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_INDEX_GENERATED_FORWARDS_H
20 #define SEQAN_HEADER_INDEX_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 {
35 //____________________________________________________________________________
36 // substringHelperPizzaChili
38 template <typename TValue, typename TSpec, typename TPos> struct substringHelperPizzaChili; // "projects/library/seqan/index/index_pizzachili_string.h"(520)
41 } //namespace SEQAN_NAMESPACE_MAIN
42 //////////////////////////////////////////////////////////////////////////////
44 namespace SEQAN_NAMESPACE_MAIN {
46 //____________________________________________________________________________
49 template <typename TSource, typename TSpec> class Align; // "projects/library/seqan/index/index_esa_base.h"(189)
51 //____________________________________________________________________________
54 struct ArrayGaps; // "projects/library/seqan/index/index_esa_base.h"(186)
56 //____________________________________________________________________________
59 template <unsigned BlockSize > struct BTree; // "projects/library/seqan/index/index_esa_find.h"(70)
61 //____________________________________________________________________________
64 struct BWT; // "projects/library/seqan/index/index_base.h"(46)
65 struct BWT; // "projects/library/seqan/index/index_bwt.h"(30)
67 //____________________________________________________________________________
70 template <typename TSpec > struct BottomUp; // "projects/library/seqan/index/index_esa_base.h"(125)
72 //____________________________________________________________________________
75 struct ChildTab; // "projects/library/seqan/index/index_childtab.h"(30)
76 struct ChildTab; // "projects/library/seqan/index/index_base.h"(45)
78 //____________________________________________________________________________
79 // CompareSkewDCStream
81 template <typename TValue> struct CompareSkewDCStream; // "projects/library/seqan/index/pipe_merger7.h"(95)
83 //____________________________________________________________________________
86 struct DeepShallow; // "projects/library/seqan/index/index_shawarma.h"(42)
88 //____________________________________________________________________________
89 // DefaultIndexCreator
91 template <typename TIndex, typename TFibre > struct DefaultIndexCreator; // "projects/library/seqan/index/index_base.h"(177)
93 //____________________________________________________________________________
96 template <typename TObject > struct DefaultIndexSpec; // "projects/library/seqan/index/index_base.h"(63)
98 //____________________________________________________________________________
99 // DefaultIndexStringSpec
101 template <typename TIndex > struct DefaultIndexStringSpec; // "projects/library/seqan/index/index_base.h"(78)
103 //____________________________________________________________________________
106 struct DivSufSort; // "projects/library/seqan/index/index_shawarma.h"(41)
108 //____________________________________________________________________________
111 struct EmptyEdges; // "projects/library/seqan/index/index_esa_base.h"(102)
113 //____________________________________________________________________________
116 struct Extender3; // "projects/library/seqan/index/pump_extender3.h"(30)
118 //____________________________________________________________________________
121 template <typename TCompression > struct Extender7; // "projects/library/seqan/index/pump_extender7.h"(33)
123 //____________________________________________________________________________
126 template <typename TPair, typename TCompression > struct Extender7Multi; // "projects/library/seqan/index/pump_extender7.h"(228)
128 //____________________________________________________________________________
131 template <typename TIndex, typename TSpec > struct Fibre; // "projects/library/seqan/index/index_base.h"(141)
133 //____________________________________________________________________________
136 struct FibreLess; // "projects/library/seqan/index/index_base.h"(158)
138 //____________________________________________________________________________
141 struct FibreRecord; // "projects/library/seqan/index/index_base.h"(150)
143 //____________________________________________________________________________
146 template <typename TSpec> struct FixedGappedShape; // "projects/library/seqan/index/shape_base.h"(32)
148 //____________________________________________________________________________
151 template <unsigned q> struct FixedShape; // "projects/library/seqan/index/shape_base.h"(28)
153 //____________________________________________________________________________
156 template <typename InType, typename TLimitsString, typename Result > struct FunctorGlobalize; // "projects/library/seqan/index/index_base.h"(386)
158 //____________________________________________________________________________
159 // GetVSTreeIteratorTraits
161 template <typename TIterator> struct GetVSTreeIteratorTraits; // "projects/library/seqan/index/index_esa_base.h"(148)
163 //____________________________________________________________________________
166 template <int P00 , int P01 , int P02 , int P03 , int P04 , int P05 , int P06 , int P07 , int P08 , int P09 , int P10 , int P11 , int P12 , int P13 , int P14 , int P15 , int P16 , int P17 , int P18 , int P19 > struct HardwiredShape; // "projects/library/seqan/index/shape_gapped.h"(50)
168 //____________________________________________________________________________
171 struct HideEmptyEdges; // "projects/library/seqan/index/index_esa_base.h"(101)
173 //____________________________________________________________________________
176 template <typename TObject, typename TSpec > class Index; // "projects/library/seqan/index/index_base.h"(114)
178 //____________________________________________________________________________
181 template <typename TSpec > struct Index_ESA; // "projects/library/seqan/index/index_base.h"(49)
183 //____________________________________________________________________________
186 template <typename TShapeSpec, typename TSpec > struct Index_QGram; // "projects/library/seqan/index/index_qgram.h"(100)
188 //____________________________________________________________________________
191 template <typename TSpec > struct Index_Wotd; // "projects/library/seqan/index/index_wotd.h"(56)
193 //____________________________________________________________________________
194 // InvalidPizzaChiliSpec
196 struct InvalidPizzaChiliSpec; // "projects/library/seqan/index/pizzachili_api.h"(37)
198 //____________________________________________________________________________
201 struct Kasai; // "projects/library/seqan/index/index_base.h"(41)
202 struct Kasai; // "projects/library/seqan/index/index_lcp.h"(30)
204 //____________________________________________________________________________
207 struct KasaiOriginal; // "projects/library/seqan/index/index_base.h"(42)
208 struct KasaiOriginal; // "projects/library/seqan/index/index_lcp.h"(31)
210 //____________________________________________________________________________
213 struct LarssonSadakane; // "projects/library/seqan/index/index_sa_lss.h"(336)
214 struct LarssonSadakane; // "projects/library/seqan/index/index_base.h"(35)
216 //____________________________________________________________________________
219 struct LcpConfig; // "projects/library/seqan/index/pump_lcp_core.h"(31)
221 //____________________________________________________________________________
224 struct LeftCompleteTree; // "projects/library/seqan/index/index_esa_find.h"(67)
226 //____________________________________________________________________________
229 struct MSufSort; // "projects/library/seqan/index/index_shawarma.h"(40)
231 //____________________________________________________________________________
234 struct MUMs; // "projects/library/seqan/index/index_esa_base.h"(129)
236 //____________________________________________________________________________
239 struct ManberMyers; // "projects/library/seqan/index/index_sa_mm.h"(27)
240 struct ManberMyers; // "projects/library/seqan/index/index_base.h"(36)
242 //____________________________________________________________________________
245 template <typename TSTree> struct MaxRepeat; // "projects/library/seqan/index/index_esa_algs.h"(602)
247 //____________________________________________________________________________
248 // MaxRepeatOccurrences
250 struct MaxRepeatOccurrences; // "projects/library/seqan/index/index_esa_base.h"(132)
252 //____________________________________________________________________________
255 struct Merger3; // "projects/library/seqan/index/pipe_merger3.h"(30)
257 //____________________________________________________________________________
260 struct Merger7; // "projects/library/seqan/index/pipe_merger7.h"(178)
262 //____________________________________________________________________________
265 template <typename TLimitsString> struct Merger7Multi; // "projects/library/seqan/index/pipe_merger7.h"(187)
267 //____________________________________________________________________________
270 template <typename TSTree> struct MultiMEM; // "projects/library/seqan/index/index_esa_algs_multi.h"(385)
272 //____________________________________________________________________________
273 // MultiMEMOccurences
275 struct MultiMEMOccurences; // "projects/library/seqan/index/index_esa_base.h"(134)
277 //____________________________________________________________________________
280 template <typename TSpec > struct ParentLinks; // "projects/library/seqan/index/index_esa_base.h"(121)
282 //____________________________________________________________________________
285 template <typename TSpec> struct PizzaChili; // "projects/library/seqan/index/index_pizzachili_string.h"(47)
287 //____________________________________________________________________________
288 // PizzaChiliCodeProvider
290 template <typename TSpec> struct PizzaChiliCodeProvider; // "projects/library/seqan/index/pizzachili_api.h"(40)
292 //____________________________________________________________________________
295 struct Postorder; // "projects/library/seqan/index/index_esa_base.h"(96)
297 //____________________________________________________________________________
298 // PostorderEmptyEdges
300 struct PostorderEmptyEdges; // "projects/library/seqan/index/index_esa_base.h"(98)
302 //____________________________________________________________________________
305 struct Preorder; // "projects/library/seqan/index/index_esa_base.h"(95)
307 //____________________________________________________________________________
308 // PreorderEmptyEdges
310 struct PreorderEmptyEdges; // "projects/library/seqan/index/index_esa_base.h"(97)
312 //____________________________________________________________________________
315 struct QGram_Alg; // "projects/library/seqan/index/index_base.h"(38)
317 //____________________________________________________________________________
320 struct QSufSort; // "projects/library/seqan/index/index_shawarma.h"(43)
322 //____________________________________________________________________________
325 template <typename TPos, typename TPeriod> struct Repeat; // "projects/library/seqan/index/repeat_base.h"(28)
327 //____________________________________________________________________________
328 // RepeatFinderParams
330 template <typename TSize> struct RepeatFinderParams; // "projects/library/seqan/index/repeat_base.h"(47)
332 //____________________________________________________________________________
335 struct SAQSort; // "projects/library/seqan/index/index_base.h"(37)
336 struct SAQSort; // "projects/library/seqan/index/index_sa_qsort.h"(27)
338 //____________________________________________________________________________
341 template <typename TObject> struct SAValue; // "projects/library/seqan/index/index_base.h"(288)
343 //____________________________________________________________________________
344 // SearchTreeIterator
346 template <typename TString, typename TSpec > class SearchTreeIterator; // "projects/library/seqan/index/index_esa_find.h"(73)
348 //____________________________________________________________________________
351 template <typename TValue , typename TSpec > class Shape; // "projects/library/seqan/index/shape_base.h"(54)
353 //____________________________________________________________________________
356 template <typename TSpec> struct Shawarma; // "projects/library/seqan/index/index_shawarma.h"(38)
358 //____________________________________________________________________________
361 struct Skew3; // "projects/library/seqan/index/index_base.h"(33)
362 struct Skew3; // "projects/library/seqan/index/index_skew3.h"(30)
364 //____________________________________________________________________________
367 struct Skew7; // "projects/library/seqan/index/index_base.h"(34)
368 struct Skew7; // "projects/library/seqan/index/index_skew7.h"(30)
370 //____________________________________________________________________________
373 template <typename TValue> struct SkewDCStream; // "projects/library/seqan/index/pipe_merger7.h"(71)
375 //____________________________________________________________________________
378 struct SortedList; // "projects/library/seqan/index/index_esa_find.h"(66)
380 //____________________________________________________________________________
383 struct SuperMaxRepeats; // "projects/library/seqan/index/index_esa_base.h"(127)
385 //____________________________________________________________________________
386 // SuperMaxRepeatsFast
388 struct SuperMaxRepeatsFast; // "projects/library/seqan/index/index_esa_base.h"(128)
390 //____________________________________________________________________________
393 struct TRepeatFinder; // "projects/library/seqan/index/repeat_base.h"(53)
395 //____________________________________________________________________________
398 template <typename TSpec > struct TopDown; // "projects/library/seqan/index/index_esa_base.h"(117)
400 //____________________________________________________________________________
403 template <typename TSpec > struct VSTree; // "projects/library/seqan/index/index_esa_base.h"(113)
405 //____________________________________________________________________________
406 // VSTreeIteratorTraits
408 template <typename TDFSOrder , typename THideEmptyEdges > struct VSTreeIteratorTraits; // "projects/library/seqan/index/index_esa_base.h"(32)
410 //____________________________________________________________________________
413 template <typename TSize> struct VertexESA; // "projects/library/seqan/index/index_esa_base.h"(153)
415 //____________________________________________________________________________
418 template <typename TPredHull , typename TPred > struct WotdDFI; // "projects/library/seqan/index/index_dfi.h"(74)
420 //____________________________________________________________________________
423 struct WotdOriginal_; // "projects/library/seqan/index/index_wotd.h"(52)
425 //____________________________________________________________________________
428 template <typename TValue, typename TSpec> struct _AllocHelper; // "projects/library/seqan/index/index_pizzachili_string.h"(283)
430 //____________________________________________________________________________
433 template <typename TValue> struct _Context_LSS; // "projects/library/seqan/index/index_sa_lss.h"(40)
435 //____________________________________________________________________________
438 struct _DFIEntry; // "projects/library/seqan/index/index_dfi.h"(32)
440 //____________________________________________________________________________
443 template <bool RESULT> struct _DFIPredDefault; // "projects/library/seqan/index/index_dfi.h"(44)
445 //____________________________________________________________________________
448 struct _Fibre_BWT; // "projects/library/seqan/index/index_base.h"(245)
450 //____________________________________________________________________________
453 struct _Fibre_ChildTab; // "projects/library/seqan/index/index_base.h"(244)
455 //____________________________________________________________________________
458 struct _Fibre_Counts; // "projects/library/seqan/index/index_qgram.h"(64)
460 //____________________________________________________________________________
463 struct _Fibre_CountsDir; // "projects/library/seqan/index/index_qgram.h"(65)
465 //____________________________________________________________________________
468 struct _Fibre_Dir; // "projects/library/seqan/index/index_qgram.h"(61)
470 //____________________________________________________________________________
473 struct _Fibre_LCP; // "projects/library/seqan/index/index_base.h"(242)
475 //____________________________________________________________________________
478 struct _Fibre_LCPE; // "projects/library/seqan/index/index_base.h"(243)
480 //____________________________________________________________________________
481 // _Fibre_PizzaChili_Compressed
483 struct _Fibre_PizzaChili_Compressed; // "projects/library/seqan/index/index_pizzachili.h"(41)
485 //____________________________________________________________________________
488 struct _Fibre_RawSA; // "projects/library/seqan/index/index_base.h"(240)
490 //____________________________________________________________________________
493 struct _Fibre_RawText; // "projects/library/seqan/index/index_base.h"(238)
495 //____________________________________________________________________________
498 struct _Fibre_SA; // "projects/library/seqan/index/index_base.h"(239)
500 //____________________________________________________________________________
503 struct _Fibre_SADir; // "projects/library/seqan/index/index_qgram.h"(62)
505 //____________________________________________________________________________
508 struct _Fibre_SAE; // "projects/library/seqan/index/index_base.h"(241)
510 //____________________________________________________________________________
513 struct _Fibre_Shape; // "projects/library/seqan/index/index_qgram.h"(63)
515 //____________________________________________________________________________
518 struct _Fibre_Text; // "projects/library/seqan/index/index_base.h"(237)
520 //____________________________________________________________________________
523 struct _Finder_LCPE; // "projects/library/seqan/index/index_esa_find.h"(49)
525 //____________________________________________________________________________
528 struct _Finder_MLR; // "projects/library/seqan/index/index_esa_find.h"(48)
530 //____________________________________________________________________________
531 // _Finder_QGramLookup
533 struct _Finder_QGramLookup; // "projects/library/seqan/index/index_qgram_find.h"(30)
535 //____________________________________________________________________________
538 template <typename TValue, typename TSize> struct _FractionCompound; // "projects/library/seqan/index/index_esa_algs.h"(250)
540 //____________________________________________________________________________
543 template <typename TSize> struct _FractionHeader; // "projects/library/seqan/index/index_esa_algs.h"(239)
545 //____________________________________________________________________________
546 // _FractionMultiCompound
548 template <typename TValue, typename TSize> struct _FractionMultiCompound; // "projects/library/seqan/index/index_esa_algs_multi.h"(132)
550 //____________________________________________________________________________
551 // _HistoryStackEntry
553 template <typename TVSTreeIter > struct _HistoryStackEntry; // "projects/library/seqan/index/index_esa_stree.h"(125)
555 //____________________________________________________________________________
556 // _HistoryStackWotdModified
558 template <typename TSize> struct _HistoryStackWotdModified; // "projects/library/seqan/index/index_wotd.h"(209)
560 //____________________________________________________________________________
561 // _HistoryStackWotdOriginal
563 template <typename TSize> struct _HistoryStackWotdOriginal; // "projects/library/seqan/index/index_wotd.h"(202)
565 //____________________________________________________________________________
568 template <typename TSpec > struct _MaxRepeats; // "projects/library/seqan/index/index_esa_base.h"(106)
570 //____________________________________________________________________________
573 struct _MultiMEMs; // "projects/library/seqan/index/index_esa_base.h"(107)
575 //____________________________________________________________________________
578 struct _PizzaChiliFinder; // "projects/library/seqan/index/index_pizzachili_find.h"(26)
580 //____________________________________________________________________________
583 struct _PizzaChili_AF; // "projects/library/seqan/index/pizzachili_api.h"(67)
585 //____________________________________________________________________________
588 struct _PizzaChili_CCSA; // "projects/library/seqan/index/pizzachili_api.h"(70)
590 //____________________________________________________________________________
593 struct _PizzaChili_FM; // "projects/library/seqan/index/pizzachili_api.h"(73)
595 //____________________________________________________________________________
598 struct _PizzaChili_LZ; // "projects/library/seqan/index/pizzachili_api.h"(76)
600 //____________________________________________________________________________
603 struct _PizzaChili_RLFM; // "projects/library/seqan/index/pizzachili_api.h"(82)
605 //____________________________________________________________________________
608 struct _PizzaChili_RSA; // "projects/library/seqan/index/pizzachili_api.h"(79)
610 //____________________________________________________________________________
613 struct _PizzaChili_SA; // "projects/library/seqan/index/pizzachili_api.h"(85)
615 //____________________________________________________________________________
618 struct _PizzaChili_SADA; // "projects/library/seqan/index/pizzachili_api.h"(88)
620 //____________________________________________________________________________
623 struct _PizzaChili_SSA; // "projects/library/seqan/index/pizzachili_api.h"(91)
625 //____________________________________________________________________________
628 struct _PizzaChili_Test; // "projects/library/seqan/index/pizzachili_api.h"(94)
630 //____________________________________________________________________________
633 struct _Postorder; // "projects/library/seqan/index/index_esa_base.h"(29)
635 //____________________________________________________________________________
638 struct _Preorder; // "projects/library/seqan/index/index_esa_base.h"(28)
640 //____________________________________________________________________________
643 template <typename TSAValue, typename TText > struct _QGramLess; // "projects/library/seqan/index/index_qgram.h"(347)
