1 /*==========================================================================
2 SeqAn - The Library for Sequence Analysis
4 ============================================================================
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.
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.
17 ==========================================================================*/
19 #ifndef SEQAN_HEADER_FIND_GENERATED_FORWARDS_H
20 #define SEQAN_HEADER_FIND_GENERATED_FORWARDS_H
22 //////////////////////////////////////////////////////////////////////////////
23 // NOTE: This file is automatically generated by build_forwards.py
24 // Do not edit this file manually!
25 //////////////////////////////////////////////////////////////////////////////
28 //////////////////////////////////////////////////////////////////////////////
30 //////////////////////////////////////////////////////////////////////////////
32 namespace SEQAN_NAMESPACE_MAIN {
34 //____________________________________________________________________________
37 struct AbndmAlgo; // "projects/library/seqan/find/find_abndm.h"(76)
39 //____________________________________________________________________________
42 struct AlignTextBanded; // "projects/library/seqan/find/find_myers_ukkonen.h"(46)
44 //____________________________________________________________________________
47 struct AlignTextGlobal; // "projects/library/seqan/find/find_myers_ukkonen.h"(45)
49 //____________________________________________________________________________
52 struct AlignTextLocal; // "projects/library/seqan/find/find_myers_ukkonen.h"(44)
54 //____________________________________________________________________________
57 template <typename TScore> struct DPSearch; // "projects/library/seqan/find/find_score.h"(32)
59 //____________________________________________________________________________
62 template <typename TObject > struct DefaultFinder; // "projects/library/seqan/find/find_base.h"(41)
64 //____________________________________________________________________________
67 class DefaultHash; // "projects/library/seqan/find/find_wumanber.h"(63)
69 //____________________________________________________________________________
72 template <typename TObject > struct DefaultPattern; // "projects/library/seqan/find/find_base.h"(54)
74 //____________________________________________________________________________
77 template <typename TFormat, typename TFile, typename TSpec> struct FileReader; // "projects/library/seqan/find/find_horspool.h"(308)
79 //____________________________________________________________________________
82 template <typename THaystack, typename TSpec > class Finder; // "projects/library/seqan/find/find_base.h"(343)
84 //____________________________________________________________________________
87 template <typename TFinder> struct Haystack; // "projects/library/seqan/find/find_base.h"(69)
89 //____________________________________________________________________________
92 struct Hierarchical; // "projects/library/seqan/find/find_pex.h"(30)
94 //____________________________________________________________________________
97 template <typename TObject, typename TSpec > class Index; // "projects/library/seqan/find/find_swift.h"(34)
99 //____________________________________________________________________________
102 template <typename TPattern> struct Needle; // "projects/library/seqan/find/find_base.h"(84)
104 //____________________________________________________________________________
107 struct NonHierarchical; // "projects/library/seqan/find/find_pex.h"(31)
109 //____________________________________________________________________________
112 template <typename TNeedle, typename TSpec > class Pattern; // "projects/library/seqan/find/find_base.h"(114)
114 //____________________________________________________________________________
117 template <typename TVerification, typename TMultiFinder > struct Pex; // "projects/library/seqan/find/find_pex.h"(34)
119 //____________________________________________________________________________
122 template <typename T> struct PexMultiFinder; // "projects/library/seqan/find/find_pex.h"(53)
124 //____________________________________________________________________________
127 //template <typename TInput, typename TSpec > struct Pipe; // "projects/library/seqan/find/find_swift.h"(179)
129 //____________________________________________________________________________
132 template <typename TSpec > struct Swift; // "projects/library/seqan/find/find_swift.h"(44)
134 //____________________________________________________________________________
137 struct SwiftParameters; // "projects/library/seqan/find/find_swift.h"(65)
139 //____________________________________________________________________________
142 template <typename THash > class WuManber; // "projects/library/seqan/find/find_wumanber.h"(238)
144 //____________________________________________________________________________
147 struct _AhoCorasick; // "projects/library/seqan/find/find_ahocorasick.h"(46)
149 //____________________________________________________________________________
152 struct _BndmAlgo; // "projects/library/seqan/find/find_bndm.h"(44)
154 //____________________________________________________________________________
157 struct _BomAlgo; // "projects/library/seqan/find/find_bom.h"(44)
159 //____________________________________________________________________________
162 struct _Horspool; // "projects/library/seqan/find/find_horspool.h"(43)
164 //____________________________________________________________________________
165 // _MultipatternFinder
167 struct _MultipatternFinder; // "projects/library/seqan/find/find_multi.h"(29)
169 //____________________________________________________________________________
172 struct _MultipleShiftAnd; // "projects/library/seqan/find/find_multiple_shiftand.h"(44)
174 //____________________________________________________________________________
177 template <typename TSpec> struct _MyersUkkonen; // "projects/library/seqan/find/find_myers_ukkonen.h"(49)
