects/library/seqan/find/find_pex.h"(266)
 475 template <typename TNeedle, typename TFinder, typename TMultiFinder> void _patternInit(Pattern<TNeedle, Pex<Hierarchical, TMultiFinder > > &me, TFinder &);             // "projects/library/seqan/find/find_pex.h"(479)
 476 template <typename TNeedle> inline void _patternInit (Pattern<TNeedle, ShiftAnd> & me);         // "projects/library/seqan/find/find_shiftand.h"(130)
 477 template <typename TNeedle> inline void _patternInit (Pattern<TNeedle, Horspool> &);            // "projects/library/seqan/find/find_horspool.h"(125)
 478 template <typename TNeedle, typename TScore> inline void _patternInit (Pattern<TNeedle, DPSearch<TScore> > & me);               // "projects/library/seqan/find/find_score.h"(299)
 479 template <typename TNeedle> inline void _patternInit (Pattern<TNeedle, MultipleShiftAnd> & me);         // "projects/library/seqan/find/find_multiple_shiftand.h"(218)
 480 template <typename TNeedle> inline void _patternInit (Pattern<TNeedle, BomAlgo> & me);          // "projects/library/seqan/find/find_bom.h"(129)
 481 template <typename TNeedle> inline void _patternInit (Pattern<TNeedle, ShiftOr> & me);          // "projects/library/seqan/find/find_shiftor.h"(129)
 482 template <typename TNeedle> inline void _patternInit (Pattern<TNeedle, WildShiftAnd> & me);             // "projects/library/seqan/find/find_wild_shiftand.h"(518)
 483 template <typename TNeedle> inline void _patternInit (Pattern<TNeedle, SetHorspool> & me);              // "projects/library/seqan/find/find_set_horspool.h"(175)
 484 template <typename TNeedle> inline void _patternInit (Pattern<TNeedle, BndmAlgo> & me);         // "projects/library/seqan/find/find_bndm.h"(131)
 485 template <typename TNeedle> inline void _patternInit (Pattern<TNeedle, AhoCorasick> & me);              // "projects/library/seqan/find/find_ahocorasick.h"(225)
 486 template <typename TNeedle> inline void _patternInit (Pattern<TNeedle, AbndmAlgo> & me);        // "projects/library/seqan/find/find_abndm.h"(196)
 487
 488 //____________________________________________________________________________
 489 // _printMask
 490
 491 inline void _printMask(String <unsigned> const & mask,String <char> name);              // "projects/library/seqan/find/find_abndm.h"(33)
 492 inline void _printMask(String <unsigned> const & mask,unsigned start, unsigned len,String <char> name);         // "projects/library/seqan/find/find_abndm.h"(46)
 493
 494 //____________________________________________________________________________
 495 // _printR
 496
 497 template <typename TNeedle> void _printR(Pattern<TNeedle, AbndmAlgo> & me);             // "projects/library/seqan/find/find_abndm.h"(127)
 498
 499 //____________________________________________________________________________
 500 // _printSwiftBuckets
 501
 502 template <typename TNeedle, typename TIndexSpec, typename TSpec > inline void _printSwiftBuckets(Pattern< Index<TNeedle, TIndexSpec>, Swift<TSpec> > &p);               // "projects/library/seqan/find/find_swift.h"(288)
 503
 504 //____________________________________________________________________________
 505 // _printSwiftParams
 506
 507 template <typename TParams> inline void _printSwiftParams(TParams &bucketParams);               // "projects/library/seqan/find/find_swift.h"(276)
 508
 509 //____________________________________________________________________________
 510 // _swiftBucketNo
 511
 512 template <typename TIndex, typename TSpec, typename TParams, typename TSize> inline unsigned _swiftBucketNo(Pattern<TIndex, Swift<TSpec> > const &, TParams &bucketParams, TSize seqNo);        // "projects/library/seqan/find/find_swift.h"(324)
 513
 514 //____________________________________________________________________________
 515 // _swiftBucketParams
 516
 517 template <typename TIndex, typename TSpec, typename TSize> inline typename Pattern<TIndex, Swift<TSpec> >::TBucketParams & _swiftBucketParams(Pattern<TIndex, Swift<TSpec> > & pattern, TSize seqNo);           // "projects/library/seqan/find/find_swift.h"(314)
 518
 519 //____________________________________________________________________________
 520 // _swiftMultiFlushBuckets
 521
 522 template <typename THaystack, typename TIndex, typename TSpec > inline bool _swiftMultiFlushBuckets( Finder<THaystack, Swift<TSpec> > &finder, Pattern<TIndex, Swift<TSpec> > &pattern);        // "projects/library/seqan/find/find_swift.h"(612)
 523
 524 //____________________________________________________________________________
 525 // _swiftMultiProcessQGram
 526
 527 template <typename THaystack, typename TIndex, typename TSpec, typename THValue > inline bool _swiftMultiProcessQGram( Finder<THaystack, Swift<TSpec> > &finder, Pattern<TIndex, Swift<TSpec> > &pattern, THValue hash);        // "projects/library/seqan/find/find_swift.h"(491)
 528
 529 //____________________________________________________________________________
 530 // _validate
 531
 532 template <typename TNeedle2> bool _validate(TNeedle2 const & needle);           // "projects/library/seqan/find/find_wild_shiftand.h"(111)