645 //____________________________________________________________________________
648 template <typename TSAValue, typename TText > struct _QGramLessNoCheck; // "projects/library/seqan/index/index_qgram.h"(506)
650 //____________________________________________________________________________
651 // _QGramLessNoCheckOffset
653 template <typename TSAValue, typename TText > struct _QGramLessNoCheckOffset; // "projects/library/seqan/index/index_qgram.h"(588)
655 //____________________________________________________________________________
658 template <typename TSAValue, typename TText > struct _QGramLessOffset; // "projects/library/seqan/index/index_qgram.h"(442)
660 //____________________________________________________________________________
663 template <typename TPos> struct _RepeatLess; // "projects/library/seqan/index/repeat_base.h"(82)
665 //____________________________________________________________________________
668 template <typename TOccValue> struct _SAValueLess; // "projects/library/seqan/index/index_shims.h"(449)
670 //____________________________________________________________________________
673 template <int I, typename T > struct _SkewNIndx; // "projects/library/seqan/index/pipe_merger7.h"(34)
675 //____________________________________________________________________________
678 template <int I, typename T > struct _SkewShift; // "projects/library/seqan/index/pipe_merger7.h"(31)
680 //____________________________________________________________________________
683 template <typename TSAValue, typename TText > struct _SuffixLess; // "projects/library/seqan/index/index_sa_qsort.h"(33)
685 //____________________________________________________________________________
688 template <typename TSAValue, typename TText > struct _SuffixLessOffset; // "projects/library/seqan/index/index_sa_qsort.h"(71)
690 //____________________________________________________________________________
691 // _VertexWotdModified
693 template <typename TSize> struct _VertexWotdModified; // "projects/library/seqan/index/index_wotd.h"(163)
695 //____________________________________________________________________________
696 // _VertexWotdOriginal
698 template <typename TSize> struct _VertexWotdOriginal; // "projects/library/seqan/index/index_wotd.h"(148)
700 //____________________________________________________________________________
703 template <typename InType, typename Result > struct _qgram_comp; // "projects/library/seqan/index/index_qgram.h"(1227)
705 //____________________________________________________________________________
708 template <typename TValue, typename TResult > struct _qgram_hash; // "projects/library/seqan/index/index_qgram.h"(1262)
710 //____________________________________________________________________________
713 template <typename InType, typename TLimitsString, typename Result > struct filter_globalizer; // "projects/library/seqan/index/index_bwt.h"(130)
715 //____________________________________________________________________________
718 template <typename InType, typename Result > struct map_inverse; // "projects/library/seqan/index/index_lcp.h"(45)
720 //____________________________________________________________________________
723 template <typename InType, typename TLimitsString, typename Result > struct map_inverse_multi; // "projects/library/seqan/index/index_lcp.h"(148)
725 //____________________________________________________________________________
728 template <typename InType, typename Result > struct skew3_extend_comp; // "projects/library/seqan/index/index_skew3.h"(107)
730 //____________________________________________________________________________
733 template <typename InType, typename Result > struct skew3_ncomp; // "projects/library/seqan/index/index_skew3.h"(49)
735 //____________________________________________________________________________
736 // skew3_nmap_extended
738 template <typename InType, typename Result > struct skew3_nmap_extended; // "projects/library/seqan/index/index_skew3.h"(101)
740 //____________________________________________________________________________
743 template <typename InType, typename Result > struct skew3_nmap_linear; // "projects/library/seqan/index/index_skew3.h"(72)
745 //____________________________________________________________________________
748 template <typename InType, typename Result > struct skew3_nmap_sliced; // "projects/library/seqan/index/index_skew3.h"(80)
750 //____________________________________________________________________________
751 // skew3_unslicer_func
753 template <typename InType, typename Result > struct skew3_unslicer_func; // "projects/library/seqan/index/index_skew3.h"(89)
755 //____________________________________________________________________________
758 template <typename InType, const int EXT_LENGTH, typename Result > struct skew7_extend_comp; // "projects/library/seqan/index/index_skew7.h"(137)
760 //____________________________________________________________________________
761 // skew7_global_sliced_multi
763 template <typename InType, typename TLimitsString, typename TResultSize , typename Result > struct skew7_global_sliced_multi; // "projects/library/seqan/index/index_skew7_multi.h"(109)
765 //____________________________________________________________________________
768 template <typename InType, typename Result > struct skew7_ncomp; // "projects/library/seqan/index/index_skew7.h"(49)
770 //____________________________________________________________________________
773 template <typename InType, typename Result > struct skew7_ncomp_multi; // "projects/library/seqan/index/index_skew7_multi.h"(42)
775 //____________________________________________________________________________
776 // skew7_nmap_extended
778 template <typename InType, typename Result > struct skew7_nmap_extended; // "projects/library/seqan/index/index_skew7.h"(131)
780 //____________________________________________________________________________
783 template <typename InType, typename Result > struct skew7_nmap_linear; // "projects/library/seqan/index/index_skew7.h"(91)
785 //____________________________________________________________________________
788 template <typename InType, typename Result > struct skew7_nmap_sliced; // "projects/library/seqan/index/index_skew7.h"(99)
790 //____________________________________________________________________________
791 // skew7_unslicer_func
793 template <typename InType, typename Result > struct skew7_unslicer_func; // "projects/library/seqan/index/index_skew7.h"(115)
795 } //namespace SEQAN_NAMESPACE_MAIN
798 //////////////////////////////////////////////////////////////////////////////
800 //////////////////////////////////////////////////////////////////////////////
802 namespace SEQAN_NAMESPACE_MAIN {
805 //____________________________________________________________________________
808 typedef int error_t; // "projects/library/seqan/index/pizzachili_api.h"(34)
810 //____________________________________________________________________________
813 typedef void* index_t; // "projects/library/seqan/index/pizzachili_api.h"(33)
815 //____________________________________________________________________________
818 typedef unsigned char uchar_t; // "projects/library/seqan/index/pizzachili_api.h"(31)
820 //____________________________________________________________________________
823 typedef unsigned long ulong_t; // "projects/library/seqan/index/pizzachili_api.h"(32)
826 } //namespace SEQAN_NAMESPACE_MAIN
827 //////////////////////////////////////////////////////////////////////////////
829 namespace SEQAN_NAMESPACE_MAIN {
831 //____________________________________________________________________________
834 typedef Fibre_BWT ESA_BWT; // "projects/library/seqan/index/index_esa_base.h"(239)
836 //____________________________________________________________________________
839 typedef Fibre_ChildTab ESA_ChildTab; // "projects/library/seqan/index/index_esa_base.h"(238)
841 //____________________________________________________________________________
844 typedef Tag<_Finder_LCPE> const ESA_FIND_LCPE; // "projects/library/seqan/index/index_esa_find.h"(52)
846 //____________________________________________________________________________
849 typedef Tag<_Finder_MLR> const ESA_FIND_MLR; // "projects/library/seqan/index/index_esa_find.h"(51)
851 //____________________________________________________________________________
854 typedef Fibre_LCP ESA_LCP; // "projects/library/seqan/index/index_esa_base.h"(236)
856 //____________________________________________________________________________
859 typedef Fibre_LCPE ESA_LCPE; // "projects/library/seqan/index/index_esa_base.h"(237)
861 //____________________________________________________________________________
864 typedef Fibre_RawSA ESA_RawSA; // "projects/library/seqan/index/index_esa_base.h"(234)
866 //____________________________________________________________________________
869 typedef Fibre_RawText ESA_RawText; // "projects/library/seqan/index/index_esa_base.h"(232)
871 //____________________________________________________________________________
874 typedef Fibre_SA ESA_SA; // "projects/library/seqan/index/index_esa_base.h"(233)
876 //____________________________________________________________________________
879 typedef Fibre_SAE ESA_SAE; // "projects/library/seqan/index/index_esa_base.h"(235)
881 //____________________________________________________________________________
884 typedef Fibre_Text ESA_Text; // "projects/library/seqan/index/index_esa_base.h"(231)
886 //____________________________________________________________________________
889 typedef Tag<_Fibre_BWT> const Fibre_BWT; // "projects/library/seqan/index/index_base.h"(255)
891 //____________________________________________________________________________
894 typedef Tag<_Fibre_ChildTab> const Fibre_ChildTab; // "projects/library/seqan/index/index_base.h"(254)
896 //____________________________________________________________________________
899 typedef Tag<_Fibre_Counts> const Fibre_Counts; // "projects/library/seqan/index/index_qgram.h"(70)
901 //____________________________________________________________________________
904 typedef Tag<_Fibre_CountsDir> const Fibre_CountsDir; // "projects/library/seqan/index/index_qgram.h"(71)
906 //____________________________________________________________________________
909 typedef Tag<_Fibre_Dir> const Fibre_Dir; // "projects/library/seqan/index/index_qgram.h"(67)
911 //____________________________________________________________________________
914 typedef Tag<_Fibre_LCP> const Fibre_LCP; // "projects/library/seqan/index/index_base.h"(252)
916 //____________________________________________________________________________
919 typedef Tag<_Fibre_LCPE> const Fibre_LCPE; // "projects/library/seqan/index/index_base.h"(253)
921 //____________________________________________________________________________
922 // Fibre_PizzaChili_Compressed
924 typedef Tag<_Fibre_PizzaChili_Compressed> const Fibre_PizzaChili_Compressed; // "projects/library/seqan/index/index_pizzachili.h"(44)
926 //____________________________________________________________________________
927 // Fibre_PizzaChili_Text
929 typedef Tag<_Fibre_Text> const Fibre_PizzaChili_Text; // "projects/library/seqan/index/index_pizzachili.h"(43)
931 //____________________________________________________________________________
934 typedef Tag<_Fibre_RawSA> const Fibre_RawSA; // "projects/library/seqan/index/index_base.h"(250)
936 //____________________________________________________________________________
939 typedef Tag<_Fibre_RawText> const Fibre_RawText; // "projects/library/seqan/index/index_base.h"(248)
941 //____________________________________________________________________________
944 typedef Tag<_Fibre_SA> const Fibre_SA; // "projects/library/seqan/index/index_base.h"(249)
946 //____________________________________________________________________________
949 typedef Tag<_Fibre_SADir> const Fibre_SADir; // "projects/library/seqan/index/index_qgram.h"(68)
951 //____________________________________________________________________________
954 typedef Tag<_Fibre_SAE> const Fibre_SAE; // "projects/library/seqan/index/index_base.h"(251)
956 //____________________________________________________________________________
959 typedef Tag<_Fibre_Shape> const Fibre_Shape; // "projects/library/seqan/index/index_qgram.h"(69)
961 //____________________________________________________________________________
964 typedef Tag<_Fibre_Text> const Fibre_Text; // "projects/library/seqan/index/index_base.h"(247)
966 //____________________________________________________________________________
969 typedef FixedGappedShape<Default> GappedShape; // "projects/library/seqan/index/shape_base.h"(33)
971 //____________________________________________________________________________
974 typedef _MaxRepeats<void> MaxRepeats; // "projects/library/seqan/index/index_esa_base.h"(131)
976 //____________________________________________________________________________
979 typedef _MaxRepeats<_MultiMEMs> MultiMEMs; // "projects/library/seqan/index/index_esa_base.h"(133)
981 //____________________________________________________________________________
984 typedef Tag<_PizzaChiliFinder> const PizzaChiliFinder; // "projects/library/seqan/index/index_pizzachili_find.h"(36)
986 //____________________________________________________________________________
989 typedef Tag<_PizzaChili_AF> const PizzaChili_AF; // "projects/library/seqan/index/pizzachili_api.h"(68)
991 //____________________________________________________________________________
994 typedef Tag<_PizzaChili_CCSA> const PizzaChili_CCSA; // "projects/library/seqan/index/pizzachili_api.h"(71)
996 //____________________________________________________________________________
997 // PizzaChili_Compressed
999 typedef Fibre_PizzaChili_Compressed PizzaChili_Compressed; // "projects/library/seqan/index/index_pizzachili.h"(47)
1001 //____________________________________________________________________________
1004 typedef Tag<_PizzaChili_FM> const PizzaChili_FM; // "projects/library/seqan/index/pizzachili_api.h"(74)
1006 //____________________________________________________________________________
1009 typedef Tag<_PizzaChili_LZ> const PizzaChili_LZ; // "projects/library/seqan/index/pizzachili_api.h"(77)
1011 //____________________________________________________________________________
1014 typedef Tag<_PizzaChili_RLFM> const PizzaChili_RLFM; // "projects/library/seqan/index/pizzachili_api.h"(83)
1016 //____________________________________________________________________________
1019 typedef Tag<_PizzaChili_RSA> const PizzaChili_RSA; // "projects/library/seqan/index/pizzachili_api.h"(80)
1021 //____________________________________________________________________________
1024 typedef Tag<_PizzaChili_SA> const PizzaChili_SA; // "projects/library/seqan/index/pizzachili_api.h"(86)
1026 //____________________________________________________________________________
1029 typedef Tag<_PizzaChili_SADA> const PizzaChili_SADA; // "projects/library/seqan/index/pizzachili_api.h"(89)
1031 //____________________________________________________________________________
1034 typedef Tag<_PizzaChili_SSA> const PizzaChili_SSA; // "projects/library/seqan/index/pizzachili_api.h"(92)
1036 //____________________________________________________________________________
1039 typedef Tag<_PizzaChili_Test> const PizzaChili_Test; // "projects/library/seqan/index/pizzachili_api.h"(95)
1041 //____________________________________________________________________________
1044 typedef Fibre_PizzaChili_Text PizzaChili_Text; // "projects/library/seqan/index/index_pizzachili.h"(46)
1046 //____________________________________________________________________________
1049 typedef Fibre_Counts QGram_Counts; // "projects/library/seqan/index/index_qgram.h"(82)
1051 //____________________________________________________________________________
1054 typedef Fibre_CountsDir QGram_CountsDir; // "projects/library/seqan/index/index_qgram.h"(83)
1056 //____________________________________________________________________________
1059 typedef Fibre_Dir QGram_Dir; // "projects/library/seqan/index/index_qgram.h"(79)
1061 //____________________________________________________________________________
1062 // QGram_FIND_Lookup
1064 typedef Tag<_Finder_QGramLookup> const QGram_FIND_Lookup; // "projects/library/seqan/index/index_qgram_find.h"(38)
1066 //____________________________________________________________________________
1069 typedef Fibre_RawSA QGram_RawSA; // "projects/library/seqan/index/index_qgram.h"(78)
1071 //____________________________________________________________________________
1074 typedef Fibre_RawText QGram_RawText; // "projects/library/seqan/index/index_qgram.h"(76)
1076 //____________________________________________________________________________
1079 typedef Fibre_SA QGram_SA; // "projects/library/seqan/index/index_qgram.h"(77)
1081 //____________________________________________________________________________
1084 typedef Fibre_SADir QGram_SADir; // "projects/library/seqan/index/index_qgram.h"(80)
1086 //____________________________________________________________________________
1089 typedef Fibre_Shape QGram_Shape; // "projects/library/seqan/index/index_qgram.h"(81)
1091 //____________________________________________________________________________
1094 typedef Fibre_Text QGram_Text; // "projects/library/seqan/index/index_qgram.h"(75)
1096 //____________________________________________________________________________
1099 typedef FixedShape<0> SimpleShape; // "projects/library/seqan/index/shape_base.h"(29)
1101 //____________________________________________________________________________
1104 typedef Tag<WotdOriginal_> const WotdOriginal; // "projects/library/seqan/index/index_wotd.h"(53)
1106 //____________________________________________________________________________
1109 typedef Fibre_Dir Wotd_Dir; // "projects/library/seqan/index/index_wotd.h"(35)
1111 //____________________________________________________________________________
1114 typedef Fibre_RawSA Wotd_RawSA; // "projects/library/seqan/index/index_wotd.h"(34)
1116 //____________________________________________________________________________
1119 typedef Fibre_RawText Wotd_RawText; // "projects/library/seqan/index/index_wotd.h"(32)
1121 //____________________________________________________________________________
1124 typedef Fibre_SA Wotd_SA; // "projects/library/seqan/index/index_wotd.h"(33)
1126 //____________________________________________________________________________
1129 typedef Fibre_Text Wotd_Text; // "projects/library/seqan/index/index_wotd.h"(31)
1131 } //namespace SEQAN_NAMESPACE_MAIN
1134 //////////////////////////////////////////////////////////////////////////////
1136 //////////////////////////////////////////////////////////////////////////////
1138 namespace SEQAN_NAMESPACE_MAIN {
1141 //____________________________________________________________________________
1144 template <typename TText, typename TSpec> inline void clearIndex(Index<TText, PizzaChili<TSpec> >& me); // "projects/library/seqan/index/index_pizzachili.h"(132)
1146 //____________________________________________________________________________
1147 // createPizzaChiliIndex
1149 template <typename TText, typename TSpec> inline bool createPizzaChiliIndex( Index<TText, PizzaChili<TSpec> >& me, uchar_t* textstart, ulong_t textlength ); // "projects/library/seqan/index/index_pizzachili.h"(256)
1151 //____________________________________________________________________________
1154 template <typename TText, typename TSpec> inline char const* getOptionsString(Index<TText, PizzaChili<TSpec> >& ); // "projects/library/seqan/index/index_pizzachili.h"(162)
1155 template <typename TText> inline char const* getOptionsString(Index<TText, PizzaChili<PizzaChili_SA> >& ); // "projects/library/seqan/index/index_pizzachili.h"(169)
1156 template <typename TText> inline char const* getOptionsString(Index<TText, PizzaChili<PizzaChili_FM> >& ); // "projects/library/seqan/index/index_pizzachili.h"(176)
1157 template <typename TText> inline char const* getOptionsString(Index<TText, PizzaChili<PizzaChili_RSA> >& ); // "projects/library/seqan/index/index_pizzachili.h"(183)
1159 //____________________________________________________________________________
1160 // getPizzaChiliString
1162 template <typename TPattern> inline uchar_t* getPizzaChiliString(TPattern const& pattern); // "projects/library/seqan/index/index_pizzachili_find.h"(92)
1163 inline uchar_t* getPizzaChiliString(char const* pattern); // "projects/library/seqan/index/index_pizzachili_find.h"(110)
1165 //____________________________________________________________________________
1168 template <typename TValue, typename TSpec> inline void queryText(String<TValue, PizzaChili<TSpec> > const& me); // "projects/library/seqan/index/index_pizzachili_string.h"(419)
1171 } //namespace SEQAN_NAMESPACE_MAIN
1172 //////////////////////////////////////////////////////////////////////////////
1174 namespace SEQAN_NAMESPACE_MAIN {
1176 //____________________________________________________________________________
1179 template <typename Dest, typename Ofs, typename Src> static finline Src const __cp_(Dest &dst, Ofs const ofs, Src const src); // "projects/library/seqan/index/pump_extender7.h"(67)
1181 //____________________________________________________________________________
1182 // _adjustRightBorder
1184 template <typename TText, typename TSpec > inline void _adjustRightBorder( Iter< Index<TText, Index_Wotd<WotdOriginal> >, VSTree< TopDown<TSpec> > > &); // "projects/library/seqan/index/index_wotd.h"(493)
1185 template <typename TText, typename TIndexSpec, typename TSpec > inline void _adjustRightBorder( Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it); // "projects/library/seqan/index/index_wotd.h"(499)
1187 //____________________________________________________________________________
1190 template <typename TSA, typename TText > typename Size<TText>::Type _bucketLCP(TSA const &sa, TText const &text); // "projects/library/seqan/index/index_wotd.h"(1249)
1191 template <typename TSA, typename TText, typename TSize > typename Size<TText>::Type _bucketLCP(TSA const &sa, TText const &text, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(1283)
1192 template <typename TSA, typename TText, typename TSpec, typename TSize > typename Size<TText>::Type _bucketLCP(TSA const &sa, StringSet<TText, TSpec> const &stringSet, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(1315)