179 //____________________________________________________________________________
182 template <typename T> struct _MyersUkkonenHP0; // "projects/library/seqan/find/find_myers_ukkonen.h"(62)
184 //____________________________________________________________________________
187 template <typename TPosition,typename TScore,typename TVerifier,typename TNeedle> struct _PexRange; // "projects/library/seqan/find/find_pex.h"(64)
189 //____________________________________________________________________________
192 struct _Quasar; // "projects/library/seqan/find/find_quasar.h"(33)
194 //____________________________________________________________________________
197 struct _SetHorspool; // "projects/library/seqan/find/find_set_horspool.h"(44)
199 //____________________________________________________________________________
202 struct _ShiftAnd; // "projects/library/seqan/find/find_shiftand.h"(44)
204 //____________________________________________________________________________
207 struct _ShiftOr; // "projects/library/seqan/find/find_shiftor.h"(44)
209 //____________________________________________________________________________
212 template <typename TSpec, typename TSize, typename TShortSize > struct _SwiftBucket; // "projects/library/seqan/find/find_swift.h"(79)
214 //____________________________________________________________________________
215 // _SwiftBucketParams
217 template <typename TSpec, typename TSize, typename TShortSize > struct _SwiftBucketParams; // "projects/library/seqan/find/find_swift.h"(98)
219 //____________________________________________________________________________
222 template <typename THstkPos> struct _SwiftHit; // "projects/library/seqan/find/find_swift.h"(113)
224 //____________________________________________________________________________
227 struct _SwiftLocal; // "projects/library/seqan/find/find_swift.h"(36)
229 //____________________________________________________________________________
232 struct _SwiftSemiGlobal; // "projects/library/seqan/find/find_swift.h"(39)
234 //____________________________________________________________________________
237 struct _WildShiftAnd; // "projects/library/seqan/find/find_wild_shiftand.h"(31)
239 } //namespace SEQAN_NAMESPACE_MAIN
242 //////////////////////////////////////////////////////////////////////////////
244 //////////////////////////////////////////////////////////////////////////////
246 namespace SEQAN_NAMESPACE_MAIN {
248 //____________________________________________________________________________
251 typedef Tag<_AhoCorasick> AhoCorasick; // "projects/library/seqan/find/find_ahocorasick.h"(47)
253 //____________________________________________________________________________
256 typedef Tag<_BndmAlgo> BndmAlgo; // "projects/library/seqan/find/find_bndm.h"(45)
258 //____________________________________________________________________________
261 typedef Tag<_BomAlgo> BomAlgo; // "projects/library/seqan/find/find_bom.h"(45)
263 //____________________________________________________________________________
266 typedef Tag<_Horspool> Horspool; // "projects/library/seqan/find/find_horspool.h"(44)
268 //____________________________________________________________________________
269 // MultipatternFinder
271 typedef Tag<_MultipatternFinder> MultipatternFinder; // "projects/library/seqan/find/find_multi.h"(30)
273 //____________________________________________________________________________
276 typedef Tag<_MultipleShiftAnd> MultipleShiftAnd; // "projects/library/seqan/find/find_multiple_shiftand.h"(45)
278 //____________________________________________________________________________
281 typedef Tag<_MyersUkkonen<AlignTextLocal> > MyersUkkonen; // "projects/library/seqan/find/find_myers_ukkonen.h"(51)
283 //____________________________________________________________________________
284 // MyersUkkonenBanded
286 typedef Tag<_MyersUkkonen<AlignTextBanded> > MyersUkkonenBanded; // "projects/library/seqan/find/find_myers_ukkonen.h"(53)
288 //____________________________________________________________________________
289 // MyersUkkonenGlobal
291 typedef Tag<_MyersUkkonen<AlignTextGlobal> > MyersUkkonenGlobal; // "projects/library/seqan/find/find_myers_ukkonen.h"(52)
293 //____________________________________________________________________________
296 typedef Pex<Hierarchical,AhoCorasick> PexHierarchical; // "projects/library/seqan/find/find_pex.h"(36)
298 //____________________________________________________________________________
299 // PexNonHierarchical
301 typedef Pex<NonHierarchical,AhoCorasick> PexNonHierarchical; // "projects/library/seqan/find/find_pex.h"(37)
303 //____________________________________________________________________________
306 typedef Tag<_Quasar> Quasar; // "projects/library/seqan/find/find_quasar.h"(34)
308 //____________________________________________________________________________
311 typedef Tag<_SetHorspool> SetHorspool; // "projects/library/seqan/find/find_set_horspool.h"(45)
313 //____________________________________________________________________________
316 typedef Tag<_ShiftAnd> ShiftAnd; // "projects/library/seqan/find/find_shiftand.h"(45)
318 //____________________________________________________________________________
321 typedef Tag<_ShiftOr> ShiftOr; // "projects/library/seqan/find/find_shiftor.h"(45)
323 //____________________________________________________________________________
326 typedef Tag<_SwiftLocal> SwiftLocal; // "projects/library/seqan/find/find_swift.h"(37)
328 //____________________________________________________________________________
331 typedef Tag<_SwiftSemiGlobal> SwiftSemiGlobal; // "projects/library/seqan/find/find_swift.h"(40)
333 //____________________________________________________________________________
336 typedef Tag<_WildShiftAnd> WildShiftAnd; // "projects/library/seqan/find/find_wild_shiftand.h"(32)
338 } //namespace SEQAN_NAMESPACE_MAIN
341 //////////////////////////////////////////////////////////////////////////////
343 //////////////////////////////////////////////////////////////////////////////
345 namespace SEQAN_NAMESPACE_MAIN {