 533
 534 //____________________________________________________________________________
 535 // atBegin
 536
 537 template <typename THaystack, typename TSpec> inline bool atBegin(Finder<THaystack, TSpec> & me);               // "projects/library/seqan/find/find_base.h"(513)
 538
 539 //____________________________________________________________________________
 540 // atEnd
 541
 542 template <typename THaystack, typename TSpec> inline bool atEnd(Finder<THaystack, Swift<TSpec> > & me);         // "projects/library/seqan/find/find_swift.h"(218)
 543 template <typename THaystack, typename TSpec> inline bool atEnd(Finder<THaystack, TSpec> & me);         // "projects/library/seqan/find/find_base.h"(521)
 544
 545 //____________________________________________________________________________
 546 // beginPosition
 547
 548 template <typename THaystack, typename TSpec> inline typename Position<Finder<THaystack, Swift<TSpec> > >::Type beginPosition(Finder<THaystack, Swift<TSpec> > & finder);               // "projects/library/seqan/find/find_swift.h"(720)
 549 template <typename THaystack, typename TSpec> inline typename Position<Finder<THaystack, Swift<TSpec> > >::Type beginPosition(Finder<THaystack, Swift<TSpec> > const & finder);         // "projects/library/seqan/find/find_swift.h"(728)
 550 template <typename TNeedle, typename TSpec> inline typename Position<Pattern<TNeedle, TSpec> >::Type & beginPosition(Pattern<TNeedle, TSpec> & me);             // "projects/library/seqan/find/find_base.h"(176)
 551 template <typename TNeedle, typename TSpec> inline typename Position<Pattern<TNeedle, TSpec> const >::Type & beginPosition(Pattern<TNeedle, TSpec> const & me);         // "projects/library/seqan/find/find_base.h"(182)
 552
 553 //____________________________________________________________________________
 554 // clear
 555
 556 template <typename TNeedle, typename TIndexSpec, typename TSpec> inline void clear(Pattern<Index<TNeedle, TIndexSpec>, Swift<TSpec> > & me);            // "projects/library/seqan/find/find_swift.h"(692)
 557 template <typename THaystack, typename TSpec> inline void clear(Finder<THaystack, TSpec> & me);         // "projects/library/seqan/find/find_base.h"(484)
 558
 559 //____________________________________________________________________________
 560 // container
 561
 562 template <typename THaystack, typename TSpec> inline typename _Parameter<THaystack>::Type container(Finder<THaystack, TSpec> & me);             // "projects/library/seqan/find/find_base.h"(420)
 563 template <typename THaystack, typename TSpec> inline typename _Parameter<THaystack>::Type container(Finder<THaystack, TSpec> const & me);               // "projects/library/seqan/find/find_base.h"(428)
 564
 565 //____________________________________________________________________________
 566 // empty
 567
 568 template <typename TNeedle, typename TIndexSpec, typename TSpec> inline bool empty(Pattern<Index<TNeedle, TIndexSpec>, Swift<TSpec> > & me);            // "projects/library/seqan/find/find_swift.h"(685)
 569 template <typename THaystack, typename TSpec> inline bool empty(Finder<THaystack, TSpec> & me);         // "projects/library/seqan/find/find_base.h"(476)
 570
 571 //____________________________________________________________________________
 572 // endPosition
 573
 574 template <typename THaystack, typename TSpec> inline typename Position<Finder<THaystack, Swift<TSpec> > >::Type endPosition(Finder<THaystack, Swift<TSpec> > & finder);         // "projects/library/seqan/find/find_swift.h"(738)
 575 template <typename THaystack, typename TSpec> inline typename Position<Finder<THaystack, Swift<TSpec> > >::Type endPosition(Finder<THaystack, Swift<TSpec> > const & finder);           // "projects/library/seqan/find/find_swift.h"(746)
 576 template <typename TNeedle, typename TSpec> inline typename Position<Pattern<TNeedle, TSpec> >::Type & endPosition(Pattern<TNeedle, TSpec> & me);               // "projects/library/seqan/find/find_base.h"(200)
 577 template <typename TNeedle, typename TSpec> inline typename Position<Pattern<TNeedle, TSpec> const >::Type & endPosition(Pattern<TNeedle, TSpec> const & me);           // "projects/library/seqan/find/find_base.h"(206)
 578
 579 //____________________________________________________________________________
 580 // find
 581
 582 template <typename TFinder, typename TNeedle, typename TSpec> inline bool find (TFinder & finder, Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > & me);          // "projects/library/seqan/find/find_myers_ukkonen.h"(961)
 583 template <typename TFinder, typename TNeedle, typename TSpec> inline bool find (TFinder & finder, Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > & me, int const k);             // "projects/library/seqan/find/find_myers_ukkonen.h"(997)
 584 template <typename THaystack, typename TNeedle, typename TIndexSpec, typename TSpec> inline bool find( Finder<THaystack, Swift<TSpec> > &finder, Pattern<Index<TNeedle, TIndexSpec>, Swift<TSpec> > &pattern, double errorRate);        // "projects/library/seqan/find/find_swift.h"(799)