1194 //____________________________________________________________________________
1195 // _createBWTableWrapper
1197 template <typename TBWT, typename TText, typename TSA, typename _TTextRandom > inline void _createBWTableWrapper(TBWT &bwt, TText const &s, TSA const &sa, _TTextRandom const); // "projects/library/seqan/index/index_shims.h"(424)
1198 template <typename TBWT, typename TText, typename TSA > inline void _createBWTableWrapper(TBWT &bwt, TText const &s, TSA const &sa, True const); // "projects/library/seqan/index/index_shims.h"(432)
1200 //____________________________________________________________________________
1203 template <typename TText, typename TSpec> inline Holder<TText> & _dataHost(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_base.h"(464)
1204 template <typename TText, typename TSpec> inline Holder<TText> const & _dataHost(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(468)
1206 //____________________________________________________________________________
1207 // _deallocateStorage
1209 template <typename TValue, typename TSpec> inline void _deallocateStorage( String<TValue, PizzaChili<TSpec> >& , TValue* begin, typename Size<String<TValue, PizzaChili<TSpec> > >::Type ); // "projects/library/seqan/index/index_pizzachili_string.h"(370)
1211 //____________________________________________________________________________
1214 template <typename TIndex, class TSpec > inline void _dfsClear(Iter<TIndex, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(1393)
1216 //____________________________________________________________________________
1219 template <typename TIndex, class TSpec > inline typename Size<TIndex>::Type & _dfsLCP(Iter< TIndex, VSTree< BottomUp<TSpec> > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1860)
1220 template <typename TIndex, class TSpec > inline typename Size<TIndex>::Type _dfsLCP(Iter< TIndex, VSTree< BottomUp<TSpec> > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1866)
1222 //____________________________________________________________________________
1225 template <typename TIndex, typename TSpec > inline void _dfsOnLeaf(Iter<TIndex, VSTree< BottomUp<TSpec> > > &it); // "projects/library/seqan/index/index_esa_stree.h"(274)
1226 template <typename TSTree, typename TSpec > inline void _dfsOnLeaf(Iter<TSTree, VSTree< BottomUp<_MaxRepeats<TSpec> > > > &it); // "projects/library/seqan/index/index_esa_algs.h"(496)
1227 template <typename TSTree > inline void _dfsOnLeaf(Iter<TSTree, VSTree< BottomUp<MultiMEMs> > > &it); // "projects/library/seqan/index/index_esa_algs_multi.h"(338)
1229 //____________________________________________________________________________
1232 template <typename TIndex, typename TSpec, typename TSize > inline void _dfsOnPop(Iter<TIndex, VSTree< BottomUp<TSpec> > > &it, TSize const); // "projects/library/seqan/index/index_esa_stree.h"(262)
1234 //____________________________________________________________________________
1237 template <typename TIndex, typename TSpec, typename TElement > inline void _dfsOnPush(Iter<TIndex, VSTree< BottomUp<TSpec> > > &it, TElement const &e); // "projects/library/seqan/index/index_esa_stree.h"(269)
1238 template <typename TSTree, typename TElement, typename TSpec > inline void _dfsOnPush(Iter<TSTree, VSTree< BottomUp<_MaxRepeats<TSpec> > > > &it, TElement const &e); // "projects/library/seqan/index/index_esa_algs.h"(482)
1240 //____________________________________________________________________________
1243 template <typename TIndex, class TSpec > inline Pair<typename Size<TIndex>::Type> & _dfsRange(Iter< TIndex, VSTree< BottomUp<TSpec> > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1847)
1244 template <typename TIndex, class TSpec > inline Pair<typename Size<TIndex>::Type> const & _dfsRange(Iter< TIndex, VSTree< BottomUp<TSpec> > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1854)
1246 //____________________________________________________________________________
1247 // _dfsReversedOrder
1249 template <typename TIndex, typename TSpec > inline bool _dfsReversedOrder(Iter<TIndex, VSTree< BottomUp<TSpec> > > &it); // "projects/library/seqan/index/index_esa_stree.h"(256)
1251 //____________________________________________________________________________
1254 template <typename TText, typename TPredHull, typename TPred> inline void _dump(Index<TText, Index_Wotd< WotdDFI<TPredHull, TPred> > > &index); // "projects/library/seqan/index/index_dfi.h"(470)
1255 template <typename TText, typename TSpec> inline void _dump(Index<TText, Index_Wotd<TSpec> > &index); // "projects/library/seqan/index/index_wotd.h"(1580)
1256 template <typename TText, typename TSpec> inline void _dump(Index<TText, Index_ESA<TSpec> > &index); // "projects/library/seqan/index/index_esa_stree.h"(238)
1258 //____________________________________________________________________________
1261 template <typename TText, typename TPredHull, typename TPred> inline void _dumpFreq(Index<TText, Index_Wotd< WotdDFI<TPredHull, TPred> > > &index); // "projects/library/seqan/index/index_dfi.h"(497)
1263 //____________________________________________________________________________
1264 // _dumpHistoryStack
1266 template <typename TIndex, typename TSpec > inline void _dumpHistoryStack(Iter<TIndex, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(229)
1268 //____________________________________________________________________________
1271 template <typename TText, typename TSA, typename TLCP, typename TSpec, typename TQuery > inline Pair< typename Iterator<TSA, Standard>::Type > _equalRangeLCPE( TText &text, TSA &sa, SearchTreeIterator< TLCP, TSpec > treeIter, TQuery &query); // "projects/library/seqan/index/index_esa_find.h"(1362)
1272 template <typename TText, typename TSA, typename TLCP, typename TQuery > inline Pair< typename Iterator<TSA, Standard>::Type > _equalRangeLCPE( TText &text, TSA &sa, TLCP &lcp, TQuery &query); // "projects/library/seqan/index/index_esa_find.h"(1514)
1274 //____________________________________________________________________________
1277 template <typename TText, typename TSA, typename TSpec, typename TQuery > inline Pair< typename Iterator<TSA, Standard>::Type > _equalRangeSA( TText &text, SearchTreeIterator< TSA, TSpec > treeIter, TQuery &query); // "projects/library/seqan/index/index_esa_find.h"(632)
1279 //____________________________________________________________________________
1282 template <typename TText, typename TSpec, typename TSpecFinder, typename TPattern> inline void _findFirstIndex( Finder<Index<TText, PizzaChili<TSpec> >, TSpecFinder>& finder, TPattern const& pattern, PizzaChiliFinder const ); // "projects/library/seqan/index/index_pizzachili_find.h"(123)
1283 template <typename TText, typename TSpec, typename TSpecFinder, typename TPattern > inline void _findFirstIndex( Finder< Index<TText, TSpec>, TSpecFinder > &finder, TPattern const &pattern, QGram_FIND_Lookup const); // "projects/library/seqan/index/index_qgram_find.h"(57)
1284 template <typename TText, typename TSpec, typename TSpecFinder, typename TPattern > inline void _findFirstIndex( Finder< Index<TText, TSpec>, TSpecFinder > &finder, TPattern const &pattern, ESA_FIND_MLR const); // "projects/library/seqan/index/index_esa_find.h"(1742)
1285 template <typename TText, typename TSpec, typename TSpecFinder, typename TPattern > inline void _findFirstIndex( Finder< Index<TText, TSpec>, TSpecFinder > &finder, TPattern const &pattern, ESA_FIND_LCPE const); // "projects/library/seqan/index/index_esa_find.h"(1754)
1287 //____________________________________________________________________________
1290 template <typename TSTree, typename TSpec, typename TValue, typename TSize > inline void _fractionMerge( Iter<TSTree, VSTree< BottomUp<TSpec> > > &it, _FractionCompound<TValue, TSize> &parent, _FractionCompound<TValue, TSize> &child); // "projects/library/seqan/index/index_esa_algs.h"(451)
1291 template <typename TSTree, typename TSpec, typename TValue, typename TSize > inline void _fractionMerge( Iter<TSTree, VSTree< BottomUp<TSpec> > > &it, _FractionMultiCompound<TValue, TSize> &parent, _FractionMultiCompound<TValue, TSize> &child); // "projects/library/seqan/index/index_esa_algs_multi.h"(317)
1293 //____________________________________________________________________________
1296 template <typename TIndex> inline int _fullDir2Length(TIndex const &index); // "projects/library/seqan/index/index_qgram.h"(330)
1298 //____________________________________________________________________________
1301 template <typename TIndex> inline int _fullDirLength(TIndex const &index); // "projects/library/seqan/index/index_qgram.h"(322)
1303 //____________________________________________________________________________
1306 template <typename TSize, typename TIndex > inline TSize _getDown(TSize i, TIndex const &index); // "projects/library/seqan/index/index_esa_stree.h"(1836)
1308 //____________________________________________________________________________
1311 template <typename TSize, typename TIndex > inline TSize _getNextl(TSize i, TIndex const &index); // "projects/library/seqan/index/index_esa_stree.h"(1821)
1313 //____________________________________________________________________________
1316 template <typename TText, class TSpec, typename TValue > inline bool _getNodeByChar( Iter< Index<TText, Index_ESA<TSpec> >, VSTree<TSpec> > const &it, TValue c, typename VertexDescriptor< Index<TText, Index_ESA<TSpec> > >::Type &childDesc); // "projects/library/seqan/index/index_esa_stree.h"(787)
1318 //____________________________________________________________________________
1321 template <typename TText, typename TSpec, typename TPos> inline TPos _getNodeLP( Index<TText, Index_Wotd<TSpec> > const &index, TPos pos); // "projects/library/seqan/index/index_wotd.h"(1366)
1323 //____________________________________________________________________________
1326 template <typename TSize, typename TIndex > inline TSize _getUp(TSize i, TIndex const &index); // "projects/library/seqan/index/index_esa_stree.h"(1827)
1328 //____________________________________________________________________________
1331 template <typename TText, typename TSpec, typename TDFSOrder, typename THideEmptyEdges > inline bool _goDown( Iter< Index<TText, Index_Wotd<WotdOriginal> >, VSTree< TopDown<TSpec> > > &it, VSTreeIteratorTraits<TDFSOrder, THideEmptyEdges> const); // "projects/library/seqan/index/index_wotd.h"(524)
1332 template <typename TText, typename TIndexSpec, typename TSpec, typename TDFSOrder, typename THideEmptyEdges > inline bool _goDown( Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it, VSTreeIteratorTraits<TDFSOrder, THideEmptyEdges> const); // "projects/library/seqan/index/index_wotd.h"(560)
1333 template <typename TText, class TIndexSpec, class TSpec, typename TDFSOrder > inline bool _goDown( Iter< Index<TText, Index_ESA<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it, VSTreeIteratorTraits<TDFSOrder, False> const); // "projects/library/seqan/index/index_esa_stree.h"(1035)
1334 template <typename TText, class TIndexSpec, class TSpec, typename TDFSOrder > inline bool _goDown( Iter< Index<TText, Index_ESA<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it, VSTreeIteratorTraits<TDFSOrder, True> const); // "projects/library/seqan/index/index_esa_stree.h"(1055)
1336 //____________________________________________________________________________
1339 template <typename TText, class TSpec, typename TValue > inline bool _goDownChar( Iter<Index<TText, Index_Wotd<WotdOriginal> >, VSTree< TopDown<TSpec> > > &it, TValue c); // "projects/library/seqan/index/index_wotd.h"(1609)
1340 template <typename TText, class TIndexSpec, class TSpec, typename TValue > inline bool _goDownChar( Iter<Index<TText, Index_Wotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it, TValue c); // "projects/library/seqan/index/index_wotd.h"(1631)
1341 template <typename TIndex, class TSpec, typename TValue > inline bool _goDownChar(Iter< TIndex, VSTree< TopDown<TSpec> > > &it, TValue c); // "projects/library/seqan/index/index_esa_stree.h"(1100)
1343 //____________________________________________________________________________
1346 template <typename TIndex, typename TSpec, typename TObject > inline bool _goDownObject( Iter< TIndex, VSTree< TopDown<TSpec> > > &it, TObject const &obj, False); // "projects/library/seqan/index/index_esa_stree.h"(1168)
1347 template <typename TIndex, typename TSpec, typename TObject > inline bool _goDownObject( Iter< TIndex, VSTree< TopDown<TSpec> > > &it, TObject const &obj, True); // "projects/library/seqan/index/index_esa_stree.h"(1178)
1349 //____________________________________________________________________________
1352 template <typename TIndex, typename TSpec, typename TString, typename TSize > inline bool _goDownString( Iter< TIndex, VSTree< TopDown<TSpec> > > &node, TString const &pattern, TSize &lcp); // "projects/library/seqan/index/index_esa_stree.h"(1118)
1354 //____________________________________________________________________________
1357 template <typename TText, typename TSpec, typename TDFSOrder, typename THideEmptyEdges > inline bool _goRight( Iter< Index<TText, Index_Wotd<WotdOriginal> >, VSTree< TopDown<TSpec> > > &it, VSTreeIteratorTraits<TDFSOrder, THideEmptyEdges> const); // "projects/library/seqan/index/index_wotd.h"(596)
1358 template <typename TText, typename TIndexSpec, typename TSpec, typename TDFSOrder, typename THideEmptyEdges > inline bool _goRight( Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it, VSTreeIteratorTraits<TDFSOrder, THideEmptyEdges> const); // "projects/library/seqan/index/index_wotd.h"(620)
1359 template <typename TText, class TIndexSpec, class TSpec, typename TDFSOrder, typename THideEmptyEdges > inline bool _goRight( Iter< Index<TText, Index_ESA<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it, VSTreeIteratorTraits<TDFSOrder, THideEmptyEdges> const); // "projects/library/seqan/index/index_esa_stree.h"(1289)
1361 //____________________________________________________________________________
1364 template <typename TText, typename TWotdSpec, typename TSpec > inline bool _goUp(Iter< Index<TText, Index_Wotd<TWotdSpec> >, VSTree< TopDown<TSpec> > > &it); // "projects/library/seqan/index/index_wotd.h"(645)
1365 template <typename TText, typename TSpec > inline bool _goUp(Iter< Index<TText, Index_Wotd<WotdOriginal> >, VSTree< TopDown< ParentLinks<TSpec> > > > &it); // "projects/library/seqan/index/index_wotd.h"(657)
1366 template <typename TText, typename TIndexSpec, typename TSpec > inline bool _goUp(Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > &it); // "projects/library/seqan/index/index_wotd.h"(674)
1367 template <typename TIndex, class TSpec > inline bool _goUp(Iter< TIndex, VSTree< TopDown<TSpec> > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1219)
1368 template <typename TIndex, class TSpec > inline bool _goUp(Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1231)
1370 //____________________________________________________________________________
1373 template <typename THValue, typename TValue, typename TIter> inline THValue _hashFixedShape(THValue hash, TIter &, TValue const, FixedShape<1> const); // "projects/library/seqan/index/shape_base.h"(290)
1374 template <typename THValue, typename TValue, typename TIter, unsigned q> inline THValue _hashFixedShape(THValue hash, TIter &it, TValue const, FixedShape<q> const); // "projects/library/seqan/index/shape_base.h"(296)
1376 //____________________________________________________________________________
1377 // _hashHardwiredShape
1379 template <typename THValue, typename TValue, typename TIter> inline THValue _hashHardwiredShape(THValue hash, TIter &, TValue const, HardwiredShape< 0,0,0,0,0, 0,0,0,0,0, 0,0,0,0,0, 0,0,0,0,0 > const); // "projects/library/seqan/index/shape_gapped.h"(448)
1380 template <int P01, int P02, int P03, int P04, int P05, int P06, int P07, int P08, int P09, int P10, int P11, int P12, int P13, int P14, int P15, int P16, int P17, int P18, int P19, typename THValue, typename TValue, typename TIter > inline THValue _hashHardwiredShape(THValue hash, TIter &it, TValue const, HardwiredShape< 1 ,P01,P02,P03,P04, P05,P06,P07,P08,P09, P10,P11,P12,P13,P14, P15,P16,P17,P18,P19 > const); // "projects/library/seqan/index/shape_gapped.h"(465)
1381 template <int P00, int P01, int P02, int P03, int P04, int P05, int P06, int P07, int P08, int P09, int P10, int P11, int P12, int P13, int P14, int P15, int P16, int P17, int P18, int P19, typename THValue, typename TValue, typename TIter > inline THValue _hashHardwiredShape(THValue hash, TIter &it, TValue const, HardwiredShape< P00,P01,P02,P03,P04, P05,P06,P07,P08,P09, P10,P11,P12,P13,P14, P15,P16,P17,P18,P19 > const); // "projects/library/seqan/index/shape_gapped.h"(488)
1383 //____________________________________________________________________________
1384 // _hashTuple2FixedShape
1386 template <typename THValue, typename TValue, typename TTValue, unsigned SIZE, typename TCompressed> inline THValue _hashTuple2FixedShape( THValue const, Tuple<TTValue, SIZE, TCompressed> const &tuple, TValue const, FixedShape<1> const); // "projects/library/seqan/index/shape_base.h"(353)
1387 template <typename THValue, typename TValue, typename TTValue, unsigned SIZE, typename TCompressed, unsigned q> inline THValue _hashTuple2FixedShape( THValue const, Tuple<TTValue, SIZE, TCompressed> const &tuple, TValue const, FixedShape<q> const); // "projects/library/seqan/index/shape_base.h"(364)
1389 //____________________________________________________________________________
1390 // _haveMaximalRepeats
1392 template <typename TValue, typename TSize> int _haveMaximalRepeats( _FractionCompound<TValue, TSize> const &a, _FractionCompound<TValue, TSize> const &b); // "projects/library/seqan/index/index_esa_algs.h"(268)
1393 template <typename TValue, typename TSize> int _haveMaximalRepeats( _FractionCompound<TValue, TSize> const &a, _FractionCompound<TValue, TSize> const &b, TValue &equalKey); // "projects/library/seqan/index/index_esa_algs.h"(289)
1395 //____________________________________________________________________________
1398 template <typename TIndex, class TSpec > inline void _historyClear(Iter< TIndex, VSTree<TSpec> > &); // "projects/library/seqan/index/index_esa_stree.h"(989)
1399 template <typename TIndex, class TSpec > inline void _historyClear(Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it); // "projects/library/seqan/index/index_esa_stree.h"(993)
1401 //____________________________________________________________________________
1404 template <typename TText, typename TIndexSpec, typename TSpec > inline void _historyPush(Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it); // "projects/library/seqan/index/index_wotd.h"(235)
1405 template <typename TText, typename TSpec > inline void _historyPush(Iter< Index<TText, Index_Wotd<WotdOriginal> >, VSTree< TopDown< ParentLinks<TSpec> > > > &it); // "projects/library/seqan/index/index_wotd.h"(244)
1406 template <typename TText, typename TIndexSpec, typename TSpec > inline void _historyPush(Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > &it); // "projects/library/seqan/index/index_wotd.h"(255)
1407 template <typename TText, class TIndexSpec, class TSpec > inline void _historyPush(Iter< Index<TText, Index_ESA<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1004)
1408 template <typename TText, class TIndexSpec, class TSpec > inline void _historyPush(Iter< Index<TText, Index_ESA<TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1010)
1410 //____________________________________________________________________________
1411 // _indexRequireBottomUpIteration
1413 template <typename TText, typename TSpec > void _indexRequireBottomUpIteration(Index<TText, Index_ESA<TSpec> > &index); // "projects/library/seqan/index/index_esa_base.h"(298)
1415 //____________________________________________________________________________
1416 // _indexRequireTopDownIteration
1418 template <typename TText, typename TSpec > void _indexRequireTopDownIteration(Index<TText, Index_ESA<TSpec> > &index); // "projects/library/seqan/index/index_esa_base.h"(290)
1419 template <typename TText, typename TSpec > void _indexRequireTopDownIteration(Index<TText, Index_Wotd<TSpec> > &index); // "projects/library/seqan/index/index_wotd.h"(193)
1421 //____________________________________________________________________________
1424 template <typename TText, typename TIndexSpec, typename TSpec, typename TDFSOrder > inline bool _isLeaf( Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree<TSpec> > const &it, VSTreeIteratorTraits<TDFSOrder, False> const); // "projects/library/seqan/index/index_wotd.h"(281)
1425 template <typename TText, typename TIndexSpec, typename TSpec, typename TDFSOrder > inline bool _isLeaf( Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree<TSpec> > const &it, VSTreeIteratorTraits<TDFSOrder, True> const); // "projects/library/seqan/index/index_wotd.h"(292)
1426 template <typename TSize > inline bool _isLeaf(VertexESA<TSize> const &vDesc); // "projects/library/seqan/index/index_esa_stree.h"(1750)
1427 template <typename TIndex, class TSpec, typename TDFSOrder > inline bool _isLeaf( Iter<TIndex, VSTree<TSpec> > const &it, VSTreeIteratorTraits<TDFSOrder, False> const); // "projects/library/seqan/index/index_esa_stree.h"(1760)
1428 template <typename TIndex, class TSpec, typename TDFSOrder > inline bool _isLeaf( Iter<TIndex, VSTree<TSpec> > const &it, VSTreeIteratorTraits<TDFSOrder, True> const); // "projects/library/seqan/index/index_esa_stree.h"(1769)
1430 //____________________________________________________________________________
1433 template <typename TSize, typename TIndex > inline bool _isNextl(TSize i, TIndex const &index); // "projects/library/seqan/index/index_esa_stree.h"(1805)
1435 //____________________________________________________________________________
1438 template <typename TSize > inline bool _isRoot(_VertexWotdOriginal<TSize> const &value); // "projects/library/seqan/index/index_wotd.h"(267)
1439 template <typename TSize > inline bool _isRoot(_VertexWotdModified<TSize> const &value); // "projects/library/seqan/index/index_wotd.h"(272)
1440 template <typename TSize > inline bool _isRoot(VertexESA<TSize> const &value); // "projects/library/seqan/index/index_esa_stree.h"(1501)
1442 //____________________________________________________________________________
1445 template <typename TValue> inline bool _isSizeInval(TValue const &v); // "projects/library/seqan/index/index_base.h"(794)
1447 //____________________________________________________________________________