347 //____________________________________________________________________________
350 template <typename TNeedle> inline void _createAcTrie(Pattern<TNeedle, AhoCorasick> & me); // "projects/library/seqan/find/find_ahocorasick.h"(120)
352 //____________________________________________________________________________
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)
357 //____________________________________________________________________________
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)
363 //____________________________________________________________________________
364 // _findAbndm_LargeNeedle
366 template <typename TFinder, typename TNeedle> inline bool _findAbndm_LargeNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo> & me); // "projects/library/seqan/find/find_abndm.h"(371)
368 //____________________________________________________________________________
369 // _findAbndm_SmallNeedle
371 template <typename TFinder, typename TNeedle> inline bool _findAbndm_SmallNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo> & me); // "projects/library/seqan/find/find_abndm.h"(237)
373 //____________________________________________________________________________
374 // _findBndm_LargeNeedle
376 template <typename TFinder, typename TNeedle> inline bool _findBndm_LargeNeedle(TFinder & finder, Pattern<TNeedle, BndmAlgo> & me); // "projects/library/seqan/find/find_bndm.h"(184)
378 //____________________________________________________________________________
379 // _findBndm_SmallNeedle
381 template <typename TFinder, typename TNeedle> inline bool _findBndm_SmallNeedle(TFinder & finder, Pattern<TNeedle, BndmAlgo> & me); // "projects/library/seqan/find/find_bndm.h"(160)
383 //____________________________________________________________________________
384 // _findMyersLargePatterns
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)
389 //____________________________________________________________________________
390 // _findMyersSmallPatterns
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)
395 //____________________________________________________________________________
396 // _findShiftAnd_LargeNeedle
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)
402 //____________________________________________________________________________
403 // _findShiftAnd_SmallNeedle
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)
409 //____________________________________________________________________________
410 // _findShiftOr_LargeNeedle
412 template <typename TFinder, typename TNeedle> bool _findShiftOr_LargeNeedle(TFinder & finder, Pattern<TNeedle, ShiftOr> & me); // "projects/library/seqan/find/find_shiftor.h"(212)
414 //____________________________________________________________________________
415 // _findShiftOr_SmallNeedle
417 template <typename TFinder, typename TNeedle> bool _findShiftOr_SmallNeedle(TFinder & finder, Pattern<TNeedle, ShiftOr> & me); // "projects/library/seqan/find/find_shiftor.h"(178)
419 //____________________________________________________________________________
420 // _find_score_simple_proportional
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)
424 //____________________________________________________________________________
425 // _finderSetNonEmpty
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)
430 //____________________________________________________________________________
431 // _getCharacterClass
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)
435 //____________________________________________________________________________
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)
441 //____________________________________________________________________________
444 inline bool _isInt(String<char> const & number); // "projects/library/seqan/find/find_wild_shiftand.h"(99)
446 //____________________________________________________________________________
449 template <typename TNeedle> unsigned _length_wo_wild(TNeedle const & needle); // "projects/library/seqan/find/find_wild_shiftand.h"(189)
451 //____________________________________________________________________________
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)
456 //____________________________________________________________________________
457 // _myersCoreSmallDiag
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)
461 //____________________________________________________________________________
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)
467 //____________________________________________________________________________
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)
488 //____________________________________________________________________________
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)
494 //____________________________________________________________________________
497 template <typename TNeedle> void _printR(Pattern<TNeedle, AbndmAlgo> & me); // "projects/library/seqan/find/find_abndm.h"(127)
499 //____________________________________________________________________________
500 // _printSwiftBuckets
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)
504 //____________________________________________________________________________
507 template <typename TParams> inline void _printSwiftParams(TParams &bucketParams); // "projects/library/seqan/find/find_swift.h"(276)
509 //____________________________________________________________________________
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)
514 //____________________________________________________________________________
515 // _swiftBucketParams
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)
519 //____________________________________________________________________________
520 // _swiftMultiFlushBuckets
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)
524 //____________________________________________________________________________
525 // _swiftMultiProcessQGram
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)
529 //____________________________________________________________________________