 585 //template <typename THashes, typename TPipeSpec, typename TNeedle, typename TIndexSpec, typename TSpec> inline bool find( Finder<Pipe<THashes, TPipeSpec>, Swift<TSpec> > &finder, Pattern<Index<TNeedle, TIndexSpec>, Swift<TSpec> > &pattern, double errorRate, bool printDots);             // "projects/library/seqan/find/find_swift.h"(843)
 586 template <typename TFinder, typename TNeedle> inline bool find(TFinder & finder, Pattern<TNeedle, Quasar> & me);        // "projects/library/seqan/find/find_quasar.h"(138)
 587 template <typename TFinder, typename TNeedle, typename TMultiFinder> inline bool find (TFinder & finder, Pattern<TNeedle, Pex<NonHierarchical, TMultiFinder > > & me);          // "projects/library/seqan/find/find_pex.h"(335)
 588 template <typename TFinder, typename TNeedle, typename TMultiFinder> inline bool find (TFinder & finder, Pattern<TNeedle, Pex<Hierarchical, TMultiFinder > > & me);             // "projects/library/seqan/find/find_pex.h"(520)
 589 template <typename TFinder, typename TNeedle> inline bool find(TFinder & finder, Pattern<TNeedle, ShiftAnd> & me);              // "projects/library/seqan/find/find_shiftand.h"(217)
 590 template <typename TFinder, typename TNeedle2> bool find(TFinder & finder, Pattern<TNeedle2, Horspool> & me);           // "projects/library/seqan/find/find_horspool.h"(448)
 591 template <typename TFinder, typename TNeedle, typename TScore> inline bool find(TFinder & finder, Pattern<TNeedle, DPSearch<TScore> > & me);            // "projects/library/seqan/find/find_score.h"(430)
 592 template <typename TFinder, typename TNeedle, typename TScore> inline bool find(TFinder & finder, Pattern<TNeedle, DPSearch<TScore> > & me, int const limit_);          // "projects/library/seqan/find/find_score.h"(440)
 593 template <typename TFinder, typename TNeedle> inline bool find(TFinder & finder, Pattern<TNeedle, MultipleShiftAnd> & me);              // "projects/library/seqan/find/find_multiple_shiftand.h"(386)
 594 template <typename TFinder, typename TNeedle> inline bool find(TFinder & finder, Pattern<TNeedle, BomAlgo> & me);               // "projects/library/seqan/find/find_bom.h"(159)
 595 template <typename TFinder, typename TNeedle> inline bool find(TFinder & finder, Pattern<TNeedle, ShiftOr> & me);               // "projects/library/seqan/find/find_shiftor.h"(248)
 596 template <typename TFinder, typename TNeedle> inline bool find(TFinder & finder, Pattern<TNeedle, WildShiftAnd> & me);          // "projects/library/seqan/find/find_wild_shiftand.h"(631)
 597 template <typename TFinder, typename TNeedle> inline bool find(TFinder & finder, Pattern<TNeedle, SetHorspool> & me);           // "projects/library/seqan/find/find_set_horspool.h"(213)
 598 template <typename TFinder, typename TNeedle> inline bool find(TFinder & finder, Pattern<TNeedle, BndmAlgo> & me);              // "projects/library/seqan/find/find_bndm.h"(229)
 599 template <typename TFinder, typename TNeedle> inline bool find(TFinder & finder, Pattern<TNeedle, AhoCorasick> & me);           // "projects/library/seqan/find/find_ahocorasick.h"(263)
 600 template <typename TFinder, typename TNeedle> inline bool find (TFinder & finder, Pattern<TNeedle, AbndmAlgo > & me);           // "projects/library/seqan/find/find_abndm.h"(575)
 601 template <typename TFinder, typename TNeedle> inline bool find (TFinder & finder, Pattern<TNeedle, AbndmAlgo > & me, int const k);              // "projects/library/seqan/find/find_abndm.h"(594)
 602
 603 //____________________________________________________________________________
 604 // find_horspool
 605
 606 template <typename TFinder, typename TNeedle2> bool find_horspool(TFinder & finder, Pattern<TNeedle2, Horspool> & me, bool find_first);         // "projects/library/seqan/find/find_horspool.h"(152)
 607 template <typename TValue, typename TFormat, typename TFile, typename FileReaderTSpec, typename TFinderSpec, typename TNeedle2> bool find_horspool(Finder<String<TValue, FileReader<TFormat, TFile, FileReaderTSpec> >, TFinderSpec > & finder, Pattern<TNeedle2, Horspool> & me, bool find_first);             // "projects/library/seqan/find/find_horspool.h"(315)
 608
 609 //____________________________________________________________________________
 610 // getScore
 611
 612 template <typename TNeedle, typename TSpec> int getScore(Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > & me);           // "projects/library/seqan/find/find_myers_ukkonen.h"(271)
 613 template <typename TNeedle, typename TVerification, typename TMultiFinder> int getScore(Pattern<TNeedle, Pex<TVerification,TMultiFinder > > & me);              // "projects/library/seqan/find/find_pex.h"(230)
 614 template <typename TNeedle, typename TScore> inline typename Value<TScore>::Type getScore(Pattern<TNeedle, DPSearch<TScore> > & me);            // "projects/library/seqan/find/find_score.h"(290)
 615 template <typename TNeedle> int getScore(Pattern<TNeedle, AbndmAlgo > & me);            // "projects/library/seqan/find/find_abndm.h"(228)
 616
 617 //____________________________________________________________________________