1450 template <typename TSize, typename TIndex > inline bool _isUp(TSize i, TIndex const &index); // "projects/library/seqan/index/index_esa_stree.h"(1813)
1452 //____________________________________________________________________________
1455 template <typename T, typename ST> inline bool _leqSkew3(T a1, ST a2, T b1, ST b2); // "projects/library/seqan/index/index_skew3.h"(313)
1456 template <typename T, typename ST> inline bool _leqSkew3(T a1, T a2, ST a3, T b1, T b2, ST b3); // "projects/library/seqan/index/index_skew3.h"(319)
1458 //____________________________________________________________________________
1461 template <typename TTextIter, typename TSize> inline bool _leqSkew7(TTextIter a1, TSize a2, TTextIter b1, TSize b2, TSize n); // "projects/library/seqan/index/index_skew7.h"(414)
1462 template <typename TTextIter, typename TSize> inline bool _leqSkew7(TTextIter a, TTextIter b, TSize n); // "projects/library/seqan/index/index_skew7.h"(425)
1463 template <typename TTextIter, typename TSize, typename TString> inline bool _leqSkew7(unsigned a, unsigned b, TTextIter spos[], const TSize tpos[], const bool islast[], const TString &s124, const long adjust[7][7]); // "projects/library/seqan/index/index_skew7.h"(436)
1465 //____________________________________________________________________________
1468 template <typename TText, typename TSA, typename TLCP, typename TSpec, typename TQuery, typename TDiff_ > inline typename Iterator<TSA, Standard>::Type _lowerBoundLCPE( TText &text, TSA &sa, SearchTreeIterator< TLCP, TSpec > treeIter, TQuery &query, TDiff_ lcpLower, TDiff_ lcpUpper); // "projects/library/seqan/index/index_esa_find.h"(992)
1469 template <typename TText, typename TSA, typename TLCP, typename TSpec, typename TQuery > inline typename Iterator<TSA, Standard>::Type _lowerBoundLCPE( TText &text, TSA &sa, SearchTreeIterator< TLCP, TSpec > &treeIter, TQuery &query); // "projects/library/seqan/index/index_esa_find.h"(1169)
1471 //____________________________________________________________________________
1474 template <typename TText, typename TSA, typename TSpec, typename TQuery > inline typename Iterator<TSA, Standard>::Type _lowerBoundSA( TText &text, SearchTreeIterator< TSA, TSpec > treeIter, TQuery &query); // "projects/library/seqan/index/index_esa_find.h"(524)
1476 //____________________________________________________________________________
1479 template <typename TIndex, typename TSpec > inline void _onGoDown(Iter<TIndex, VSTree< TopDown<TSpec> > > &); // "projects/library/seqan/index/index_esa_stree.h"(1018)
1481 //____________________________________________________________________________
1484 template <typename TIndex, typename TSpec > inline void _onGoRight(Iter<TIndex, VSTree< TopDown<TSpec> > > &); // "projects/library/seqan/index/index_esa_stree.h"(1021)
1486 //____________________________________________________________________________
1489 template <typename TIndex, typename TSpec > inline void _onGoUp(Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &); // "projects/library/seqan/index/index_esa_stree.h"(1024)
1491 //____________________________________________________________________________
1492 // _pizzaChiliDeallocate
1494 template <typename TValue> inline void _pizzaChiliDeallocate(TValue* begin); // "projects/library/seqan/index/index_pizzachili_string.h"(276)
1496 //____________________________________________________________________________
1497 // _pizzaChiliReallocate
1499 template <typename TValue, typename TSpec> inline typename Value<String<TValue, PizzaChili<TSpec> > >::Type* _pizzaChiliReallocate( String<TValue, PizzaChili<TSpec> >& me, typename Size<String<TValue, PizzaChili<TSpec> > >::Type new_capacity ); // "projects/library/seqan/index/index_pizzachili_string.h"(259)
1501 //____________________________________________________________________________
1502 // _qgramCountQGrams
1504 template <typename TDir, typename TText, typename TShape > inline void _qgramCountQGrams(TDir &dir, TText const &text, TShape &shape); // "projects/library/seqan/index/index_qgram.h"(640)
1505 template <typename TDir, typename TString, typename TSpec, typename TShape > inline void _qgramCountQGrams(TDir &dir, StringSet<TString, TSpec> const &stringSet, TShape &shape); // "projects/library/seqan/index/index_qgram.h"(660)
1507 //____________________________________________________________________________
1508 // _qgramCummulativeSum
1510 template <typename TDir, typename TWithConstraints > inline typename Value<TDir>::Type _qgramCummulativeSum(TDir &dir, TWithConstraints); // "projects/library/seqan/index/index_qgram.h"(690)
1512 //____________________________________________________________________________
1513 // _qgramCummulativeSumAlt
1515 template <typename TDir, typename TWithConstraints > inline typename Value<TDir>::Type _qgramCummulativeSumAlt(TDir &dir, TWithConstraints const); // "projects/library/seqan/index/index_qgram.h"(722)
1517 //____________________________________________________________________________
1518 // _qgramDisableBuckets
1520 template <typename TIndex > inline bool _qgramDisableBuckets(TIndex &); // "projects/library/seqan/index/index_qgram.h"(863)
1522 //____________________________________________________________________________
1523 // _qgramFillSuffixArray
1525 template <typename TSA, typename TText, typename TShape, typename TDir, typename TWithConstraints > inline void _qgramFillSuffixArray(TSA &sa, TText const &text, TShape &shape, TDir &dir, TWithConstraints const); // "projects/library/seqan/index/index_qgram.h"(748)
1526 template <typename TSA, typename TString, typename TSpec, typename TShape, typename TDir, typename TWithConstraints > inline void _qgramFillSuffixArray( TSA &sa, StringSet<TString, TSpec> const &stringSet, TShape &shape, TDir &dir, TWithConstraints const); // "projects/library/seqan/index/index_qgram.h"(790)
1528 //____________________________________________________________________________
1529 // _qgramPostprocessBuckets
1531 template <typename TDir > inline void _qgramPostprocessBuckets(TDir &dir); // "projects/library/seqan/index/index_qgram.h"(831)
1533 //____________________________________________________________________________
1534 // _reallocateStorage
1536 template <typename TValue, typename TSpec> inline typename Value<String<TValue, PizzaChili<TSpec> > >::Type* _reallocateStorage( String<TValue, PizzaChili<TSpec> >& me, typename Size<String<TValue, PizzaChili<TSpec> > >::Type new_capacity, Exact ); // "projects/library/seqan/index/index_pizzachili_string.h"(359)
1538 //____________________________________________________________________________
1539 // _refineQGramIndex
1541 template <typename TSA, typename TDir, typename TText, typename TSize1, typename TSize2 > void _refineQGramIndex( TSA &sa, TDir &dir, TText const &text, TSize1 oldQ, TSize2 newQ); // "projects/library/seqan/index/index_qgram.h"(1033)
1543 //____________________________________________________________________________
1546 template <typename TValue, typename TSpec> inline void _setLength( String<TValue, PizzaChili<TSpec> >& me, size_t new_length ); // "projects/library/seqan/index/index_pizzachili_string.h"(409)
1548 //____________________________________________________________________________
1551 template <typename TValue> inline void _setSizeInval(TValue &v); // "projects/library/seqan/index/index_base.h"(789)
1553 //____________________________________________________________________________
1554 // _sortBucketQuickSort
1556 template <typename TSA, typename TText, typename TSize> void _sortBucketQuickSort( TSA &sa, TText &text, TSize lcp); // "projects/library/seqan/index/index_sa_qsort.h"(87)
1558 //____________________________________________________________________________
1559 // _sortFirstWotdBucket
1561 template <typename TText, typename TSpec, typename TPredHull, typename TPred > typename Size< Index<StringSet<TText, TSpec>, Index_Wotd<WotdDFI<TPredHull, TPred> > > >::Type _sortFirstWotdBucket(Index<StringSet<TText, TSpec>, Index_Wotd<WotdDFI<TPredHull, TPred> > > &index); // "projects/library/seqan/index/index_dfi.h"(171)
1562 template <typename TIndex > typename Size<TIndex>::Type _sortFirstWotdBucket(TIndex &index); // "projects/library/seqan/index/index_wotd.h"(890)
1563 template <typename TText, typename TSpec, typename TIndexSpec > typename Size< Index<StringSet<TText, TSpec>, TIndexSpec> >::Type _sortFirstWotdBucket(Index<StringSet<TText, TSpec>, TIndexSpec> &index); // "projects/library/seqan/index/index_wotd.h"(935)
1565 //____________________________________________________________________________
1568 template <typename TText, typename TSpec, typename TPredHull, typename TPred, typename TSize > TSize _sortWotdBucket( Index<StringSet<TText, TSpec>, Index_Wotd<WotdDFI<TPredHull, TPred> > > &index, TSize left, TSize right, TSize prefixLen); // "projects/library/seqan/index/index_dfi.h"(260)
1569 template <typename TText, typename TSize > TSize _sortWotdBucket( Index<TText, Index_Wotd<WotdOriginal> > &index, TSize left, TSize right, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(999)
1570 template <typename TIndex, typename TSize > TSize _sortWotdBucket( TIndex &index, TSize left, TSize right, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(1108)
1571 template <typename TText, typename TSpec, typename TIndexSpec, typename TSize > TSize _sortWotdBucket( Index<StringSet<TText, TSpec>, TIndexSpec> &index, TSize left, TSize right, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(1171)
1573 //____________________________________________________________________________
1574 // _storeWotdChildren
1576 template <typename TText, typename TPredHull, typename TPred, typename TSize> inline void _storeWotdChildren( Index<TText, Index_Wotd<WotdDFI<TPredHull, TPred> > > &index, TSize dirOfs, TSize lcp); // "projects/library/seqan/index/index_dfi.h"(397)
1577 template <typename TText, typename TPos> inline void _storeWotdChildren( Index<TText, Index_Wotd<WotdOriginal> > &index, TPos dirOfs); // "projects/library/seqan/index/index_wotd.h"(1385)
1578 template <typename TText, typename TSpec, typename TSize> inline void _storeWotdChildren( Index<TText, Index_Wotd<TSpec> > &index, TSize dirOfs, TSize lcp); // "projects/library/seqan/index/index_wotd.h"(1441)
1580 //____________________________________________________________________________
1583 template <typename TSize > inline unsigned _treeLevels(TSize lcpSize); // "projects/library/seqan/index/index_lcp_tree.h"(146)
1585 //____________________________________________________________________________
1588 template <typename TText, typename TSA, typename TLCP, typename TSpec, typename TQuery, typename TDiff_ > inline typename Iterator<TSA, Standard>::Type _upperBoundLCPE( TText &text, TSA &sa, SearchTreeIterator< TLCP, TSpec > treeIter, TQuery &query, TDiff_ lcpLower, TDiff_ lcpUpper); // "projects/library/seqan/index/index_esa_find.h"(1192)
1589 template <typename TText, typename TSA, typename TLCP, typename TSpec, typename TQuery > inline typename Iterator<TSA, Standard>::Type _upperBoundLCPE( TText &text, TSA &sa, SearchTreeIterator< TLCP, TSpec > &treeIter, TQuery &query); // "projects/library/seqan/index/index_esa_find.h"(1342)
1591 //____________________________________________________________________________
1594 template <typename TText, typename TSA, typename TSpec, typename TQuery > inline typename Iterator<TSA, Standard>::Type _upperBoundSA( TText &text, SearchTreeIterator< TSA, TSpec > treeIter, TQuery &query); // "projects/library/seqan/index/index_esa_find.h"(578)
1596 //____________________________________________________________________________
1599 template <typename TBuckets, typename TText > inline void _wotdCountChars(TBuckets &buckets, TText const &text); // "projects/library/seqan/index/index_wotd.h"(700)
1600 template <typename TBuckets, typename TText, typename TSpec > inline void _wotdCountChars(TBuckets &buckets, StringSet<TText, TSpec> const &stringSet); // "projects/library/seqan/index/index_wotd.h"(714)
1601 template <typename TBuckets, typename TText, typename TSA, typename TSize > inline typename Size<TText>::Type _wotdCountChars( TBuckets &buckets, TText const &text, TSA const &sa, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(767)
1602 template <typename TBuckets, typename TText, typename TSpec, typename TSA, typename TSize > inline typename Size<TText>::Type _wotdCountChars( TBuckets &buckets, StringSet<TText, TSpec> const &stringSet, TSA const &sa, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(803)
1604 //____________________________________________________________________________
1605 // _wotdCountCharsWotdOriginal
1607 template <typename TBuckets, typename TText, typename TSA, typename TSize > inline typename Size<TText>::Type _wotdCountCharsWotdOriginal( TBuckets &buckets, TText const &text, TSA &sa, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(736)
1609 //____________________________________________________________________________
1610 // _wotdCreateFirstLevel
1612 template <typename TText, typename TSpec> inline void _wotdCreateFirstLevel(Index<TText, Index_Wotd<TSpec> > &index); // "projects/library/seqan/index/index_wotd.h"(1681)
1614 //____________________________________________________________________________
1615 // _wotdCummulativeSum
1617 template <typename TBounds, typename TBuckets, typename TSize > inline typename Size<TBuckets>::Type _wotdCummulativeSum(TBounds &bounds, TBuckets const &buckets, TSize offset); // "projects/library/seqan/index/index_wotd.h"(844)
1618 template <typename TBounds, typename TBuckets > inline typename Size<TBuckets>::Type _wotdCummulativeSum(TBounds &bounds, TBuckets const &buckets); // "projects/library/seqan/index/index_wotd.h"(870)
1620 //____________________________________________________________________________
1623 template <typename TText, typename TSpec > inline typename Size< Index<TText, Index_Wotd<WotdOriginal> > >::Type _wotdEvaluate(Iter< Index<TText, Index_Wotd<WotdOriginal> >, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_wotd.h"(1497)
1624 template <typename TText, typename TIndexSpec, typename TSpec > inline typename Size< Index<TText, Index_Wotd<TIndexSpec> > >::Type _wotdEvaluate(Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_wotd.h"(1538)
1626 //____________________________________________________________________________
1629 template <typename TString, typename TSSetSpec, typename TIndexSpec, class TSpec > inline Align<TString, ArrayGaps> alignment(Iter< Index< StringSet<TString, TSSetSpec>, TIndexSpec >, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(643)
1630 template <typename TString, typename TConcSpec, typename TIndexSpec, class TSpec > inline Align<TString, ArrayGaps> alignment(Iter< Index< StringSet<TString, Owner<ConcatDirect<TConcSpec> > >, TIndexSpec >, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(689)
1632 //____________________________________________________________________________
1635 template <typename TValue, typename TSpec, typename TSource, typename TExpand> inline void assign( String<TValue, PizzaChili<TSpec> >& target, TSource const& source, Tag<TExpand> const ); // "projects/library/seqan/index/index_pizzachili_string.h"(196)
1636 template <typename TValue, typename TSpec, typename TSource, typename TExpand> inline void assign( String<TValue, PizzaChili<TSpec> >& target, TSource const* source, Tag<TExpand> const ); // "projects/library/seqan/index/index_pizzachili_string.h"(210)
1637 template <typename TValue, typename TSpec, typename TExpand> inline void assign( String<TValue, PizzaChili<TSpec> >& target, String<TValue, PizzaChili<TSpec> > const& source, Tag<TExpand> const ); // "projects/library/seqan/index/index_pizzachili_string.h"(224)
1639 //____________________________________________________________________________
1642 template <typename TText, typename TSpec, typename TSpecFinder > inline bool atBegin(Finder< Index<TText, TSpec>, TSpecFinder > & me); // "projects/library/seqan/index/index_find.h"(180)
1644 //____________________________________________________________________________
1647 template <typename TText, typename TSpec > inline bool atEnd(Iter<Index<TText, Index_Wotd<WotdOriginal> >, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_wotd.h"(477)
1648 template <typename TText, typename TSpec > inline bool atEnd(Iter<Index<TText, Index_Wotd<WotdOriginal> >, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_wotd.h"(483)
1649 template <typename TText, typename TSpec, typename TSpecFinder > inline bool atEnd(Finder< Index<TText, TSpec>, TSpecFinder > & me); // "projects/library/seqan/index/index_find.h"(188)
1650 template <typename TIndex, class TSpec > inline bool atEnd(Iter<TIndex, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(1467)
1651 template <typename TIndex, class TSpec > inline bool atEnd(Iter<TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1473)
1652 template <typename TRepeat > inline bool atEnd(Iter<TRepeat, MaxRepeatOccurrences> const &it); // "projects/library/seqan/index/index_esa_algs.h"(824)
1653 template <typename TRepeat > inline bool atEnd(Iter<TRepeat, MaxRepeatOccurrences> &it); // "projects/library/seqan/index/index_esa_algs.h"(829)
1654 template <typename TRepeat > inline bool atEnd(Iter<TRepeat, MultiMEMOccurences> const &it); // "projects/library/seqan/index/index_esa_algs_multi.h"(644)
1655 template <typename TRepeat > inline bool atEnd(Iter<TRepeat, MultiMEMOccurences> &it); // "projects/library/seqan/index/index_esa_algs_multi.h"(649)
1657 //____________________________________________________________________________
1660 template <typename TValue, typename TSpec, typename TTag> inline typename Iterator<String<TValue, PizzaChili<TSpec> >, Tag<TSpec> const>::Type begin( String<TValue, PizzaChili<TSpec> >& me, Tag<TTag> const ); // "projects/library/seqan/index/index_pizzachili_string.h"(464)
1661 template <typename TValue, typename TSpec, typename TTag> inline typename Iterator<String<TValue, PizzaChili<TSpec> > const, Tag<TSpec> const>::Type begin( String<TValue, PizzaChili<TSpec> > const& me, Tag<TTag> const ); // "projects/library/seqan/index/index_pizzachili_string.h"(475)
1662 template <typename TText, typename TIndexSpec, class TSpec > inline typename Iterator<Index<TText, TIndexSpec>, TSpec >::Type begin(Index<TText, TIndexSpec> &index, TSpec const); // "projects/library/seqan/index/index_esa_stree.h"(877)
1663 template <typename TSTree, class TSpec > inline typename Iterator< Iter< TSTree, VSTree< BottomUp<_MaxRepeats<TSpec> > > > >::Type begin(Iter< TSTree, VSTree< BottomUp<_MaxRepeats<TSpec> > > > &it); // "projects/library/seqan/index/index_esa_algs.h"(579)
1665 //____________________________________________________________________________
1668 template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex, Fibre_BWT>::Type>::Type bwtAt(TPos i, TIndex &index); // "projects/library/seqan/index/index_base.h"(777)
1669 template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex const, Fibre_BWT>::Type>::Type bwtAt(TPos i, TIndex const &index); // "projects/library/seqan/index/index_base.h"(781)
1671 //____________________________________________________________________________
1674 template <typename TText, typename TSpec> inline typename Reference< typename Cargo<Index<TText, TSpec> >::Type >::Type cargo(Index<TText, TSpec> & me); // "projects/library/seqan/index/index_shims.h"(595)
1675 template <typename TText, typename TSpec> inline typename Reference< typename Cargo<Index<TText, TSpec> const>::Type >::Type cargo(Index<TText, TSpec> const & me); // "projects/library/seqan/index/index_shims.h"(603)
1677 //____________________________________________________________________________
1680 template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex, Fibre_ChildTab>::Type>::Type childAt(TPos i, TIndex &index); // "projects/library/seqan/index/index_base.h"(756)
1681 template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex const, Fibre_ChildTab>::Type>::Type childAt(TPos i, TIndex const &index); // "projects/library/seqan/index/index_base.h"(760)
1683 //____________________________________________________________________________
1684 // childrenAreLeaves
1686 template <typename TIndex, class TSpec > inline bool childrenAreLeaves(Iter<TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1734)
1688 //____________________________________________________________________________
1691 template <typename TLCPInput, typename TDest > inline void childtab_process(TLCPInput &lcpIn, TDest &dest); // "projects/library/seqan/index/index_childtab.h"(44)
1693 //____________________________________________________________________________
1696 template <typename TText, typename TSpec> inline void clear(Index<TText, Index_ESA<TSpec> > &index); // "projects/library/seqan/index/index_esa_base.h"(307)
1697 template <typename TText, typename TSpec> inline void clear(Index<TText, PizzaChili<TSpec> >& me); // "projects/library/seqan/index/index_pizzachili.h"(150)
1698 template <typename TText, typename TSpec, typename TSpecFinder > inline void clear(Finder< Index<TText, TSpec>, TSpecFinder > & me); // "projects/library/seqan/index/index_find.h"(167)
1699 template <typename TValue, typename TSpec> inline void clear(String<TValue, PizzaChili<TSpec> >& me); // "projects/library/seqan/index/index_pizzachili_string.h"(178)
1700 template <typename TIndex, class TSpec > inline void clear(Iter<TIndex, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(1387)
1702 //____________________________________________________________________________
1705 template <typename TText, typename TSpec, typename TSpecFinder > inline typename _Parameter< Index<TText, TSpec> >::Type container(Finder< Index<TText, TSpec>, TSpecFinder > & me); // "projects/library/seqan/index/index_find.h"(100)
1706 template <typename TText, typename TSpec, typename TSpecFinder > inline typename _Parameter< Index<TText, TSpec> >::Type container(Finder< Index<TText, TSpec>, TSpecFinder > const & me); // "projects/library/seqan/index/index_find.h"(108)
1707 template <typename TIndex, class TSpec > inline TIndex const & container(Iter< TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(543)
1708 template <typename TIndex, class TSpec > inline TIndex & container(Iter< TIndex, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(548)
1710 //____________________________________________________________________________
1713 //template <typename TInput > inline bool control(Pipe< TInput, LarssonSadakane > &me, ControlBeginRead const &command); // "projects/library/seqan/index/index_sa_lss.h"(413)