532 template <typename TNeedle2> bool _validate(TNeedle2 const & needle); // "projects/library/seqan/find/find_wild_shiftand.h"(111)
534 //____________________________________________________________________________
537 template <typename THaystack, typename TSpec> inline bool atBegin(Finder<THaystack, TSpec> & me); // "projects/library/seqan/find/find_base.h"(513)
539 //____________________________________________________________________________
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)
545 //____________________________________________________________________________
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)
553 //____________________________________________________________________________
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)
559 //____________________________________________________________________________
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)
565 //____________________________________________________________________________
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)
571 //____________________________________________________________________________
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)
579 //____________________________________________________________________________
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)
603 //____________________________________________________________________________
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)
609 //____________________________________________________________________________
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)
617 //____________________________________________________________________________
620 template <typename THaystack, typename TSpec> inline void goBegin(Finder<THaystack, TSpec> & me); // "projects/library/seqan/find/find_base.h"(531)
622 //____________________________________________________________________________
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)
628 //____________________________________________________________________________
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)
634 //____________________________________________________________________________
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)
668 //____________________________________________________________________________
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)
674 //____________________________________________________________________________
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)
682 //____________________________________________________________________________
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)
687 //____________________________________________________________________________
690 template <typename THaystack, typename TSpec> inline Finder<THaystack, TSpec> & operator++(Finder<THaystack, TSpec> & me); // "projects/library/seqan/find/find_base.h"(601)
692 //____________________________________________________________________________
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)
697 //____________________________________________________________________________
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)
703 //____________________________________________________________________________
706 template <typename THaystack, typename TSpec> inline Finder<THaystack, TSpec> & operator--(Finder<THaystack, TSpec> & me); // "projects/library/seqan/find/find_base.h"(592)
708 //____________________________________________________________________________
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)
713 //____________________________________________________________________________
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)
724 //____________________________________________________________________________
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)
731 //____________________________________________________________________________
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)
739 //____________________________________________________________________________
742 template <typename TNeedle, typename TScore> inline TScore const & scoringScheme(Pattern<TNeedle, DPSearch<TScore> > & me); // "projects/library/seqan/find/find_score.h"(193)
744 //____________________________________________________________________________
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)
750 //____________________________________________________________________________
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)
755 //____________________________________________________________________________
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)
760 //____________________________________________________________________________
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)
765 //____________________________________________________________________________
768 template <typename THaystack, typename TSpec > inline void setHaystack(Finder<THaystack, TSpec> &obj, THaystack const &hstk); // "projects/library/seqan/find/find_base.h"(686)
770 //____________________________________________________________________________
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)
805 //____________________________________________________________________________
808 template <typename TNeedle, typename TSpec > inline void setNeedle(Pattern<TNeedle, TSpec> &obj, TNeedle const &ndl); // "projects/library/seqan/find/find_base.h"(293)
810 //____________________________________________________________________________
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)
815 //____________________________________________________________________________
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)
823 //____________________________________________________________________________
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)
829 //____________________________________________________________________________
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)
835 } //namespace SEQAN_NAMESPACE_MAIN