 618 // goBegin
 619
 620 template <typename THaystack, typename TSpec> inline void goBegin(Finder<THaystack, TSpec> & me);               // "projects/library/seqan/find/find_base.h"(531)
 621
 622 //____________________________________________________________________________
 623 // goEnd
 624
 625 template <typename THaystack, typename TSpec> inline void goEnd(Finder<THaystack, Swift<TSpec> > & me);         // "projects/library/seqan/find/find_swift.h"(225)
 626 template <typename THaystack, typename TSpec> inline void goEnd(Finder<THaystack, TSpec> & me);         // "projects/library/seqan/find/find_base.h"(540)
 627
 628 //____________________________________________________________________________
 629 // haystack
 630
 631 template <typename TObject > inline typename Haystack<TObject>::Type & haystack(TObject &obj);          // "projects/library/seqan/find/find_base.h"(703)
 632 template <typename TObject > inline typename Haystack<TObject const>::Type & haystack(TObject const &obj);              // "projects/library/seqan/find/find_base.h"(709)
 633
 634 //____________________________________________________________________________
 635 // host
 636
 637 template <typename TNeedle, typename TSpec> inline typename Host<Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > >::Type & host(Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > & me);              // "projects/library/seqan/find/find_myers_ukkonen.h"(227)
 638 template <typename TNeedle, typename TSpec> inline typename Host<Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > const>::Type & host(Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > const & me);           // "projects/library/seqan/find/find_myers_ukkonen.h"(235)
 639 template <typename TNeedle> inline typename Host<Pattern<TNeedle, Quasar>const>::Type & host(Pattern<TNeedle, Quasar> & me);            // "projects/library/seqan/find/find_quasar.h"(119)
 640 template <typename TNeedle> inline typename Host<Pattern<TNeedle, Quasar>const>::Type & host(Pattern<TNeedle, Quasar> const & me);              // "projects/library/seqan/find/find_quasar.h"(127)
 641 template <typename TNeedle, typename TVerification, typename TMultiFinder> inline typename Host<Pattern<TNeedle, Pex<TVerification,TMultiFinder > > const>::Type & host(Pattern<TNeedle, Pex<TVerification,TMultiFinder > > & me);              // "projects/library/seqan/find/find_pex.h"(196)
 642 template <typename TNeedle, typename TVerification, typename TMultiFinder> inline typename Host<Pattern<TNeedle, Pex<TVerification,TMultiFinder > > const>::Type & host(Pattern<TNeedle, Pex<TVerification,TMultiFinder > > const & me);        // "projects/library/seqan/find/find_pex.h"(204)
 643 template <typename TNeedle> inline typename Host<Pattern<TNeedle, ShiftAnd>const>::Type & host(Pattern<TNeedle, ShiftAnd> & me);        // "projects/library/seqan/find/find_shiftand.h"(142)
 644 template <typename TNeedle> inline typename Host<Pattern<TNeedle, ShiftAnd>const>::Type & host(Pattern<TNeedle, ShiftAnd> const & me);          // "projects/library/seqan/find/find_shiftand.h"(150)
 645 template <typename TNeedle> inline typename Host<Pattern<TNeedle, Horspool> >::Type & host(Pattern<TNeedle, Horspool> & me);            // "projects/library/seqan/find/find_horspool.h"(132)
 646 template <typename TNeedle> inline typename Host<Pattern<TNeedle, Horspool> const>::Type & host(Pattern<TNeedle, Horspool> const & me);         // "projects/library/seqan/find/find_horspool.h"(140)
 647 template <typename THaystack, typename TSpec> inline typename _Parameter<THaystack>::Type host(Finder<THaystack, TSpec> & me);          // "projects/library/seqan/find/find_base.h"(404)
 648 template <typename THaystack, typename TSpec> inline typename _Parameter<THaystack>::Type host(Finder<THaystack, TSpec> const & me);            // "projects/library/seqan/find/find_base.h"(412)
 649 template <typename TNeedle, typename TScore> inline typename Host<Pattern<TNeedle, DPSearch<TScore> > >::Type & host(Pattern<TNeedle, DPSearch<TScore> > & me);         // "projects/library/seqan/find/find_score.h"(144)
 650 template <typename TNeedle, typename TScore> inline typename Host<Pattern<TNeedle, DPSearch<TScore> > const>::Type & host(Pattern<TNeedle, DPSearch<TScore> > const & me);              // "projects/library/seqan/find/find_score.h"(152)
 651 template <typename TNeedle> inline typename Host<Pattern<TNeedle, MultipleShiftAnd>const>::Type & host(Pattern<TNeedle, MultipleShiftAnd> & me);        // "projects/library/seqan/find/find_multiple_shiftand.h"(236)
 652 template <typename TNeedle> inline typename Host<Pattern<TNeedle, MultipleShiftAnd>const>::Type & host(Pattern<TNeedle, MultipleShiftAnd> const & me);          // "projects/library/seqan/find/find_multiple_shiftand.h"(244)
 653 template <typename TNeedle> inline typename Host<Pattern<TNeedle, BomAlgo>const>::Type & host(Pattern<TNeedle, BomAlgo> & me);          // "projects/library/seqan/find/find_bom.h"(140)