1714 //template <typename TInput > inline bool control(Pipe< TInput, Merger3 > &me, ControlBeginRead const &command); // "projects/library/seqan/index/pipe_merger3.h"(134)
1715 //template <typename TInput > inline bool control(Pipe< TInput, Merger7 > &me, ControlBeginRead const &command); // "projects/library/seqan/index/pipe_merger7.h"(475)
1716 //template <typename TInput > inline bool control(Pipe< TInput, Merger7 > &me, ControlEof const &); // "projects/library/seqan/index/pipe_merger7.h"(483)
1717 //template <typename TInput > inline bool control(Pipe< TInput, Merger7 > &me, ControlEos const &); // "projects/library/seqan/index/pipe_merger7.h"(488)
1718 //template <typename TInput, typename TLimitsString > inline bool control(Pipe< TInput, Merger7Multi<TLimitsString> > &me, ControlBeginRead const &command); // "projects/library/seqan/index/pipe_merger7.h"(506)
1719 //template <typename TInput, typename TLimitsString > inline bool control(Pipe< TInput, Merger7Multi<TLimitsString> > &me, ControlEof const &); // "projects/library/seqan/index/pipe_merger7.h"(513)
1720 //template <typename TInput, typename TLimitsString > inline bool control(Pipe< TInput, Merger7Multi<TLimitsString> > &me, ControlEos const &); // "projects/library/seqan/index/pipe_merger7.h"(518)
1722 //____________________________________________________________________________
1725 template <typename TIndex, class TSpec > inline typename Size<TIndex>::Type countChildren(Iter< TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(763)
1727 //____________________________________________________________________________
1730 template <typename TIndex, class TSpec > inline typename Size<TIndex>::Type countOccurrences(Iter< TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(600)
1732 //____________________________________________________________________________
1735 template <typename TText, typename TSpec> inline typename Size<TText>::Type countSequences(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(609)
1737 //____________________________________________________________________________
1740 template <typename TBWT, typename TText, typename TSA > inline void createBWTable(TBWT &bwt, TText const &s, TSA const &sa); // "projects/library/seqan/index/index_shims.h"(439)
1742 //____________________________________________________________________________
1745 template <typename TBWT, typename TText, typename TSA > void createBWTableExt( TBWT &bwt, TText const &s, TSA const &SA); // "projects/library/seqan/index/index_shims.h"(394)
1747 //____________________________________________________________________________
1750 template <typename TBWT, typename TText, typename TSA > void createBWTableInt( TBWT &bwt, TText const &s, TSA const &SA); // "projects/library/seqan/index/index_bwt.h"(247)
1751 template <typename TBWT, typename TString, typename TSpec, typename TSA > void createBWTableInt( TBWT &bwt, StringSet<TString, TSpec> const &s, TSA const &SA); // "projects/library/seqan/index/index_bwt.h"(275)
1753 //____________________________________________________________________________
1756 //template <typename TLCPTable, typename TValue, typename TConfig > inline void createChildTable( String<TValue, External<TConfig> > &childtab, TLCPTable &lcp); // "projects/library/seqan/index/index_childtab.h"(197)
1757 template <typename TLCPInput, typename TDest > inline void createChildTable(TDest &dest, TLCPInput const &lcpIn); // "projects/library/seqan/index/index_childtab.h"(209)
1759 //____________________________________________________________________________
1760 // createChildTableExt
1762 template <typename TLCPTable, typename TChildTable > void createChildTableExt( TChildTable &childtab, TLCPTable &lcp); // "projects/library/seqan/index/index_childtab.h"(171)
1764 //____________________________________________________________________________
1765 // createCountsArray
1767 template <typename TCounts, typename TDir, typename TString, typename TSpec, typename TShape > void createCountsArray( TCounts &counts, TDir &dir, StringSet<TString, TSpec> const &stringSet, TShape &shape); // "projects/library/seqan/index/index_qgram.h"(1150)
1769 //____________________________________________________________________________
1772 template <class LCPFwdIt, class FlatOutIt > inline FlatOutIt createLCPBinTree( LCPFwdIt _First, LCPFwdIt _Last, FlatOutIt _Dest); // "projects/library/seqan/index/index_lcp_tree.h"(33)
1773 template <typename TLCPE, typename TLCP > inline void createLCPBinTree(TLCPE &lcp_enhanced, TLCP &lcp); // "projects/library/seqan/index/index_lcp_tree.h"(139)
1774 //template <typename TValue, typename TConfig, typename TLCP > inline void createLCPBinTree(String<TValue, External<TConfig> > &lcp_enhanced, TLCP &lcp); // "projects/library/seqan/index/index_lcp_tree.h"(155)
1776 //____________________________________________________________________________
1779 template <typename TValue, typename TSpec, typename TText, typename TSA, typename TAlgSpec > void createLCPETable( String< TValue, TSpec > &LCPE, TText const &s, TSA const &SA, TAlgSpec const alg); // "projects/library/seqan/index/index_shims.h"(334)
1780 //template <typename TValue, typename TConfig, typename TText, typename TSA, typename TAlgSpec > void createLCPETable( String< TValue, External<TConfig> > &LCPE, TText const &s, TSA const &SA, TAlgSpec const alg); // "projects/library/seqan/index/index_shims.h"(359)
1781 template <typename TValue, typename TSpec, typename TText, typename TSA> inline void createLCPETable( String< TValue, TSpec > &LCPE, TText &s, TSA &SA); // "projects/library/seqan/index/index_shims.h"(373)
1783 //____________________________________________________________________________
1784 // createLCPETableExt
1786 template <typename TValue, typename TSpec, typename TObject, typename TSA, typename TAlgSpec > void createLCPETableExt( String< TValue, TSpec > &LCPE, TObject const &text, TSA const &suffixArray, TAlgSpec const); // "projects/library/seqan/index/index_shims.h"(301)
1788 //____________________________________________________________________________
1791 //template <typename TLCPTable, typename TText, typename TSA > void createLCPTable( TLCPTable &LCP, TText const &s, TSA const &SA, KasaiOriginal const); // "projects/library/seqan/index/index_lcp.h"(253)
1792 //template <typename TLCPTable, typename TText, typename TSA > void createLCPTable( TLCPTable &LCP, TText const &s, TSA const &SA, Kasai const); // "projects/library/seqan/index/index_lcp.h"(315)
1793 template <typename TLCPTable, typename TString, typename TSpec, typename TSA > void createLCPTable( TLCPTable &LCP, StringSet<TString, TSpec> const &sset, TSA const &SA, Kasai const); // "projects/library/seqan/index/index_lcp.h"(398)
1795 //____________________________________________________________________________
1796 // createLCPTableExt
1798 template <typename TLCPTable, typename TObject, typename TSA, typename TAlgSpec > void createLCPTableExt( TLCPTable &LCP, TObject const &text, TSA const &suffixArray, TAlgSpec const); // "projects/library/seqan/index/index_shims.h"(179)
1799 template <typename TLCPTable, typename TString, typename TSpec, typename TSA, typename TAlgSpec > void createLCPTableExt( TLCPTable &LCP, StringSet<TString, TSpec> const &stringSet, TSA const &suffixArray, TAlgSpec const); // "projects/library/seqan/index/index_shims.h"(210)
1801 //____________________________________________________________________________
1804 template <typename TIndex > void createQGramIndex(TIndex &index); // "projects/library/seqan/index/index_qgram.h"(869)
1805 template <typename TSA, typename TDir, typename TText, typename TShape > void createQGramIndex( TSA &sa, TDir &dir, TText const &text, TShape &shape); // "projects/library/seqan/index/index_qgram.h"(915)
1807 //____________________________________________________________________________
1808 // createQGramIndexDirOnly
1810 template <typename TDir, typename TText, typename TShape > void createQGramIndexDirOnly( TDir &dir, TText const &text, TShape &shape); // "projects/library/seqan/index/index_qgram.h"(1089)
1811 template <typename TDir, typename TString, typename TSpec, typename TShape > void createQGramIndexDirOnly( TDir &dir, StringSet<TString, TSpec> const &stringSet, TShape &shape); // "projects/library/seqan/index/index_qgram.h"(1111)
1813 //____________________________________________________________________________
1814 // createQGramIndexExt
1816 template <typename TSA, typename TDir, typename TText, typename TShape > void createQGramIndexExt( TSA &suffixArray, TDir &dir, TText &text, TShape &shape); // "projects/library/seqan/index/index_qgram.h"(1287)
1817 template <typename TSA, typename TDir, typename TString, typename TSpec, typename TShape, typename TLimitsString > void createQGramIndexExt( TSA &suffixArray, TDir &dir, StringSet<TString, TSpec> const &stringSet, TShape &shape, TLimitsString &limits); // "projects/library/seqan/index/index_qgram.h"(1374)
1819 //____________________________________________________________________________
1820 // createQGramIndexSAOnly
1822 template <typename TSA, typename TText, typename TShape > void createQGramIndexSAOnly( TSA &sa, TText const &text, TShape &shape); // "projects/library/seqan/index/index_qgram.h"(951)
1823 template <typename TSA, typename TString, typename TSpec, typename TShape > void createQGramIndexSAOnly( TSA &sa, StringSet<TString, TSpec> const &stringSet, TShape &shape); // "projects/library/seqan/index/index_qgram.h"(986)
1825 //____________________________________________________________________________
1828 template <class SAFwdIt, class FlatOutIt > inline FlatOutIt createSABTree( SAFwdIt _First, SAFwdIt _Last, FlatOutIt _Dest, unsigned BlockSize); // "projects/library/seqan/index/index_sa_btree.h"(33)
1829 template <typename TSAB, typename TSA > inline void createSABTree(TSAB &sa_btree, TSA &sa, unsigned BlockSize); // "projects/library/seqan/index/index_sa_btree.h"(96)
1830 //template <typename TValue, typename TConfig, typename TSA > inline void createSABTree(String<TValue, External<TConfig> > &sa_btree, TSA &sa, unsigned BlockSize); // "projects/library/seqan/index/index_sa_btree.h"(110)
1832 //____________________________________________________________________________
1833 // createSuffixArray
1835 template <typename TSA, typename TText > void createSuffixArray( TSA &SA, TText &s, Shawarma<DeepShallow> const); // "projects/library/seqan/index/index_shawarma.h"(58)
1836 template <typename TSA, typename TText, typename TAlgSpec > inline void createSuffixArray( TSA &SA, TText const &s, TAlgSpec const &alg); // "projects/library/seqan/index/index_shims.h"(121)
1837 //template <typename TSA, typename TValue, typename TConfig, typename TAlgSpec > inline void createSuffixArray( TSA &SA, String< TValue, External<TConfig> > const &s, TAlgSpec const alg); // "projects/library/seqan/index/index_shims.h"(139)
1838 template <typename TSA, typename TValue, typename TSpec, typename TSSetSpec, typename TAlgSpec > inline void createSuffixArray( TSA &SA, StringSet< String<TValue, TSpec>, TSSetSpec > const &s, TAlgSpec const); // "projects/library/seqan/index/index_shims.h"(155)
1839 template <typename TSA, typename TText > void createSuffixArray( TSA &SA, TText &s, LarssonSadakane const &, unsigned K); // "projects/library/seqan/index/index_sa_lss.h"(352)
1840 template <typename TSA, typename TText > void createSuffixArray( TSA &SA, TText &s, ManberMyers const &, unsigned K, unsigned maxdepth); // "projects/library/seqan/index/index_sa_mm.h"(42)
1841 template <typename TSA, typename TText > inline void createSuffixArray( TSA &SA, TText &s, SAQSort const &); // "projects/library/seqan/index/index_sa_qsort.h"(102)
1842 //template <typename TSA, typename TValue, typename TConfig > inline void createSuffixArray( TSA &SA, String< TValue, External<TConfig> > &s, Skew3 const &spec, unsigned K, unsigned maxdepth); // "projects/library/seqan/index/index_skew3.h"(299)
1843 template <typename TSA, typename TText > void createSuffixArray( TSA &SA, TText &s, Skew3 const &, unsigned K, unsigned maxdepth, unsigned depth); // "projects/library/seqan/index/index_skew3.h"(342)
1844 template <typename TSA, typename TText > inline void createSuffixArray( TSA &SA, TText &s, Skew3 const &alg, unsigned K, unsigned maxdepth); // "projects/library/seqan/index/index_skew3.h"(494)
1845 //template <typename TSA, typename TValue, typename TConfig > inline void createSuffixArray( TSA &SA, String< TValue, External<TConfig> > &s, Skew7 const &spec, unsigned K, unsigned maxdepth); // "projects/library/seqan/index/index_skew7.h"(399)
1846 template <typename TSA, typename TText > void createSuffixArray( TSA &SA, TText &s, Skew7 const &, unsigned K, unsigned maxdepth, unsigned depth); // "projects/library/seqan/index/index_skew7.h"(472)
1847 template <typename TSA, typename TText > inline void createSuffixArray( TSA &SA, TText &s, Skew7 const &alg, unsigned K, unsigned maxdepth); // "projects/library/seqan/index/index_skew7.h"(795)
1849 //____________________________________________________________________________
1850 // createSuffixArrayExt
1852 template <typename TSA, typename TObject, typename TAlgSpec > void createSuffixArrayExt( TSA &suffixArray, TObject const &text, TAlgSpec const); // "projects/library/seqan/index/index_shims.h"(40)
1853 template <typename TSA, typename TString, typename TSpec, typename TAlgSpec > void createSuffixArrayExt( TSA &suffixArray, StringSet<TString, TSpec> const &stringSet, TAlgSpec const); // "projects/library/seqan/index/index_shims.h"(74)
1855 //____________________________________________________________________________
1856 // createSuffixArrayPart
1858 template <typename TSA, typename TText, typename TSize > inline void createSuffixArrayPart( TSA &SA, TText &s, ManberMyers const &alg, TSize maxLCP, unsigned K ); // "projects/library/seqan/index/index_sa_mm.h"(167)
1859 template <typename TSA, typename TText, typename TSize > inline void createSuffixArrayPart( TSA &SA, TText &s, Skew3 const &_dummy, TSize maxLCP, unsigned K ); // "projects/library/seqan/index/index_skew3.h"(508)
1860 template <typename TSA, typename TText, typename TSize > inline void createSuffixArrayPart( TSA &SA, TText &s, Skew7 const &_dummy, TSize maxLCP, unsigned K ); // "projects/library/seqan/index/index_skew7.h"(809)
1862 //____________________________________________________________________________
1865 template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex, Fibre_Dir>::Type>::Type dirAt(TPos i, TIndex &index); // "projects/library/seqan/index/index_qgram.h"(265)
1866 template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex const, Fibre_Dir>::Type>::Type dirAt(TPos i, TIndex const &index); // "projects/library/seqan/index/index_qgram.h"(269)
1868 //____________________________________________________________________________
1871 template <typename TText, typename TSpec, typename TSpecFinder > inline bool empty(Finder< Index<TText, TSpec>, TSpecFinder > & me); // "projects/library/seqan/index/index_find.h"(159)
1872 template <typename TIndex, class TSpec > inline bool empty(Iter<TIndex, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(1452)
1873 template <typename TIndex, class TSpec > inline bool empty(Iter<TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1458)
1875 //____________________________________________________________________________
1878 template <typename TText, typename TIndexSpec, typename TSpec > inline bool emptyParentEdge(Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree<TopDown<TSpec> > > const &it); // "projects/library/seqan/index/index_wotd.h"(425)
1879 template <typename TText, typename TIndexSpec, typename TSpec > inline bool emptyParentEdge(Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree<TopDown<ParentLinks<TSpec> > > > const &it); // "projects/library/seqan/index/index_wotd.h"(438)
1880 template <typename TIndex, typename TSpec > inline bool emptyParentEdge(Iter< TIndex, VSTree<TopDown<TSpec> > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(427)
1882 //____________________________________________________________________________
1885 template <typename TValue, typename TSpec, typename TTag> inline typename Iterator<String<TValue, PizzaChili<TSpec> >, Tag<TSpec> const>::Type end( String<TValue, PizzaChili<TSpec> >& me, Tag<TTag> const ); // "projects/library/seqan/index/index_pizzachili_string.h"(486)
1886 template <typename TValue, typename TSpec, typename TTag> inline typename Iterator<String<TValue, PizzaChili<TSpec> > const, Tag<TSpec> const>::Type end( String<TValue, PizzaChili<TSpec> > const& me, Tag<TTag> const ); // "projects/library/seqan/index/index_pizzachili_string.h"(497)
1887 template <typename TText, typename TIndexSpec, class TSpec > inline typename Iterator<Index<TText, TIndexSpec>, TSpec >::Type end(Index<TText, TIndexSpec> &index, TSpec const); // "projects/library/seqan/index/index_esa_stree.h"(927)
1888 template <typename TSTree, class TSpec > inline typename Iterator< Iter< TSTree, VSTree< BottomUp<_MaxRepeats<TSpec> > > > >::Type end(Iter< TSTree, VSTree< BottomUp<_MaxRepeats<TSpec> > > > &it); // "projects/library/seqan/index/index_esa_algs.h"(589)
1890 //____________________________________________________________________________
1893 template <typename TIndex, class TSpec > inline bool eof(Iter<TIndex, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(1440)
1894 template <typename TIndex, class TSpec > inline bool eof(Iter<TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1446)
1896 //____________________________________________________________________________
1899 template <typename TText, typename TSA, typename TLCPE, typename TQuery > inline Pair< typename Position<TSA>::Type > equalRangeLCPE( TText const &text, TSA const &sa, TLCPE const &lcpe, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(1586)
1900 template <typename TText, typename TSA, typename TLCPE, typename TQuery > inline Pair< typename Position<TSA>::Type > equalRangeLCPE( TText const &text, TSA const &sa, TLCPE const &lcpe, TQuery *query); // "projects/library/seqan/index/index_esa_find.h"(1688)
1902 //____________________________________________________________________________
1903 // equalRangeLCPEIterator
1905 template <typename TText, typename TSA, typename TLCPE, typename TQuery > inline Pair< typename Iterator<TSA, Standard>::Type > equalRangeLCPEIterator( TText const &text, TSA const &sa, TLCPE const &lcpe, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(1637)
1906 template <typename TText, typename TSA, typename TLCPE, typename TQuery > inline Pair< typename Iterator<TSA, Standard>::Type > equalRangeLCPEIterator( TText const &text, TSA const &sa, TLCPE const &lcpe, TQuery *query); // "projects/library/seqan/index/index_esa_find.h"(1707)
1908 //____________________________________________________________________________
1911 template <typename TText, typename TSA, typename TQuery, typename TFlatTreeSpec > inline Pair< typename Position<TSA>::Type > equalRangeSA( TText const &text, TSA const &sa, TQuery const &query, TFlatTreeSpec const); // "projects/library/seqan/index/index_esa_find.h"(853)
1912 template <typename TText, typename TSA, typename TQuery > inline Pair< typename Position<TSA>::Type > equalRangeSA( TText const &text, TSA const &sa, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(870)
1913 template <typename TText, typename TSA, typename TQuery, typename TFlatTreeSpec > inline Pair< typename Position<TSA>::Type > equalRangeSA( TText const &text, TSA const &sa, TQuery *query, TFlatTreeSpec const); // "projects/library/seqan/index/index_esa_find.h"(950)
1914 template <typename TText, typename TSA, typename TQuery > inline Pair< typename Position<TSA>::Type > equalRangeSA( TText const &text, TSA const &sa, TQuery *query); // "projects/library/seqan/index/index_esa_find.h"(967)
1916 //____________________________________________________________________________
1917 // equalRangeSAIterator
1919 template <typename TText, typename TSA, typename TQuery > inline Pair< typename Iterator<TSA const, Standard>::Type > equalRangeSAIterator( TText const &text, TSA const &sa, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(727)
1920 template <typename TText, typename TSA, typename TQuery > inline Pair< typename Iterator<TSA const, Standard>::Type > equalRangeSAIterator( TText const &text, TSA const &sa, TQuery *query); // "projects/library/seqan/index/index_esa_find.h"(773)
1922 //____________________________________________________________________________
1925 template <typename TText, typename TSpec, typename TSpecFinder, typename TPattern > inline bool find( Finder<Index<TText, TSpec>, TSpecFinder> &finder, TPattern const &pattern); // "projects/library/seqan/index/index_find.h"(249)
1926 template <typename TText, typename TSpec, typename TSpecFinder > inline bool find(Finder<Index<TText, TSpec>, TSpecFinder> &finder); // "projects/library/seqan/index/index_find.h"(260)
1928 //____________________________________________________________________________
1931 template <typename TRepeatStore, typename TText, typename TRepeatSize, typename TPeriodSize> void findRepeats(TRepeatStore &repString, TText const &text, TRepeatSize minRepeatLen, TPeriodSize maxPeriod); // "projects/library/seqan/index/repeat_base.h"(92)
1932 template <typename TRepeatStore, typename TString, typename TSpec, typename TRepeatSize> void findRepeats(TRepeatStore &repString, StringSet<TString, TSpec> const &text, TRepeatSize minRepeatLen); // "projects/library/seqan/index/repeat_base.h"(189)
1934 //____________________________________________________________________________
1937 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, PizzaChili<TSpec> > const, PizzaChili_Text>::Type getFibre(Index<TText, PizzaChili<TSpec> > const& me, PizzaChili_Text const); // "projects/library/seqan/index/index_pizzachili.h"(210)
1938 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, PizzaChili<TSpec> >, PizzaChili_Text>::Type getFibre(Index<TText, PizzaChili<TSpec> >& me, PizzaChili_Text const); // "projects/library/seqan/index/index_pizzachili.h"(217)
1939 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_Dir>::Type & getFibre(Index<TText, TSpec> &index, Fibre_Dir); // "projects/library/seqan/index/index_qgram.h"(188)
1940 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_Dir>::Type & getFibre(Index<TText, TSpec> const &index, Fibre_Dir); // "projects/library/seqan/index/index_qgram.h"(193)
1941 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_Counts>::Type & getFibre(Index<TText, TSpec> &index, Fibre_Counts); // "projects/library/seqan/index/index_qgram.h"(199)
1942 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_Counts>::Type & getFibre(Index<TText, TSpec> const &index, Fibre_Counts); // "projects/library/seqan/index/index_qgram.h"(204)
1943 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_CountsDir>::Type & getFibre(Index<TText, TSpec> &index, Fibre_CountsDir); // "projects/library/seqan/index/index_qgram.h"(210)
1944 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_CountsDir>::Type & getFibre(Index<TText, TSpec> const &index, Fibre_CountsDir); // "projects/library/seqan/index/index_qgram.h"(215)
1945 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_Shape>::Type & getFibre(Index<TText, TSpec> &index, Fibre_Shape); // "projects/library/seqan/index/index_qgram.h"(221)
1946 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_Shape>::Type & getFibre(Index<TText, TSpec> const &index, Fibre_Shape); // "projects/library/seqan/index/index_qgram.h"(226)
1947 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_Text>::Type & getFibre(Index<TText, TSpec> &index, Fibre_Text); // "projects/library/seqan/index/index_base.h"(476)
1948 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_Text>::Type & getFibre(Index<TText, TSpec> const &index, Fibre_Text); // "projects/library/seqan/index/index_base.h"(481)
1949 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_RawText>::Type & getFibre(Index<TText, TSpec> &index, Fibre_RawText); // "projects/library/seqan/index/index_base.h"(489)
1950 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_RawText>::Type & getFibre(Index<TText, TSpec> const &index, Fibre_RawText); // "projects/library/seqan/index/index_base.h"(494)
1951 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_SA>::Type & getFibre(Index<TText, TSpec> &index, Fibre_SA); // "projects/library/seqan/index/index_base.h"(502)
1952 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_SA>::Type & getFibre(Index<TText, TSpec> const &index, Fibre_SA); // "projects/library/seqan/index/index_base.h"(507)
1953 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_SA>::Type & getFibre(Index<TText, TSpec> &index, Fibre_RawSA); // "projects/library/seqan/index/index_base.h"(515)
1954 template <typename TString, typename TSSetSpec, typename TSpec> inline typename Fibre<Index<StringSet<TString, TSSetSpec>, TSpec>, Fibre_RawSA>::Type getFibre(Index<StringSet<TString, TSSetSpec>, TSpec> &index, Fibre_RawSA); // "projects/library/seqan/index/index_base.h"(528)
1955 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_LCP>::Type & getFibre(Index<TText, TSpec> &index, Fibre_LCP); // "projects/library/seqan/index/index_base.h"(548)
1956 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_LCP>::Type & getFibre(Index<TText, TSpec> const &index, Fibre_LCP); // "projects/library/seqan/index/index_base.h"(553)
1957 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_LCPE>::Type & getFibre(Index<TText, TSpec> &index, Fibre_LCPE); // "projects/library/seqan/index/index_base.h"(561)
1958 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_LCPE>::Type & getFibre(Index<TText, TSpec> const &index, Fibre_LCPE); // "projects/library/seqan/index/index_base.h"(566)
1959 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_ChildTab>::Type & getFibre(Index<TText, TSpec> &index, Fibre_ChildTab); // "projects/library/seqan/index/index_base.h"(574)
1960 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_ChildTab>::Type & getFibre(Index<TText, TSpec> const &index, Fibre_ChildTab); // "projects/library/seqan/index/index_base.h"(579)
1961 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_BWT>::Type & getFibre(Index<TText, TSpec> &index, Fibre_BWT); // "projects/library/seqan/index/index_base.h"(587)
1962 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_BWT>::Type & getFibre(Index<TText, TSpec> const &index, Fibre_BWT); // "projects/library/seqan/index/index_base.h"(592)
1964 //____________________________________________________________________________
1967 template <typename TIndex, class TSpec, typename TSet > inline typename Size<TIndex>::Type getFrequency(Iter<TIndex, VSTree<TSpec> > const &it, TSet &set); // "projects/library/seqan/index/index_esa_stree.h"(1686)
1968 template <typename TIndex, class TSpec > inline typename Size<TIndex>::Type getFrequency(Iter<TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1714)
1970 //____________________________________________________________________________
1971 // getKmerSimilarityMatrix
1973 template <typename TObject, typename TShapeSpec, typename TSpec, typename TDistMatrix > inline void getKmerSimilarityMatrix( Index< TObject, Index_QGram<TShapeSpec, TSpec> > &index, TDistMatrix &distMat); // "projects/library/seqan/index/index_qgram.h"(1538)
1974 template <typename TObject, typename TShapeSpec, typename TSpec, typename TDistMatrix, typename TSeqNoString > inline void getKmerSimilarityMatrix( Index< TObject, Index_QGram<TShapeSpec, TSpec> > &index, TDistMatrix &distMat, TSeqNoString const &seqNo); // "projects/library/seqan/index/index_qgram.h"(1638)
1976 //____________________________________________________________________________
1979 template <typename TText, typename TSpec > inline typename SAValue<Index<TText, Index_Wotd<WotdOriginal> > >::Type getOccurrence(Iter< Index<TText, Index_Wotd<WotdOriginal> >, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_wotd.h"(418)
1980 template <typename TIndex, class TSpec > inline typename SAValue<TIndex>::Type getOccurrence(Iter< TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(581)
1982 //____________________________________________________________________________
1985 template <typename TIndex, class TSpec > inline typename Infix< typename Fibre<TIndex, Fibre_SA>::Type const >::Type getOccurrences(Iter< TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(621)
1987 //____________________________________________________________________________
1988 // getOccurrencesBWT
1990 template <typename TIndex, class TSpec > inline typename Infix< typename Fibre<TIndex, ESA_BWT>::Type const >::Type getOccurrencesBWT(Iter< TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(723)
1992 //____________________________________________________________________________
1995 template <typename TText, typename TSpec, typename TSpecFinder > inline void goBegin(Finder< Index<TText, TSpec>, TSpecFinder > & me); // "projects/library/seqan/index/index_find.h"(198)
1996 template <typename TText, typename TIndexSpec, class TSpec > inline void goBegin(Iter<Index<TText, TIndexSpec>, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(887)
1997 template <typename TText, typename TIndexSpec, class TSpec > inline void goBegin(Iter<Index<TText, Index_ESA<TIndexSpec> >, VSTree< BottomUp<TSpec> > > &it); // "projects/library/seqan/index/index_esa_stree.h"(906)
1998 template <typename TRepeat > inline Iter<TRepeat, MaxRepeatOccurrences> & goBegin(Iter<TRepeat, MaxRepeatOccurrences> &it); // "projects/library/seqan/index/index_esa_algs.h"(810)
2000 //____________________________________________________________________________
2003 template <typename TIndex, class TSpec > inline bool goDown(Iter< TIndex, VSTree< TopDown<TSpec> > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1085)
2004 template <typename TIndex, typename TSpec, typename TObject > inline bool goDown( Iter< TIndex, VSTree< TopDown<TSpec> > > &it, TObject const &obj); // "projects/library/seqan/index/index_esa_stree.h"(1190)
2005 template <typename TIndex, typename TSpec, typename TString, typename TSize > inline bool goDown( Iter< TIndex, VSTree< TopDown<TSpec> > > &it, TString const &pattern, TSize &lcp); // "projects/library/seqan/index/index_esa_stree.h"(1200)
2007 //____________________________________________________________________________
2010 template <typename TText, typename TSpec, typename TSpecFinder > inline void goEnd(Finder< Index<TText, TSpec>, TSpecFinder > & me); // "projects/library/seqan/index/index_find.h"(206)
2011 template <typename TText, typename TIndexSpec, class TSpec > inline void goEnd(Iter<Index<TText, Index_ESA<TIndexSpec> >, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(938)
2012 template <typename TText, typename TIndexSpec, class TSpec > inline void goEnd(Iter<Index<TText, Index_ESA<TIndexSpec> >, VSTree< BottomUp<TSpec> > > &it); // "projects/library/seqan/index/index_esa_stree.h"(945)
2013 template <typename TRepeat > inline Iter<TRepeat, MaxRepeatOccurrences> & goEnd(Iter<TRepeat, MaxRepeatOccurrences> &it); // "projects/library/seqan/index/index_esa_algs.h"(819)
2015 //____________________________________________________________________________
2018 template <typename TIndex, typename TSpec > inline void goNext(Iter<TIndex, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(956)
2019 template <typename TIndex, typename TSpec, typename TTraits > inline void goNext(Iter<TIndex, VSTree<TSpec> > &it, TTraits const traits); // "projects/library/seqan/index/index_esa_stree.h"(961)
2020 template <typename TSTree > inline void goNext(Iter< TSTree, VSTree< BottomUp<SuperMaxRepeats> > > &it); // "projects/library/seqan/index/index_esa_algs.h"(96)
2021 template <typename TText, typename TSpec > inline void goNext(Iter< Index<TText, Index_ESA<TSpec> >, VSTree< BottomUp<SuperMaxRepeatsFast> > > &it); // "projects/library/seqan/index/index_esa_algs.h"(187)
2022 template <typename TSTree, typename TSpec > inline void goNext(Iter< TSTree, VSTree< BottomUp<_MaxRepeats<TSpec> > > > &it); // "projects/library/seqan/index/index_esa_algs.h"(533)
2023 template <typename TRepeat > inline Iter<TRepeat, MaxRepeatOccurrences> & goNext(Iter<TRepeat, MaxRepeatOccurrences> &it); // "projects/library/seqan/index/index_esa_algs.h"(793)
2024 template <typename TSTree > inline void goNext(Iter< TSTree, VSTree< BottomUp<MUMs> > > &it); // "projects/library/seqan/index/index_esa_algs_multi.h"(100)
2025 template <typename TRepeat > inline Iter<TRepeat, MultiMEMOccurences> & goNext(Iter<TRepeat, MultiMEMOccurences> &it); // "projects/library/seqan/index/index_esa_algs_multi.h"(630)
2027 //____________________________________________________________________________
2030 template <typename TIndex, typename TSpec, typename THideEmptyEdges > inline void goNextImpl( Iter<TIndex, VSTree< BottomUp<TSpec> > > &it, VSTreeIteratorTraits<_Postorder, THideEmptyEdges> const); // "projects/library/seqan/index/index_esa_stree.h"(284)
2031 template <typename TIndex, typename TSpec, typename THideEmptyEdges > inline void goNextImpl( Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it, VSTreeIteratorTraits<_Preorder, THideEmptyEdges> const); // "projects/library/seqan/index/index_esa_stree.h"(1405)
2032 template <typename TIndex, typename TSpec, typename THideEmptyEdges > inline void goNextImpl( Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it, VSTreeIteratorTraits<_Postorder, THideEmptyEdges> const); // "projects/library/seqan/index/index_esa_stree.h"(1421)
2034 //____________________________________________________________________________
2037 template <typename TIndex, class TSpec > inline bool goRight(Iter< TIndex, VSTree< TopDown<TSpec> > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1316)
2039 //____________________________________________________________________________
2042 template <typename TText, typename TSpec > inline void goRoot(Iter< Index<TText, Index_Wotd<WotdOriginal> >, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_wotd.h"(454)
2043 template <typename TText, typename TIndexSpec, typename TSpec > inline void goRoot(Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_wotd.h"(466)
2044 template <typename TText, typename TIndexSpec, class TSpec > inline void goRoot(Iter<Index<TText, TIndexSpec>, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(865)
2046 //____________________________________________________________________________
2049 template <typename TIndex, class TSpec > inline bool goUp(Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1244)
2051 //____________________________________________________________________________
2054 template <typename TValue, typename TIter> inline typename Value< Shape<TValue, GappedShape> >::Type hash(Shape<TValue, GappedShape> &me, TIter it); // "projects/library/seqan/index/shape_gapped.h"(368)
2055 template <typename TValue, typename TSpec, typename TIter, typename TSize> inline typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type hash(Shape<TValue, FixedGappedShape<TSpec> > &me, TIter it, TSize charsLeft); // "projects/library/seqan/index/shape_gapped.h"(385)
2056 template <int P00, int P01, int P02, int P03, int P04, int P05, int P06, int P07, int P08, int P09, int P10, int P11, int P12, int P13, int P14, int P15, int P16, int P17, int P18, int P19, typename TValue, typename TIter > inline typename Value< Shape<TValue, FixedGappedShape< HardwiredShape< P00,P01,P02,P03,P04, P05,P06,P07,P08,P09, P10,P11,P12,P13,P14, P15,P16,P17,P18,P19 > > > >::Type hash(Shape<TValue, FixedGappedShape< HardwiredShape< P00,P01,P02,P03,P04, P05,P06,P07,P08,P09, P10,P11,P12,P13,P14, P15,P16,P17,P18,P19 > > > &me, TIter it); // "projects/library/seqan/index/shape_gapped.h"(517)
2057 template <typename TValue, typename TIter> typename Value< Shape<TValue, SimpleShape> >::Type hash(Shape<TValue, SimpleShape> &me, TIter it); // "projects/library/seqan/index/shape_base.h"(271)
2058 template <typename TValue, unsigned q, typename TIter> inline typename Value< Shape<TValue, FixedShape<q> > >::Type hash(Shape<TValue, FixedShape<q> > &me, TIter it); // "projects/library/seqan/index/shape_base.h"(307)
2059 template <typename TValue, typename TSpec, typename TIter, typename TSize> inline typename Value< Shape<TValue, TSpec> >::Type hash(Shape<TValue, TSpec> &me, TIter it, TSize charsLeft); // "projects/library/seqan/index/shape_base.h"(320)
2060 template <typename TValue, typename TTValue, unsigned SIZE, unsigned q> typename Value< Shape<TValue, FixedShape<q> > >::Type hash( Shape<TValue, FixedShape<q> > &me, Tuple<TTValue, SIZE, Compressed> const &tuple); // "projects/library/seqan/index/shape_base.h"(379)
2061 template <typename TValue, typename TTValue, unsigned SIZE, typename TCompressed, unsigned q> typename Value< Shape<TValue, FixedShape<q> > >::Type hash( Shape<TValue, FixedShape<q> > &me, Tuple<TTValue, SIZE, TCompressed> const &tuple); // "projects/library/seqan/index/shape_base.h"(400)
2063 //____________________________________________________________________________
2066 template <typename TValue, typename TSpec, typename TIter, typename TSize> inline typename Value< Shape<TValue, TSpec> >::Type hash2(Shape<TValue, TSpec> &me, TIter it, TSize charsLeft); // "projects/library/seqan/index/shape_base.h"(490)
2068 //____________________________________________________________________________
2071 template <typename TValue, typename TSpec, typename TIter, typename TSize> inline typename Value< Shape<TValue, TSpec> >::Type hash2Next(Shape<TValue, TSpec> &me, TIter &it, TSize charsLeft); // "projects/library/seqan/index/shape_base.h"(568)
2073 //____________________________________________________________________________
2076 template <typename TValue, typename TSpec, typename TIter, typename TSize> inline typename Value< Shape<TValue, TSpec> >::Type hash2Upper(Shape<TValue, TSpec> &me, TIter it, TSize charsLeft); // "projects/library/seqan/index/shape_base.h"(519)
2078 //____________________________________________________________________________
2081 template <typename TValue, typename TSpec, typename TIter> inline typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type hashNext(Shape<TValue, FixedGappedShape<TSpec> > &me, TIter it); // "projects/library/seqan/index/shape_gapped.h"(536)
2082 template <typename TValue, typename TSpec, typename TIter> inline typename Value< Shape<TValue, TSpec> >::Type hashNext(Shape<TValue, TSpec> &me, TIter &it); // "projects/library/seqan/index/shape_base.h"(463)
2084 //____________________________________________________________________________
2087 template <typename TValue, typename TSpec, typename TIter, typename TSize> inline typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type hashUpper(Shape<TValue, FixedGappedShape<TSpec> > &me, TIter it, TSize charsLeft); // "projects/library/seqan/index/shape_gapped.h"(413)
2088 template <typename TValue, typename TSpec, typename TIter, typename TSize> inline typename Value< Shape<TValue, TSpec> >::Type hashUpper(Shape<TValue, TSpec> &me, TIter it, TSize charsLeft); // "projects/library/seqan/index/shape_base.h"(422)
2090 //____________________________________________________________________________
2093 template <typename TText, typename TSpec, typename TSpecFinder > inline typename _Parameter< Index<TText, TSpec> >::Type host(Finder< Index<TText, TSpec>, TSpecFinder > & me); // "projects/library/seqan/index/index_find.h"(84)
2094 template <typename TText, typename TSpec, typename TSpecFinder > inline typename _Parameter< Index<TText, TSpec> >::Type host(Finder< Index<TText, TSpec>, TSpecFinder > const & me); // "projects/library/seqan/index/index_find.h"(92)
2096 //____________________________________________________________________________
2099 template <typename TText, typename TSpec, typename TSpecFinder > inline typename Iterator< typename Fibre<Index<TText, TSpec>, Fibre_SA>::Type, Standard>::Type & hostIterator(Finder< Index<TText, TSpec>, TSpecFinder > & me); // "projects/library/seqan/index/index_find.h"(140)
2100 template <typename TText, typename TSpec, typename TSpecFinder > inline typename Iterator< typename Fibre<Index<TText, TSpec>, Fibre_SA>::Type, Standard>::Type const & hostIterator(Finder< Index<TText, TSpec>, TSpecFinder > const & me); // "projects/library/seqan/index/index_find.h"(148)
2102 //____________________________________________________________________________
2105 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_BWT>::Type & indexBWT(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_base.h"(932)
2106 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_BWT>::Type & indexBWT(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(934)
2108 //____________________________________________________________________________
2111 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_ChildTab>::Type & indexChildTab(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_base.h"(948)
2112 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_ChildTab>::Type & indexChildTab(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(950)
2114 //____________________________________________________________________________
2117 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_Counts>::Type & indexCounts(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_qgram.h"(289)
2118 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_Counts>::Type & indexCounts(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_qgram.h"(294)
2120 //____________________________________________________________________________
2123 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_CountsDir>::Type & indexCountsDir(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_qgram.h"(300)
2124 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_CountsDir>::Type & indexCountsDir(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_qgram.h"(305)
2126 //____________________________________________________________________________
2129 template <typename TText, typename TPredHull, typename TPred> inline bool indexCreate(Index<TText, Index_Wotd<WotdDFI<TPredHull, TPred> > > &index, Wotd_SA const, Default const); // "projects/library/seqan/index/index_dfi.h"(518)
2130 template <typename TText, typename TSpec> inline bool indexCreate(Index<TText, PizzaChili<TSpec> >& me, PizzaChili_Compressed const); // "projects/library/seqan/index/index_pizzachili.h"(278)
2131 template <typename TText, typename TSpec> inline bool indexCreate(Index<TText, Index_Wotd<TSpec> > &index, Wotd_SA const, Default const); // "projects/library/seqan/index/index_wotd.h"(1712)
2132 template <typename TText, typename TSpec, typename TSpecAlg> inline bool indexCreate(Index<TText, TSpec> &index, Fibre_SA, TSpecAlg const alg); // "projects/library/seqan/index/index_shims.h"(498)
2133 template <typename TText, typename TSpec, typename TSpecAlg> inline bool indexCreate(Index<TText, TSpec> &index, Fibre_LCP, TSpecAlg const alg); // "projects/library/seqan/index/index_shims.h"(506)
2134 template <typename TText, typename TSpec, typename TSpecAlg> inline bool indexCreate(Index<TText, TSpec> &index, Fibre_LCPE, TSpecAlg const alg); // "projects/library/seqan/index/index_shims.h"(514)
2135 template <typename TText, typename TSpec> inline bool indexCreate(Index<TText, TSpec> &index, Fibre_BWT, BWT const); // "projects/library/seqan/index/index_shims.h"(523)
2136 template <typename TText, typename TSpec> inline bool indexCreate(Index<TText, TSpec> &index, Fibre_ChildTab, ChildTab const); // "projects/library/seqan/index/index_shims.h"(531)
2137 template <typename TText, typename TSpec, typename TFibre> inline bool indexCreate(Index<TText, TSpec> &index, Tag<TFibre> const fibre); // "projects/library/seqan/index/index_shims.h"(539)
2138 template <typename TText, typename TShapeSpec, typename TSpec> inline bool indexCreate( Index<TText, Index_QGram<TShapeSpec, TSpec> > &index, Fibre_SADir, Default const); // "projects/library/seqan/index/index_qgram.h"(1459)
2139 template <typename TText, typename TShapeSpec, typename TSpec> inline bool indexCreate( Index<TText, Index_QGram<TShapeSpec, TSpec> > &index, Fibre_SA, Default const alg); // "projects/library/seqan/index/index_qgram.h"(1487)
2140 template <typename TText, typename TShapeSpec, typename TSpec> inline bool indexCreate( Index<TText, Index_QGram<TShapeSpec, TSpec> > &index, Fibre_Counts, Default const); // "projects/library/seqan/index/index_qgram.h"(1509)
2142 //____________________________________________________________________________
2145 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_Dir>::Type & indexDir(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_qgram.h"(243)
2146 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_Dir>::Type & indexDir(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_qgram.h"(248)
2148 //____________________________________________________________________________
2151 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_LCP>::Type & indexLCP(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_base.h"(900)
2152 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_LCP>::Type & indexLCP(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(902)