 654 template <typename TNeedle> inline typename Host<Pattern<TNeedle, BomAlgo>const>::Type & host(Pattern<TNeedle, BomAlgo> const & me);            // "projects/library/seqan/find/find_bom.h"(148)
 655 template <typename TNeedle> inline typename Host<Pattern<TNeedle, ShiftOr>const>::Type & host(Pattern<TNeedle, ShiftOr> & me);          // "projects/library/seqan/find/find_shiftor.h"(143)
 656 template <typename TNeedle> inline typename Host<Pattern<TNeedle, ShiftOr>const>::Type & host(Pattern<TNeedle, ShiftOr> const & me);            // "projects/library/seqan/find/find_shiftor.h"(151)
 657 template <typename TNeedle> inline typename Host<Pattern<TNeedle, WildShiftAnd>const>::Type & host(Pattern<TNeedle, WildShiftAnd> & me);        // "projects/library/seqan/find/find_wild_shiftand.h"(550)
 658 template <typename TNeedle> inline typename Host<Pattern<TNeedle, WildShiftAnd>const>::Type & host(Pattern<TNeedle, WildShiftAnd> const & me);          // "projects/library/seqan/find/find_wild_shiftand.h"(558)
 659 template <typename TNeedle> inline typename Host<Pattern<TNeedle, SetHorspool>const>::Type & host(Pattern<TNeedle, SetHorspool> & me);          // "projects/library/seqan/find/find_set_horspool.h"(188)
 660 template <typename TNeedle> inline typename Host<Pattern<TNeedle, SetHorspool>const>::Type & host(Pattern<TNeedle, SetHorspool> const & me);            // "projects/library/seqan/find/find_set_horspool.h"(196)
 661 template <typename TNeedle> inline typename Host<Pattern<TNeedle, BndmAlgo>const>::Type & host(Pattern<TNeedle, BndmAlgo> & me);        // "projects/library/seqan/find/find_bndm.h"(143)
 662 template <typename TNeedle> inline typename Host<Pattern<TNeedle, BndmAlgo>const>::Type & host(Pattern<TNeedle, BndmAlgo> const & me);          // "projects/library/seqan/find/find_bndm.h"(151)
 663 template <typename TNeedle> inline typename Host<Pattern<TNeedle, AhoCorasick>const>::Type & host(Pattern<TNeedle, AhoCorasick> & me);          // "projects/library/seqan/find/find_ahocorasick.h"(238)
 664 template <typename TNeedle> inline typename Host<Pattern<TNeedle, AhoCorasick>const>::Type & host(Pattern<TNeedle, AhoCorasick> const & me);            // "projects/library/seqan/find/find_ahocorasick.h"(246)
 665 template <typename TNeedle> inline typename Host<Pattern<TNeedle, AbndmAlgo>const>::Type & host(Pattern<TNeedle, AbndmAlgo> & me);              // "projects/library/seqan/find/find_abndm.h"(209)
 666 template <typename TNeedle> inline typename Host<Pattern<TNeedle, AbndmAlgo>const>::Type & host(Pattern<TNeedle, AbndmAlgo> const & me);        // "projects/library/seqan/find/find_abndm.h"(217)
 667
 668 //____________________________________________________________________________
 669 // hostIterator
 670
 671 template <typename THaystack, typename TSpec> inline typename Iterator<THaystack, Rooted>::Type & hostIterator(Finder<THaystack, TSpec> & me);          // "projects/library/seqan/find/find_base.h"(458)
 672 template <typename THaystack, typename TSpec> inline typename Iterator<THaystack, Rooted>::Type const & hostIterator(Finder<THaystack, TSpec> const & me);              // "projects/library/seqan/find/find_base.h"(466)
 673
 674 //____________________________________________________________________________
 675 // needle
 676
 677 template <typename TObject > inline typename Needle<TObject>::Type & needle(TObject &obj);              // "projects/library/seqan/find/find_base.h"(252)
 678 template <typename TObject > inline typename Needle<TObject const>::Type & needle(TObject const &obj);          // "projects/library/seqan/find/find_base.h"(259)
 679 template <typename TNeedle, typename TSpec > inline typename Needle< Pattern<TNeedle, TSpec> >::Type & needle(Pattern<TNeedle, TSpec> & obj);           // "projects/library/seqan/find/find_base.h"(269)
 680 template <typename TNeedle, typename TSpec > inline typename Needle< Pattern<TNeedle, TSpec> const>::Type & needle(Pattern<TNeedle, TSpec> const & obj);        // "projects/library/seqan/find/find_base.h"(276)
 681
 682 //____________________________________________________________________________
 683 // operator+
 684
 685 template <typename THaystack, typename TSpec, typename TIntegral> inline Finder<THaystack, TSpec> const operator+ (Finder<THaystack, TSpec> const & left, TIntegral right);             // "projects/library/seqan/find/find_base.h"(617)
 686
 687 //____________________________________________________________________________
 688 // operator++
 689
 690 template <typename THaystack, typename TSpec> inline Finder<THaystack, TSpec> & operator++(Finder<THaystack, TSpec> & me);              // "projects/library/seqan/find/find_base.h"(601)
 691
 692 //____________________________________________________________________________
 693 // operator+=
 694
 695 template <typename THaystack, typename TSpec, typename TIntegral> inline Finder<THaystack, TSpec> & operator+= (Finder<THaystack, TSpec> & left, TIntegral right);              // "projects/library/seqan/find/find_base.h"(630)
 696
 697 //____________________________________________________________________________
 698 // operator-
 699
 700 template <typename THaystack, typename TSpec, typename TIntegral> inline Finder<THaystack, TSpec> const operator- (Finder<THaystack, TSpec> const & left, TIntegral right);             // "projects/library/seqan/find/find_base.h"(643)
 701 template <typename THaystack, typename TSpec, typename TIntegral> inline typename Difference<Finder<THaystack, TSpec> const>::Type operator- (Finder<THaystack, TSpec> const & left, Finder<THaystack, TSpec> const & right);           // "projects/library/seqan/find/find_base.h"(651)
 702
 703 //____________________________________________________________________________
 704 // operator--
 705
 706 template <typename THaystack, typename TSpec> inline Finder<THaystack, TSpec> & operator--(Finder<THaystack, TSpec> & me);              // "projects/library/seqan/find/find_base.h"(592)
 707
 708 //____________________________________________________________________________
 709 // operator-=
 710
 711 template <typename THaystack, typename TSpec, typename TIntegral> inline Finder<THaystack, TSpec> & operator-= (Finder<THaystack, TSpec> & left, TIntegral right);              // "projects/library/seqan/find/find_base.h"(664)
 712
 713 //____________________________________________________________________________
 714 // position
 715
 716 template <typename THaystack, typename TSpec> inline typename Position<Finder<THaystack, Swift<TSpec> > >::Type position(Finder<THaystack, Swift<TSpec> > & finder);            // "projects/library/seqan/find/find_swift.h"(702)
 717 template <typename THaystack, typename TSpec> inline typename Position<Finder<THaystack, Swift<TSpec> > >::Type position(Finder<THaystack, Swift<TSpec> > const & finder);              // "projects/library/seqan/find/find_swift.h"(710)
 718 template <typename THaystack, typename TSpec> inline typename Position<Finder<THaystack, TSpec> >::Type position(Finder<THaystack, TSpec> & me);        // "projects/library/seqan/find/find_base.h"(551)
 719 template <typename THaystack, typename TSpec> inline typename Position<Finder<THaystack, TSpec> >::Type position(Finder<THaystack, TSpec> const & me);          // "projects/library/seqan/find/find_base.h"(560)
 720 template <typename TNeedle> inline typename Size<TNeedle>::Type position(Pattern<TNeedle, MultipleShiftAnd> & me);              // "projects/library/seqan/find/find_multiple_shiftand.h"(255)
 721 template <typename TNeedle> inline typename Size<TNeedle>::Type position(Pattern<TNeedle, SetHorspool> & me);           // "projects/library/seqan/find/find_set_horspool.h"(207)
 722 template <typename TNeedle> inline typename Size<TNeedle>::Type position(Pattern<TNeedle, AhoCorasick> & me);           // "projects/library/seqan/find/find_ahocorasick.h"(257)
 723
 724 //____________________________________________________________________________
 725 // range
 726
 727 template <typename THaystack, typename TSpec> inline typename Infix<THaystack>::Type range(Finder<THaystack, Swift<TSpec> > &finder);           // "projects/library/seqan/find/find_swift.h"(756)
 728 template <typename THaystack, typename TSpec, typename TText> inline typename Infix<TText>::Type range(Finder<THaystack, Swift<TSpec> > &finder, TText &text);          // "projects/library/seqan/find/find_swift.h"(772)
 729 template <typename TNeedle, typename TIndexSpec, typename TSpec> inline typename Value<TNeedle>::Type & range(Pattern<Index<TNeedle, TIndexSpec>, Swift<TSpec> > &pattern);             // "projects/library/seqan/find/find_swift.h"(788)
 730
 731 //____________________________________________________________________________
 732 // scoreLimit
 733
 734 template <typename TNeedle, typename TSpec> inline int scoreLimit(Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > const & me);            // "projects/library/seqan/find/find_myers_ukkonen.h"(247)
 735 template <typename TNeedle, typename TVerification, typename TMultiFinder> inline int scoreLimit(Pattern<TNeedle, Pex<TVerification,TMultiFinder > > const & me);               // "projects/library/seqan/find/find_pex.h"(241)
 736 template <typename TNeedle, typename TScore> inline typename Value<TScore>::Type scoreLimit(Pattern<TNeedle, DPSearch<TScore> > const & me);            // "projects/library/seqan/find/find_score.h"(245)
 737 template <typename TNeedle> inline int scoreLimit(Pattern<TNeedle, AbndmAlgo > const & me);             // "projects/library/seqan/find/find_abndm.h"(551)
 738
 739 //____________________________________________________________________________
 740 // scoringScheme
 741
 742 template <typename TNeedle, typename TScore> inline TScore const & scoringScheme(Pattern<TNeedle, DPSearch<TScore> > & me);             // "projects/library/seqan/find/find_score.h"(193)
 743
 744 //____________________________________________________________________________
 745 // segment
 746
 747 template <typename TNeedle, typename TSpec> inline typename Infix<TNeedle>::Type segment(Pattern<TNeedle, TSpec> & me);         // "projects/library/seqan/find/find_base.h"(223)