2154 //____________________________________________________________________________
2157 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_LCPE>::Type & indexLCPE(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_base.h"(916)
2158 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_LCPE>::Type & indexLCPE(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(918)
2160 //____________________________________________________________________________
2163 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_RawSA>::Type indexRawSA(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_base.h"(884)
2164 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_RawSA>::Type indexRawSA(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(886)
2166 //____________________________________________________________________________
2169 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_RawText>::Type & indexRawText(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_base.h"(852)
2170 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_RawText>::Type & indexRawText(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(854)
2172 //____________________________________________________________________________
2175 template <typename TText, typename TSpec, typename TFibre> inline bool indexRequire(Index<TText, TSpec> &index, Tag<TFibre> const fibre); // "projects/library/seqan/index/index_shims.h"(581)
2177 //____________________________________________________________________________
2180 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_SA>::Type & indexSA(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_base.h"(868)
2181 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_SA>::Type & indexSA(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(870)
2183 //____________________________________________________________________________
2186 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_Shape>::Type & indexShape(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_qgram.h"(311)
2187 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_Shape>::Type & indexShape(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_qgram.h"(316)
2189 //____________________________________________________________________________
2190 // indexSolveDependencies
2192 template <typename TText, typename TSpec> inline bool indexSolveDependencies(Index<TText, PizzaChili<TSpec> >& me, PizzaChili_Compressed const); // "projects/library/seqan/index/index_pizzachili.h"(242)
2193 template <typename TText, typename TSpec, typename TFibre> inline bool indexSolveDependencies(Index<TText, TSpec> &, Tag<TFibre> const); // "projects/library/seqan/index/index_shims.h"(612)
2194 template <typename TText, typename TSpec> inline bool indexSolveDependencies(Index<TText, TSpec> &index, Fibre_LCP); // "projects/library/seqan/index/index_shims.h"(618)
2195 template <typename TText, typename TSpec> inline bool indexSolveDependencies(Index<TText, TSpec> &index, Fibre_LCPE); // "projects/library/seqan/index/index_shims.h"(624)
2196 template <typename TText, typename TSpec> inline bool indexSolveDependencies(Index<TText, TSpec> &index, Fibre_ChildTab); // "projects/library/seqan/index/index_shims.h"(630)
2197 template <typename TText, typename TSpec> inline bool indexSolveDependencies(Index<TText, TSpec> &index, Fibre_BWT); // "projects/library/seqan/index/index_shims.h"(636)
2199 //____________________________________________________________________________
2202 template <typename TText, typename TSpec> inline bool indexSupplied(Index<TText, PizzaChili<TSpec> >& me, PizzaChili_Compressed const); // "projects/library/seqan/index/index_pizzachili.h"(226)
2203 template <typename TText, typename TSpec> inline bool indexSupplied(Index<TText, PizzaChili<TSpec> >& me, PizzaChili_Text const); // "projects/library/seqan/index/index_pizzachili.h"(233)
2204 template <typename TText, typename TSpec, typename TFibre> inline bool indexSupplied(Index<TText, TSpec> &index, Tag<TFibre> const fibre); // "projects/library/seqan/index/index_shims.h"(560)
2205 template <typename TText, typename TSpec> inline bool indexSupplied(Index<TText, TSpec> &index, Fibre_SADir); // "projects/library/seqan/index/index_qgram.h"(1478)
2207 //____________________________________________________________________________
2210 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, PizzaChili<TSpec> >, PizzaChili_Text>::Type indexText(Index<TText, PizzaChili<TSpec> >& me); // "projects/library/seqan/index/index_pizzachili.h"(194)
2211 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, PizzaChili<TSpec> > const, PizzaChili_Text>::Type indexText(Index<TText, PizzaChili<TSpec> > const& me); // "projects/library/seqan/index/index_pizzachili.h"(201)
2212 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_Text>::Type & indexText(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_base.h"(810)
2213 template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_Text>::Type & indexText(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(812)
2215 //____________________________________________________________________________
2218 template <typename TValue, typename TSpec, typename TPosBegin, typename TPosEnd> inline typename Infix<String<TValue, PizzaChili<TSpec> > >::Type infix( String<TValue, PizzaChili<TSpec> > const& me, TPosBegin begin, TPosEnd end ); // "projects/library/seqan/index/index_pizzachili_string.h"(724)
2219 template <typename TValue, typename TSpec, typename TPosBegin, typename TPosEnd> inline typename Infix<String<TValue, PizzaChili<TSpec> > >::Type infix( String<TValue, PizzaChili<TSpec> >& me, TPosBegin begin, TPosEnd end ); // "projects/library/seqan/index/index_pizzachili_string.h"(735)
2221 //____________________________________________________________________________
2224 template <typename TIndex, class TSpec > inline bool isLeaf(Iter<TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1795)
2226 //____________________________________________________________________________
2229 template <typename TIndex, class TSpec > inline bool isLeftMaximal(Iter<TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1541)
2231 //____________________________________________________________________________
2232 // isPartiallyLeftExtensible
2234 template <typename TIndex, class TSpec, typename TSet > inline bool isPartiallyLeftExtensible(Iter<TIndex, VSTree<TSpec> > const &it, TSet &charSet); // "projects/library/seqan/index/index_esa_stree.h"(1589)
2235 template <typename TIndex, class TSpec > inline bool isPartiallyLeftExtensible(Iter<TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1623)
2237 //____________________________________________________________________________
2240 template <typename TIndex, class TSpec > inline bool isRightTerminal(Iter<TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1518)
2242 //____________________________________________________________________________
2245 template <typename TIndex, class TSpec > inline bool isRoot(Iter<TIndex, VSTree< BottomUp<TSpec> > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1489)
2246 template <typename TIndex, class TSpec > inline bool isRoot(Iter<TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1495)
2248 //____________________________________________________________________________
2251 template <typename TIndex, class TSpec, typename TSet > inline bool isUnique(Iter<TIndex, VSTree<TSpec> > const &it, TSet &set); // "projects/library/seqan/index/index_esa_stree.h"(1641)
2252 template <typename TIndex, class TSpec > inline bool isUnique(Iter<TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1664)
2254 //____________________________________________________________________________
2257 template <typename TIndex, class TSpec1, class TSpec2 > inline bool lca( Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec1> > > > &a, Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec2> > > > &b, Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec1> > > > &_lca); // "projects/library/seqan/index/index_esa_stree.h"(456)
2259 //____________________________________________________________________________
2262 template <typename TIndex, class TSpec1, class TSpec2 > inline typename Size<TIndex>::Type lcp( Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec1> > > > &a, Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec2> > > > &b); // "projects/library/seqan/index/index_esa_stree.h"(507)
2264 //____________________________________________________________________________
2267 template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex, Fibre_LCP>::Type>::Type lcpAt(TPos i, TIndex &index); // "projects/library/seqan/index/index_base.h"(714)
2268 template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex const, Fibre_LCP>::Type>::Type lcpAt(TPos i, TIndex const &index); // "projects/library/seqan/index/index_base.h"(718)
2270 //____________________________________________________________________________
2273 template <typename TTextInput, typename TInvertedSAInput, typename TDest > static void lcp_process(TTextInput &textIn, TInvertedSAInput &invertedSAIn, TDest &dest, LcpConfig conf); // "projects/library/seqan/index/pump_lcp_core.h"(56)
2274 template <typename TTextInput, typename TInvertedSAInput, typename TDest > static inline void lcp_process(TTextInput &textIn, TInvertedSAInput &invertedSAIn, TDest &dest); // "projects/library/seqan/index/pump_lcp_core.h"(196)
2276 //____________________________________________________________________________
2277 // lcp_process_multi
2279 template <typename TTextInput, typename TLimitsString, typename TInvertedSAInput, typename TDest > static void lcp_process_multi( TTextInput &textIn, TLimitsString const &limits, TInvertedSAInput &invertedSAIn, TDest &dest, LcpConfig conf); // "projects/library/seqan/index/pump_lcp_core.h"(208)
2280 template <typename TTextInput, typename TLimitsString, typename TInvertedSAInput, typename TDest > static void lcp_process_multi( TTextInput &textIn, TLimitsString const &limits, TInvertedSAInput &invertedSAIn, TDest &dest); // "projects/library/seqan/index/pump_lcp_core.h"(367)
2282 //____________________________________________________________________________
2285 template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex, Fibre_LCPE>::Type>::Type lcpeAt(TPos i, TIndex &index); // "projects/library/seqan/index/index_base.h"(735)
2286 template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex const, Fibre_LCPE>::Type>::Type lcpeAt(TPos i, TIndex const &index); // "projects/library/seqan/index/index_base.h"(739)
2288 //____________________________________________________________________________
2291 //template <typename TInput > inline typename Size< Pipe< TInput, LarssonSadakane > >::Type length(Pipe< TInput, LarssonSadakane > const &me); // "projects/library/seqan/index/index_sa_lss.h"(421)
2292 template <typename TValue, typename TSpec> inline typename Size<String<TValue, PizzaChili<TSpec> > >::Type length(String<TValue, PizzaChili<TSpec> > const& me); // "projects/library/seqan/index/index_pizzachili_string.h"(379)
2293 template <typename TValue, typename TSpec> inline typename Size< Shape<TValue, TSpec> >::Type length(Shape<TValue, TSpec> const &me); // "projects/library/seqan/index/shape_base.h"(215)
2294 template <typename TText, typename TSpec> inline typename Size<Index<TText, TSpec> >::Type length(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(601)
2295 template <typename TSTree, typename TSpec > inline typename Size<TSTree>::Type length(Iter< TSTree, VSTree< BottomUp<_MaxRepeats<TSpec> > > > const &it); // "projects/library/seqan/index/index_esa_algs.h"(570)
2296 template <typename TSTree> inline typename Size< MaxRepeat<TSTree> >::Type length(MaxRepeat<TSTree> const &repeat); // "projects/library/seqan/index/index_esa_algs.h"(619)
2297 template <typename TSTree> inline typename Size< MultiMEM<TSTree> >::Type length(MultiMEM<TSTree> const &repeat); // "projects/library/seqan/index/index_esa_algs_multi.h"(402)
2298 //template <typename TInput > inline typename Size< Pipe< TInput, Merger3 > >::Type length(Pipe< TInput, Merger3 > const &me); // "projects/library/seqan/index/pipe_merger3.h"(145)
2299 //template <typename TInput > inline typename Size< Pipe< TInput, Merger7 > >::Type length(Pipe< TInput, Merger7 > const &me); // "projects/library/seqan/index/pipe_merger7.h"(494)
2300 //template <typename TInput, typename TLimitsString > inline typename Size< Pipe< TInput, Merger7Multi<TLimitsString> > >::Type length(Pipe< TInput, Merger7Multi<TLimitsString> > const &me); // "projects/library/seqan/index/pipe_merger7.h"(524)
2302 //____________________________________________________________________________
2305 template <typename TText, typename TSA, typename TLCPE, typename TQuery > inline typename Position<TLCPE>::Type lowerBoundLCPE( TText const &text, TSA const &sa, TLCPE const &lcpe, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(1554)
2306 template <typename TText, typename TSA, typename TLCPE, typename TQuery > inline typename Position<TLCPE>::Type lowerBoundLCPE( TText const &text, TSA const &sa, TLCPE const &lcpe, TQuery *query); // "projects/library/seqan/index/index_esa_find.h"(1656)
2308 //____________________________________________________________________________
2309 // lowerBoundLCPEIterator
2311 template <typename TText, typename TSA, typename TLCPE, typename TQuery > inline typename Iterator<TSA, Standard>::Type lowerBoundLCPEIterator( TText const &text, TSA const &sa, TLCPE const &lcpe, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(1605)
2313 //____________________________________________________________________________
2316 template <typename TText, typename TSA, typename TQuery, typename TFlatTreeSpec > inline typename Position<TSA>::Type lowerBoundSA( TText const &text, TSA const &sa, TQuery const &query, TFlatTreeSpec const); // "projects/library/seqan/index/index_esa_find.h"(793)
2317 template <typename TText, typename TSA, typename TQuery > inline typename Position<TSA>::Type lowerBoundSA( TText const &text, TSA const &sa, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(807)
2318 template <typename TText, typename TSA, typename TQuery, typename TFlatTreeSpec > inline typename Position<TSA>::Type lowerBoundSA( TText const &text, TSA const &sa, TQuery *query, TFlatTreeSpec const); // "projects/library/seqan/index/index_esa_find.h"(890)
2319 template <typename TText, typename TSA, typename TQuery > inline typename Position<TSA>::Type lowerBoundSA( TText const &text, TSA const &sa, TQuery *query); // "projects/library/seqan/index/index_esa_find.h"(904)
2321 //____________________________________________________________________________
2322 // lowerBoundSAIterator
2324 template <typename TText, typename TSA, typename TQuery > inline typename Iterator<TSA const, Standard>::Type lowerBoundSAIterator( TText const &text, TSA const &sa, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(699)
2325 template <typename TText, typename TSA, typename TQuery > inline typename Iterator<TSA const, Standard>::Type lowerBoundSAIterator( TText const &text, TSA const &sa, TQuery *query); // "projects/library/seqan/index/index_esa_find.h"(745)
2327 //____________________________________________________________________________
2330 template <typename TIndex, typename TSpec > inline typename Size<TIndex>::Type nodeDepth(Iter< TIndex, VSTree<TopDown<ParentLinks<TSpec> > > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(390)
2332 //____________________________________________________________________________
2333 // nodeHullPredicate
2335 template <typename TText, typename TPredHull, typename TPred, typename TSpec > inline bool nodeHullPredicate( Iter<Index<TText, Index_Wotd< WotdDFI<TPredHull, TPred> > >, TSpec> const &it); // "projects/library/seqan/index/index_dfi.h"(158)
2336 template <typename TIndex, class TSpec > inline bool nodeHullPredicate(Iter<TIndex, TSpec> &); // "projects/library/seqan/index/index_esa_stree.h"(857)
2337 template <typename TText, typename TSpec> bool nodeHullPredicate(Iter<Index<TText, Index_Wotd<TRepeatFinder> >, TSpec> &it); // "projects/library/seqan/index/repeat_base.h"(75)
2339 //____________________________________________________________________________
2342 template <typename TText, typename TPredHull, typename TPred, typename TSpec > inline bool nodePredicate( Iter<Index<TText, Index_Wotd< WotdDFI<TPredHull, TPred> > >, TSpec> const &it); // "projects/library/seqan/index/index_dfi.h"(145)
2343 template <typename TIndex, class TSpec > inline bool nodePredicate(Iter<TIndex, TSpec> &); // "projects/library/seqan/index/index_esa_stree.h"(839)
2344 template <typename TText, typename TSpec> bool nodePredicate(Iter<Index<TText, Index_Wotd<TRepeatFinder> >, TSpec> &it); // "projects/library/seqan/index/repeat_base.h"(67)
2346 //____________________________________________________________________________
2349 template <typename TIndex, class TSpec > inline typename VertexDescriptor<TIndex>::Type nodeUp(Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1256)
2350 template <typename TIndex, class TSpec > inline typename VertexDescriptor<TIndex>::Type const & nodeUp(Iter< TIndex, VSTree< TopDown<TSpec> > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1271)
2352 //____________________________________________________________________________
2355 template <typename TObject, typename TSpec > inline bool open( Index< TObject, Index_ESA<TSpec> > &index, const char *fileName, int openMode); // "projects/library/seqan/index/index_esa_base.h"(324)
2356 template <typename TObject, typename TSpec > inline bool open( Index< TObject, Index_ESA<TSpec> > &index, const char *fileName); // "projects/library/seqan/index/index_esa_base.h"(340)
2357 template <typename TText, typename TSpec> inline bool open( Index<TText, PizzaChili<TSpec> >& me, char const* filename ); // "projects/library/seqan/index/index_pizzachili.h"(334)
2358 template <typename TValue, typename TSpec > inline bool open(String<TValue, TSpec> &string, const char *fileName, int openMode); // "projects/library/seqan/index/index_shims.h"(646)
2359 template <typename TValue, typename TSpec > inline bool open(String<TValue, TSpec> &string, const char *fileName); // "projects/library/seqan/index/index_shims.h"(654)
2360 template <typename THost, typename TSpec > inline bool open(Segment<THost, TSpec> &string, const char *fileName, int openMode); // "projects/library/seqan/index/index_shims.h"(660)
2361 template <typename THost, typename TSpec > inline bool open(Segment<THost, TSpec> &string, const char *fileName); // "projects/library/seqan/index/index_shims.h"(668)
2362 template <typename TValue, typename TSpec, typename TSSSpec > inline bool open(StringSet<String<TValue, TSpec>, TSSSpec> &multi, const char *fileName, int openMode); // "projects/library/seqan/index/index_shims.h"(674)
2363 template <typename TValue, typename TSpec, typename TSSSpec> inline bool open(StringSet<String<TValue, TSpec>, TSSSpec> &multi, const char *fileName); // "projects/library/seqan/index/index_shims.h"(694)
2364 template <typename TObject, typename TShapeSpec, typename TSpec > inline bool open( Index< TObject, Index_QGram<TShapeSpec, TSpec> > &index, const char *fileName, int openMode); // "projects/library/seqan/index/index_qgram.h"(1755)
2365 template <typename TObject, typename TShapeSpec, typename TSpec > inline bool open( Index< TObject, Index_QGram<TShapeSpec, TSpec> > &index, const char *fileName); // "projects/library/seqan/index/index_qgram.h"(1769)
2367 //____________________________________________________________________________
2370 template <typename TRepeat > inline bool operator!= ( Iter<TRepeat, MaxRepeatOccurrences> const &itA, Iter<TRepeat, MaxRepeatOccurrences> const &itB); // "projects/library/seqan/index/index_esa_algs.h"(851)
2372 //____________________________________________________________________________
2375 //template <typename TInput, typename TObject, typename TPair, typename TLimitsString > inline bool operator<<(Pipe< TInput, Multi<Skew7, TPair, TLimitsString> > &me, TObject &textIn); // "projects/library/seqan/index/index_skew7_multi.h"(404)
2376 //template <typename TInput, typename _TLCPInput > inline bool operator<<(Pipe< TInput, ChildTab > &me, _TLCPInput const &in); // "projects/library/seqan/index/index_childtab.h"(162)
2377 //template <typename TInput, typename _TTextInput, typename _TSuffixArrayInput > inline bool operator<<(Pipe< TInput, Kasai > &me, Bundle2< _TTextInput, _TSuffixArrayInput > const &bundleIn); // "projects/library/seqan/index/index_lcp.h"(131)
2378 //template <typename TInput, typename _TTextInput, typename _TSuffixArrayInput, typename TPair, typename TLimitsString > inline bool operator<<(Pipe< TInput, Multi<Kasai, TPair, TLimitsString> > &me, Bundle2< _TTextInput, _TSuffixArrayInput > const &bundleIn); // "projects/library/seqan/index/index_lcp.h"(234)
2379 //template <typename TInput, typename TObject > inline bool operator<<(Pipe< TInput, Skew3 > &me, TObject &textIn); // "projects/library/seqan/index/index_skew3.h"(285)
2380 //template <typename TInput, typename _TTextInput, typename _TSuffixArrayInput > inline bool operator<<(Pipe< TInput, BWT > &me, Bundle2< _TTextInput, _TSuffixArrayInput > const &bundleIn); // "projects/library/seqan/index/index_bwt.h"(113)
2381 //template <typename TInput, typename _TTextInput, typename _TSuffixArrayInput, typename TPair, typename TLimitsString > inline bool operator<<(Pipe< TInput, Multi<BWT, TPair, TLimitsString> > &me, Bundle2< _TTextInput, _TSuffixArrayInput > const &bundleIn); // "projects/library/seqan/index/index_bwt.h"(229)
2382 //template <typename TValue> std::ostream& operator<<(std::ostream &out, const SkewDCStream<TValue> &s); // "projects/library/seqan/index/pipe_merger7.h"(77)
2383 //template <typename TInput, typename TObject > inline bool operator<<(Pipe< TInput, Skew7 > &me, TObject &textIn); // "projects/library/seqan/index/index_skew7.h"(385)
2385 //____________________________________________________________________________
2388 template <typename TRepeat > inline bool operator== ( Iter<TRepeat, MaxRepeatOccurrences> const &itA, Iter<TRepeat, MaxRepeatOccurrences> const &itB); // "projects/library/seqan/index/index_esa_algs.h"(840)
2390 //____________________________________________________________________________
2393 template <typename TValue, typename TSpec> inline void orderOccurrences(String<TValue, TSpec> &occString); // "projects/library/seqan/index/index_shims.h"(474)
2395 //____________________________________________________________________________