 748 template <typename TNeedle, typename TSpec> inline typename Infix<TNeedle>::Type segment(Pattern<TNeedle, TSpec> const & me);           // "projects/library/seqan/find/find_base.h"(230)
 749
 750 //____________________________________________________________________________
 751 // setBeginPosition
 752
 753 template <typename TNeedle, typename TSpec, typename TPosition> inline void setBeginPosition(Pattern<TNeedle, TSpec> & me, TPosition _pos);             // "projects/library/seqan/find/find_base.h"(191)
 754
 755 //____________________________________________________________________________
 756 // setContainer
 757
 758 template <typename THaystack, typename TSpec> inline void setContainer(Finder<THaystack, TSpec> & me, typename _Parameter<THaystack>::Type container_);         // "projects/library/seqan/find/find_base.h"(447)
 759
 760 //____________________________________________________________________________
 761 // setEndPosition
 762
 763 template <typename TNeedle, typename TSpec, typename TPosition> inline void setEndPosition(Pattern<TNeedle, TSpec> & me, TPosition _pos);               // "projects/library/seqan/find/find_base.h"(214)
 764
 765 //____________________________________________________________________________
 766 // setHaystack
 767
 768 template <typename THaystack, typename TSpec > inline void setHaystack(Finder<THaystack, TSpec> &obj, THaystack const &hstk);           // "projects/library/seqan/find/find_base.h"(686)
 769
 770 //____________________________________________________________________________
 771 // setHost
 772
 773 template <typename TNeedle, typename TSpec, typename TNeedle2> void setHost(Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > & me, TNeedle2 & ndl);        // "projects/library/seqan/find/find_myers_ukkonen.h"(209)
 774 template <typename TNeedle, typename TSpec, typename TNeedle2> void setHost(Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > & me, TNeedle2 const & ndl);          // "projects/library/seqan/find/find_myers_ukkonen.h"(217)
 775 template <typename TNeedle, typename TNeedle2> inline void setHost (Pattern<TNeedle, Quasar> & me, TNeedle2 const& needle);             // "projects/library/seqan/find/find_quasar.h"(92)
 776 template <typename TNeedle, typename TNeedle2> inline void setHost (Pattern<TNeedle, Quasar> & me, TNeedle2 & needle);          // "projects/library/seqan/find/find_quasar.h"(100)
 777 template <typename TNeedle, typename TNeedle2, typename TVerification, typename TMultiFinder> void setHost (Pattern<TNeedle, Pex<TVerification,TMultiFinder > > & me, TNeedle2 const & needle);         // "projects/library/seqan/find/find_pex.h"(176)
 778 template <typename TNeedle, typename TNeedle2, typename TVerification, typename TMultiFinder> void setHost (Pattern<TNeedle, Pex<TVerification,TMultiFinder > > & me, TNeedle2 & needle);               // "projects/library/seqan/find/find_pex.h"(187)
 779 template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, ShiftAnd> & me, TNeedle2 const & needle);         // "projects/library/seqan/find/find_shiftand.h"(80)
 780 template <typename TNeedle, typename TNeedle2> inline void setHost (Pattern<TNeedle, ShiftAnd> & me, TNeedle2 & needle);        // "projects/library/seqan/find/find_shiftand.h"(121)
 781 template <typename TNeedle, typename TNeedle2> void setHost(Pattern<TNeedle, Horspool> & me, TNeedle2 const & ndl);             // "projects/library/seqan/find/find_horspool.h"(86)
 782 template <typename TNeedle, typename TNeedle2> void setHost(Pattern<TNeedle, Horspool> & horsp, TNeedle2 & ndl);        // "projects/library/seqan/find/find_horspool.h"(117)
 783 template <typename TNeedle, typename TSpec, typename TNeedle2> inline void setHost(Pattern<TNeedle, TSpec> & me, TNeedle2 const & ndl);         // "projects/library/seqan/find/find_base.h"(161)
 784 template <typename TNeedle, typename TSpec, typename TNeedle2> inline void setHost(Pattern<TNeedle, TSpec> & me, TNeedle2 & ndl);               // "projects/library/seqan/find/find_base.h"(168)
 785 template <typename THaystack, typename TSpec> inline void setHost(Finder<THaystack, TSpec> & me, typename _Parameter<THaystack>::Type container_);              // "projects/library/seqan/find/find_base.h"(438)
 786 template <typename TNeedle, typename TScore, typename TNeedle2> void setHost(Pattern<TNeedle, DPSearch<TScore> > & me, TNeedle2 & ndl);         // "projects/library/seqan/find/find_score.h"(164)
 787 template <typename TNeedle, typename TScore, typename TNeedle2> void setHost(Pattern<TNeedle, DPSearch<TScore> > & me, TNeedle2 const & ndl);           // "projects/library/seqan/find/find_score.h"(172)
 788 template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, MultipleShiftAnd> & me, TNeedle2 const & needle);         // "projects/library/seqan/find/find_multiple_shiftand.h"(124)
 789 template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, MultipleShiftAnd> & me, TNeedle2 & needle);               // "projects/library/seqan/find/find_multiple_shiftand.h"(209)
 790 template <typename TNeedle, typename TNeedle2> inline void setHost (Pattern<TNeedle, BomAlgo> & me, TNeedle2 const& needle);            // "projects/library/seqan/find/find_bom.h"(108)