2396 // parentEdgeFirstChar
2398 template <typename TIndex, class TSpec > inline typename Value<TIndex>::Type parentEdgeFirstChar(Iter< TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1377)
2400 //____________________________________________________________________________
2403 template <typename TText, typename TSpec > inline typename Infix< typename Fibre<Index<TText, Index_Wotd<WotdOriginal> >, ESA_RawText>::Type const >::Type parentEdgeLabel(Iter< Index<TText, Index_Wotd<WotdOriginal> >, VSTree< TopDown<TSpec> > > const &it); // "projects/library/seqan/index/index_wotd.h"(401)
2404 template <typename TIndex, class TSpec > inline typename Infix< typename Fibre<TIndex, Fibre_Text>::Type const >::Type parentEdgeLabel(Iter< TIndex, VSTree< TopDown<TSpec> > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1357)
2406 //____________________________________________________________________________
2409 template <typename TIndex, typename TSize > inline typename Size<TIndex>::Type parentEdgeLength(TIndex const &index, _VertexWotdOriginal<TSize> &vDesc); // "projects/library/seqan/index/index_wotd.h"(309)
2410 template <typename TIndex, typename TSize > inline typename Size<TIndex>::Type parentEdgeLength(TIndex const &index, _VertexWotdModified<TSize> &vDesc); // "projects/library/seqan/index/index_wotd.h"(332)
2411 template <typename TText, typename TIndexSpec, typename TSpec > inline typename Size< Index<TText, Index_Wotd<TIndexSpec> > >::Type parentEdgeLength(Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > const &it); // "projects/library/seqan/index/index_wotd.h"(364)
2412 template <typename TText, class TIndexSpec, class TSpec > inline typename Size< Index<TText, Index_ESA<TIndexSpec> > >::Type parentEdgeLength(Iter< Index<TText, Index_ESA<TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1339)
2414 //____________________________________________________________________________
2417 template <typename TText, typename TIndexSpec, typename TSpec > inline typename Size< Index<TText, Index_Wotd<TIndexSpec> > >::Type parentRepLength(Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > const &it); // "projects/library/seqan/index/index_wotd.h"(374)
2418 template <typename TText, typename TIndexSpec, typename TSpec > inline typename Size< Index<TText, Index_Wotd<TIndexSpec> > >::Type parentRepLength(Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > const &it); // "projects/library/seqan/index/index_wotd.h"(383)
2419 template <typename TIndex, typename TSpec > inline typename Size<TIndex>::Type parentRepLength(Iter< TIndex, VSTree<TopDown<TSpec> > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(408)
2421 //____________________________________________________________________________
2424 template <typename TText, typename TSpec, typename TSpecFinder > inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type position(Finder< Index<TText, TSpec>, TSpecFinder > & me); // "projects/library/seqan/index/index_find.h"(226)
2425 template <typename TText, typename TSpec, typename TSpecFinder > inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type position(Finder< Index<TText, TSpec>, TSpecFinder > const & me); // "projects/library/seqan/index/index_find.h"(235)
2427 //____________________________________________________________________________
2430 template <typename TValue, typename TSpec, typename TPos> inline typename Prefix<String<TValue, PizzaChili<TSpec> > >::Type prefix( String<TValue, PizzaChili<TSpec> > const& me, TPos end ); // "projects/library/seqan/index/index_pizzachili_string.h"(747)
2431 template <typename TValue, typename TSpec, typename TPos> inline typename Prefix<String<TValue, PizzaChili<TSpec> > >::Type prefix( String<TValue, PizzaChili<TSpec> >& me, TPos end ); // "projects/library/seqan/index/index_pizzachili_string.h"(757)
2433 //____________________________________________________________________________
2436 template <typename TSortedArray, typename TUnsortedArray, typename TCountArray, typename TText > void radixExtend( TSortedArray &b, TUnsortedArray const &a, TText const &r, TCountArray &c, unsigned K); // "projects/library/seqan/index/radix.h"(118)
2438 //____________________________________________________________________________
2441 template <typename TSortedArray, typename TUnsortedArray, typename TCountArray, typename TText > void radixExtendClip( TSortedArray &b, TUnsortedArray const &a, TText const &r, TCountArray &c, unsigned K); // "projects/library/seqan/index/radix.h"(153)
2443 //____________________________________________________________________________
2446 template <typename TSortedArray, typename TUnsortedArray, typename TCountArray, typename TText > void radixPass( TSortedArray &b, TUnsortedArray const &a, TText const &r, TCountArray &c, unsigned K); // "projects/library/seqan/index/radix.h"(39)
2447 template <typename TSortedArray, typename TUnsortedArray, typename TCountArray, typename TText, typename TShift > void radixPass( TSortedArray &b, TUnsortedArray const &a, TText const &r, TCountArray &c, unsigned K, TShift shift); // "projects/library/seqan/index/radix.h"(75)
2449 //____________________________________________________________________________
2452 template <typename TPos, typename TIndex> inline typename Value<typename Fibre<TIndex const, Fibre_RawSA>::Type>::Type rawsaAt(TPos i, TIndex const &index); // "projects/library/seqan/index/index_base.h"(696)
2454 //____________________________________________________________________________
2457 template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex, Fibre_RawText>::Type>::Type rawtextAt(TPos i, TIndex &index); // "projects/library/seqan/index/index_base.h"(666)
2458 template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex const, Fibre_RawText>::Type>::Type rawtextAt(TPos i, TIndex const &index); // "projects/library/seqan/index/index_base.h"(670)
2460 //____________________________________________________________________________
2463 template <typename TText, typename TIndexSpec, typename TSpec > inline typename Size< Index<TText, Index_Wotd<TIndexSpec> > >::Type repLength(Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > const &it); // "projects/library/seqan/index/index_wotd.h"(392)
2464 template <typename TIndex, typename TSpec > inline typename Size<TIndex>::Type repLength(Iter< TIndex, VSTree<BottomUp<TSpec> > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(355)
2465 template <typename TIndex, typename TSize > inline typename Size<TIndex>::Type repLength(TIndex const &index, VertexESA<TSize> const &vDesc); // "projects/library/seqan/index/index_esa_stree.h"(367)
2466 template <typename TIndex, typename TSpec > inline typename Size<TIndex>::Type repLength(Iter< TIndex, VSTree<TopDown<TSpec> > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(383)
2467 template <typename TSTree, typename TSpec > inline typename Size<TSTree>::Type repLength(Iter< TSTree, VSTree< BottomUp<_MaxRepeats<TSpec> > > > const &it); // "projects/library/seqan/index/index_esa_algs.h"(562)
2469 //____________________________________________________________________________
2472 template <typename TIndex, class TSpec > inline typename Infix< typename Fibre<TIndex, Fibre_Text>::Type const >::Type representative(Iter< TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(744)
2474 //____________________________________________________________________________
2477 template <typename TValue, typename TSize> inline typename Size< Shape<TValue, SimpleShape> >::Type resize(Shape<TValue, SimpleShape> & me, TSize new_length); // "projects/library/seqan/index/shape_base.h"(246)
2479 //____________________________________________________________________________
2482 template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex, Fibre_SA>::Type>::Type saAt(TPos i, TIndex &index); // "projects/library/seqan/index/index_base.h"(687)
2483 template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex const, Fibre_SA>::Type>::Type saAt(TPos i, TIndex const &index); // "projects/library/seqan/index/index_base.h"(691)
2485 //____________________________________________________________________________
2488 template <typename TObject, typename TSpec > inline bool save( Index< TObject, Index_ESA<TSpec> > &index, const char *fileName, int openMode); // "projects/library/seqan/index/index_esa_base.h"(353)
2489 template <typename TObject, typename TSpec > inline bool save( Index< TObject, Index_ESA<TSpec> > &index, const char *fileName); // "projects/library/seqan/index/index_esa_base.h"(369)
2490 template <typename TText, typename TSpec> inline bool save( Index<TText, PizzaChili<TSpec> >& me, char const* filename ); // "projects/library/seqan/index/index_pizzachili.h"(352)
2491 template <typename TValue, typename TSpec > inline bool save(String<TValue, TSpec> const &string, const char *fileName, int openMode); // "projects/library/seqan/index/index_shims.h"(704)
2492 template <typename TValue, typename TSpec > inline bool save(String<TValue, TSpec> &string, const char *fileName); // "projects/library/seqan/index/index_shims.h"(714)
2493 template <typename THost, typename TSpec > inline bool save(Segment<THost, TSpec> const &string, const char *fileName, int openMode); // "projects/library/seqan/index/index_shims.h"(720)
2494 template <typename THost, typename TSpec > inline bool save(Segment<THost, TSpec> const &string, const char *fileName); // "projects/library/seqan/index/index_shims.h"(729)
2495 template <typename TValue, typename TSpec, typename TSSSpec> inline bool save(StringSet<String<TValue, TSpec>, TSSSpec> const &multi, const char *fileName, int openMode); // "projects/library/seqan/index/index_shims.h"(735)
2496 template <typename TValue, typename TSpec, typename TSSSpec> inline bool save(StringSet<String<TValue, TSpec>, TSSSpec> const &multi, const char *fileName); // "projects/library/seqan/index/index_shims.h"(750)
2497 template <typename TObject, typename TShapeSpec, typename TSpec > inline bool save( Index< TObject, Index_QGram<TShapeSpec, TSpec> > &index, const char *fileName, int openMode); // "projects/library/seqan/index/index_qgram.h"(1782)
2498 template <typename TObject, typename TShapeSpec, typename TSpec > inline bool save( Index< TObject, Index_QGram<TShapeSpec, TSpec> > &index, const char *fileName); // "projects/library/seqan/index/index_qgram.h"(1796)
2500 //____________________________________________________________________________
2503 template <typename TSeqNo, typename TText, typename TSpec> inline typename Size<Index<TText, TSpec> >::Type sequenceLength(TSeqNo seqNo, Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(617)
2505 //____________________________________________________________________________
2508 template <typename TText, typename TSpec, typename TSpecFinder > inline void setContainer( Finder< Index<TText, TSpec>, TSpecFinder > & me, typename _Parameter<Index<TText, TSpec> >::Type container_); // "projects/library/seqan/index/index_find.h"(130)
2510 //____________________________________________________________________________
2513 template <typename TText, typename TSpec, typename TSpecFinder > inline void setHost( Finder< Index<TText, TSpec>, TSpecFinder > & me, typename _Parameter<Index<TText, TSpec> >::Type container_); // "projects/library/seqan/index/index_find.h"(120)
2515 //____________________________________________________________________________
2518 template <typename TText, typename TSpec, typename TOtherText> inline void setIndexText(Index<TText, PizzaChili<TSpec> >& me, TOtherText& text); // "projects/library/seqan/index/index_pizzachili.h"(303)
2520 //____________________________________________________________________________
2523 template <typename TSize > inline TSize sizeofLCPE(TSize n); // "projects/library/seqan/index/index_lcp_tree.h"(105)
2524 template <class LCPFwdIt, typename TSize > inline void sizeofLCPE(LCPFwdIt _First, LCPFwdIt _Last, TSize &_Size); // "projects/library/seqan/index/index_lcp_tree.h"(124)
2526 //____________________________________________________________________________
2529 template <typename TSize > inline TSize sizeofLCPH(TSize n); // "projects/library/seqan/index/index_lcp_tree.h"(116)
2530 template <class LCPFwdIt, typename TSize > inline void sizeofLCPH(LCPFwdIt _First, LCPFwdIt _Last, TSize &_Size); // "projects/library/seqan/index/index_lcp_tree.h"(132)
2532 //____________________________________________________________________________
2535 template <typename TSize > inline TSize sizeofSAB(TSize n, unsigned BlockSize); // "projects/library/seqan/index/index_sa_btree.h"(79)
2536 template <class SAFwdIt, typename TSize > inline void sizeofSAB(SAFwdIt _First, SAFwdIt _Last, TSize &_Size, unsigned BlockSize); // "projects/library/seqan/index/index_sa_btree.h"(90)
2538 //____________________________________________________________________________
2541 template <typename TTextInput, typename TNameInput, typename TOut0, typename TOut12 > static bool skew3_extend(TTextInput &textIn, TNameInput &nameIn, TOut0 &out0, TOut12 &out12); // "projects/library/seqan/index/pump_extender3.h"(54)
2543 //____________________________________________________________________________
2546 template <typename TTextInput, typename TNameInput, typename TOut0, typename TOut3, typename TOut5, typename TOut6, typename TOut124 > static bool skew7_extend(TTextInput &textIn, TNameInput &nameIn, TOut0 &out0, TOut3 &out3, TOut5 &out5, TOut6 &out6, TOut124 &out124); // "projects/library/seqan/index/pump_extender7.h"(75)
2548 //____________________________________________________________________________
2549 // skew7_extend_multi
2551 template <typename TTextInput, typename TLimitsString, typename TNameInput, typename TOut0, typename TOut3, typename TOut5, typename TOut6, typename TOut124 > static bool skew7_extend_multi( TTextInput &textIn, TLimitsString const &limits, TNameInput &nameIn1, TNameInput &nameIn2, TNameInput &nameIn4, TOut0 &out0, TOut3 &out3, TOut5 &out5, TOut6 &out6, TOut124 &out124); // "projects/library/seqan/index/pump_extender7.h"(265)
2553 //____________________________________________________________________________
2554 // skew7_separate_slices
2556 template <typename TInput, typename TFunctor, typename TOut1, typename TOut2, typename TOut4 > static void skew7_separate_slices( TInput &in, TFunctor const &funcSlice, TOut1 &out1, TOut2 &out2, TOut4 &out4); // "projects/library/seqan/index/pump_separator7.h"(35)
2558 //____________________________________________________________________________
2561 template <typename TText, typename TSpec> inline typename StringSetLimits<TText const>::Type stringSetLimits(Index<TText, TSpec> &); // "projects/library/seqan/index/index_base.h"(818)
2562 template <typename TText, typename TSpec> inline typename StringSetLimits<TText const>::Type stringSetLimits(Index<TText, TSpec> const &); // "projects/library/seqan/index/index_base.h"(824)
2563 template <typename TString, typename TSSetSpec, typename TSpec> inline typename StringSetLimits< StringSet<TString, TSSetSpec> const >::Type & stringSetLimits(Index<StringSet<TString, TSSetSpec>, TSpec> &index); // "projects/library/seqan/index/index_base.h"(830)
2564 template <typename TString, typename TSSetSpec, typename TSpec> inline typename StringSetLimits< StringSet<TString, TSSetSpec> const >::Type & stringSetLimits(Index<StringSet<TString, TSSetSpec>, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(836)
2566 //____________________________________________________________________________
2569 template <typename TValue, typename TSpec, typename TShapeString> inline void stringToShape( Shape<TValue, FixedGappedShape<TSpec> > &me, TShapeString const &bitmap); // "projects/library/seqan/index/shape_gapped.h"(561)
2571 //____________________________________________________________________________
2574 template <typename TValue, typename TSpec, typename TPos> inline typename Suffix<String<TValue, PizzaChili<TSpec> > >::Type suffix( String<TValue, PizzaChili<TSpec> > const& me, TPos begin ); // "projects/library/seqan/index/index_pizzachili_string.h"(769)
2575 template <typename TValue, typename TSpec, typename TPos> inline typename Suffix<String<TValue, PizzaChili<TSpec> > >::Type suffix( String<TValue, PizzaChili<TSpec> >& me, TPos begin ); // "projects/library/seqan/index/index_pizzachili_string.h"(779)
2577 //____________________________________________________________________________
2580 template <typename TPos, typename TText, typename TSpec> inline typename Size<Index<TText, TSpec> >::Type suffixLength(TPos pos, Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(625)
2582 //____________________________________________________________________________
2585 template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex, Fibre_RawText>::Type>::Type textAt(TPos i, TIndex &index); // "projects/library/seqan/index/index_base.h"(635)
2586 template <typename TPos, typename TString, typename TSSetSpec, typename TSpec> inline typename Reference<typename Fibre< Index< StringSet<TString, TSSetSpec>, TSpec>, Fibre_RawText>::Type>::Type textAt(TPos i, Index< StringSet<TString, TSSetSpec>, TSpec> &index); // "projects/library/seqan/index/index_base.h"(640)
2587 template <typename TPos, typename TString, typename TSpec> inline typename Reference<typename Fibre< Index< StringSet<TString, Owner<Default> >, TSpec>, Fibre_RawText>::Type>::Type textAt(TPos i, Index< StringSet<TString, Owner<Default> >, TSpec> &index); // "projects/library/seqan/index/index_base.h"(645)
2589 //____________________________________________________________________________
2592 template <typename TSize > inline unsigned treeLevelsSAB(TSize saSize, unsigned BlockSize); // "projects/library/seqan/index/index_sa_btree.h"(103)
2594 //____________________________________________________________________________
2597 template <typename TString, typename THash> inline void unhash(TString &result, THash hash, unsigned q); // "projects/library/seqan/index/shape_base.h"(593)
2599 //____________________________________________________________________________
2602 template <typename TText, typename TSA, typename TLCPE, typename TQuery > inline typename Position<TLCPE>::Type upperBoundLCPE( TText const &text, TSA const &sa, TLCPE const &lcpe, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(1570)
2603 template <typename TText, typename TSA, typename TLCPE, typename TQuery > inline typename Position<TLCPE>::Type upperBoundLCPE( TText const &text, TSA const &sa, TLCPE const &lcpe, TQuery *query); // "projects/library/seqan/index/index_esa_find.h"(1672)
2605 //____________________________________________________________________________
2606 // upperBoundLCPEIterator
2608 template <typename TText, typename TSA, typename TLCPE, typename TQuery > inline typename Iterator<TSA, Standard>::Type upperBoundLCPEIterator( TText const &text, TSA const &sa, TLCPE const &lcpe, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(1621)
2610 //____________________________________________________________________________
2613 template <typename TText, typename TSA, typename TQuery, typename TFlatTreeSpec > inline typename Position<TSA>::Type upperBoundSA( TText const &text, TSA const &sa, TQuery const &query, TFlatTreeSpec const); // "projects/library/seqan/index/index_esa_find.h"(823)
2614 template <typename TText, typename TSA, typename TQuery > inline typename Position<TSA>::Type upperBoundSA( TText const &text, TSA const &sa, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(837)
2615 template <typename TText, typename TSA, typename TQuery, typename TFlatTreeSpec > inline typename Position<TSA>::Type upperBoundSA( TText const &text, TSA const &sa, TQuery *query, TFlatTreeSpec const); // "projects/library/seqan/index/index_esa_find.h"(920)
2616 template <typename TText, typename TSA, typename TQuery > inline typename Position<TSA>::Type upperBoundSA( TText const &text, TSA const &sa, TQuery *query); // "projects/library/seqan/index/index_esa_find.h"(934)
2618 //____________________________________________________________________________
2619 // upperBoundSAIterator
2621 template <typename TText, typename TSA, typename TQuery > inline typename Iterator<TSA const, Standard>::Type upperBoundSAIterator( TText const &text, TSA const &sa, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(713)
2622 template <typename TText, typename TSA, typename TQuery > inline typename Iterator<TSA const, Standard>::Type upperBoundSAIterator( TText const &text, TSA const &sa, TQuery *query); // "projects/library/seqan/index/index_esa_find.h"(759)
2624 //____________________________________________________________________________
2627 template <typename TValue, typename TSpec> inline typename Value< Shape<TValue, TSpec> >::Type value(Shape<TValue, TSpec> &me); // "projects/library/seqan/index/shape_base.h"(205)
2628 template <typename TIndex, class TSpec > inline typename VertexDescriptor<TIndex>::Type & value(Iter< TIndex, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(557)
2629 template <typename TIndex, class TSpec > inline typename VertexDescriptor<TIndex>::Type const & value(Iter< TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(563)
2630 template <typename TSTree, typename TSpec > inline typename VertexDescriptor<TSTree>::Type value(Iter< TSTree, VSTree< BottomUp<_MaxRepeats<TSpec> > > > const &it); // "projects/library/seqan/index/index_esa_algs.h"(551)
2631 template <typename TRepeat > inline typename Value< Iter<TRepeat, MaxRepeatOccurrences> >::Type & value(Iter<TRepeat, MaxRepeatOccurrences> const &it); // "projects/library/seqan/index/index_esa_algs.h"(780)
2632 template <typename TRepeat > inline typename Value< Iter<TRepeat, MaxRepeatOccurrences> >::Type & value(Iter<TRepeat, MaxRepeatOccurrences> &it); // "projects/library/seqan/index/index_esa_algs.h"(786)
2634 //____________________________________________________________________________
2637 template <typename TValue, typename TSpec> inline typename Size< Shape<TValue, FixedGappedShape<TSpec> > >::Type weight(Shape<TValue, FixedGappedShape<TSpec> > const & me); // "projects/library/seqan/index/shape_gapped.h"(358)
2638 template <typename TValue, typename TSpec> inline typename Size< Shape<TValue, TSpec> >::Type weight(Shape<TValue, TSpec> const &me); // "projects/library/seqan/index/shape_base.h"(235)
2640 //____________________________________________________________________________
2643 template <typename TFile, typename TText, typename TESASpec> void write(TFile & file, Index<TText, Index_ESA<TESASpec> > & stree, DotDrawing); // "projects/library/seqan/index/index_esa_drawing.h"(31)
2645 } //namespace SEQAN_NAMESPACE_MAIN