 791 template <typename TNeedle, typename TNeedle2> inline void setHost (Pattern<TNeedle, BomAlgo> & me, TNeedle2 & needle);         // "projects/library/seqan/find/find_bom.h"(120)
 792 template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, ShiftOr> & me, TNeedle2 const & needle);          // "projects/library/seqan/find/find_shiftor.h"(79)
 793 template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, ShiftOr> & me, TNeedle2 & needle);        // "projects/library/seqan/find/find_shiftor.h"(120)
 794 template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, WildShiftAnd> & me, TNeedle2 const & needle);             // "projects/library/seqan/find/find_wild_shiftand.h"(289)
 795 template <typename TNeedle, typename TNeedle2> inline void setHost (Pattern<TNeedle, WildShiftAnd> & me, TNeedle2 & needle);            // "projects/library/seqan/find/find_wild_shiftand.h"(509)
 796 template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, SetHorspool> & me, TNeedle2 const & needle);              // "projects/library/seqan/find/find_set_horspool.h"(112)
 797 template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, SetHorspool> & me, TNeedle2 & needle);            // "projects/library/seqan/find/find_set_horspool.h"(166)
 798 template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, BndmAlgo> & me, TNeedle2 const& needle);          // "projects/library/seqan/find/find_bndm.h"(82)
 799 template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, BndmAlgo> & me, TNeedle2 & needle);               // "projects/library/seqan/find/find_bndm.h"(122)
 800 template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, AhoCorasick> & me, TNeedle2 const & needle);              // "projects/library/seqan/find/find_ahocorasick.h"(187)
 801 template <typename TNeedle, typename TNeedle2> inline void setHost (Pattern<TNeedle, AhoCorasick> & me, TNeedle2 & needle);             // "projects/library/seqan/find/find_ahocorasick.h"(216)
 802 template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, AbndmAlgo> & me, TNeedle2 const& needle);         // "projects/library/seqan/find/find_abndm.h"(140)
 803 template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, AbndmAlgo> & me, TNeedle2 & needle);              // "projects/library/seqan/find/find_abndm.h"(188)
 804
 805 //____________________________________________________________________________
 806 // setNeedle
 807
 808 template <typename TNeedle, typename TSpec > inline void setNeedle(Pattern<TNeedle, TSpec> &obj, TNeedle const &ndl);           // "projects/library/seqan/find/find_base.h"(293)
 809
 810 //____________________________________________________________________________
 811 // setPosition
 812
 813 template <typename THaystack, typename TSpec, typename TPosition> inline void setPosition(Finder<THaystack, TSpec> & me, TPosition pos_);               // "projects/library/seqan/find/find_base.h"(582)
 814
 815 //____________________________________________________________________________
 816 // setScoreLimit
 817
 818 template <typename TNeedle, typename TSpec, typename TScoreValue> inline void setScoreLimit(Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > & me, TScoreValue _limit);            // "projects/library/seqan/find/find_myers_ukkonen.h"(260)
 819 template <typename TNeedle, typename TScoreValue,typename TVerification, typename TMultiFinder> inline void setScoreLimit(Pattern<TNeedle, Pex<TVerification,TMultiFinder > > & me, TScoreValue _limit);        // "projects/library/seqan/find/find_pex.h"(254)
 820 template <typename TNeedle, typename TScore, typename TScoreValue> inline void setScoreLimit(Pattern<TNeedle, DPSearch<TScore> > & me, TScoreValue _limit);             // "projects/library/seqan/find/find_score.h"(266)
 821 template <typename TNeedle, typename TScoreValue> inline void setScoreLimit(Pattern<TNeedle, AbndmAlgo > & me, TScoreValue _limit);             // "projects/library/seqan/find/find_abndm.h"(564)
 822
 823 //____________________________________________________________________________
 824 // setScoringScheme
 825
 826 template <typename TNeedle, typename TScore, typename TScore2> inline void setScoringScheme(Pattern<TNeedle, DPSearch<TScore> > & me, TScore2 & score);         // "projects/library/seqan/find/find_score.h"(215)
 827 template <typename TNeedle, typename TScore, typename TScore2> inline void setScoringScheme(Pattern<TNeedle, DPSearch<TScore> > & me, TScore2 const & score);           // "projects/library/seqan/find/find_score.h"(224)
 828
 829 //____________________________________________________________________________
 830 // valid
 831
 832 template <typename TNeedle> inline bool valid(Pattern <TNeedle,WildShiftAnd> & me);             // "projects/library/seqan/find/find_wild_shiftand.h"(531)
 833 template <typename TNeedle> inline bool valid(Pattern <TNeedle,WildShiftAnd> const & me);               // "projects/library/seqan/find/find_wild_shiftand.h"(539)
 834
 835 } //namespace SEQAN_NAMESPACE_MAIN
 836
 837 #endif
 838