/*========================================================================== SeqAn - The Library for Sequence Analysis http://www.seqan.de ============================================================================ Copyright (C) 2007 This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. ==========================================================================*/ #ifndef SEQAN_HEADER_INDEX_GENERATED_FORWARDS_H #define SEQAN_HEADER_INDEX_GENERATED_FORWARDS_H ////////////////////////////////////////////////////////////////////////////// // NOTE: This file is automatically generated by build_forwards.py // Do not edit this file manually! ////////////////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////////////////////// // CLASSES ////////////////////////////////////////////////////////////////////////////// namespace SEQAN_NAMESPACE_MAIN { namespace impl { //____________________________________________________________________________ // substringHelperPizzaChili template struct substringHelperPizzaChili; // "projects/library/seqan/index/index_pizzachili_string.h"(520) } //namespace impl } //namespace SEQAN_NAMESPACE_MAIN ////////////////////////////////////////////////////////////////////////////// namespace SEQAN_NAMESPACE_MAIN { //____________________________________________________________________________ // Align template class Align; // "projects/library/seqan/index/index_esa_base.h"(189) //____________________________________________________________________________ // ArrayGaps struct ArrayGaps; // "projects/library/seqan/index/index_esa_base.h"(186) //____________________________________________________________________________ // BTree template struct BTree; // "projects/library/seqan/index/index_esa_find.h"(70) //____________________________________________________________________________ // BWT struct BWT; // "projects/library/seqan/index/index_base.h"(46) struct BWT; // "projects/library/seqan/index/index_bwt.h"(30) //____________________________________________________________________________ // BottomUp template struct BottomUp; // "projects/library/seqan/index/index_esa_base.h"(125) //____________________________________________________________________________ // ChildTab struct ChildTab; // "projects/library/seqan/index/index_childtab.h"(30) struct ChildTab; // "projects/library/seqan/index/index_base.h"(45) //____________________________________________________________________________ // CompareSkewDCStream template struct CompareSkewDCStream; // "projects/library/seqan/index/pipe_merger7.h"(95) //____________________________________________________________________________ // DeepShallow struct DeepShallow; // "projects/library/seqan/index/index_shawarma.h"(42) //____________________________________________________________________________ // DefaultIndexCreator template struct DefaultIndexCreator; // "projects/library/seqan/index/index_base.h"(177) //____________________________________________________________________________ // DefaultIndexSpec template struct DefaultIndexSpec; // "projects/library/seqan/index/index_base.h"(63) //____________________________________________________________________________ // DefaultIndexStringSpec template struct DefaultIndexStringSpec; // "projects/library/seqan/index/index_base.h"(78) //____________________________________________________________________________ // DivSufSort struct DivSufSort; // "projects/library/seqan/index/index_shawarma.h"(41) //____________________________________________________________________________ // EmptyEdges struct EmptyEdges; // "projects/library/seqan/index/index_esa_base.h"(102) //____________________________________________________________________________ // Extender3 struct Extender3; // "projects/library/seqan/index/pump_extender3.h"(30) //____________________________________________________________________________ // Extender7 template struct Extender7; // "projects/library/seqan/index/pump_extender7.h"(33) //____________________________________________________________________________ // Extender7Multi template struct Extender7Multi; // "projects/library/seqan/index/pump_extender7.h"(228) //____________________________________________________________________________ // Fibre template struct Fibre; // "projects/library/seqan/index/index_base.h"(141) //____________________________________________________________________________ // FibreLess struct FibreLess; // "projects/library/seqan/index/index_base.h"(158) //____________________________________________________________________________ // FibreRecord struct FibreRecord; // "projects/library/seqan/index/index_base.h"(150) //____________________________________________________________________________ // FixedGappedShape template struct FixedGappedShape; // "projects/library/seqan/index/shape_base.h"(32) //____________________________________________________________________________ // FixedShape template struct FixedShape; // "projects/library/seqan/index/shape_base.h"(28) //____________________________________________________________________________ // FunctorGlobalize template struct FunctorGlobalize; // "projects/library/seqan/index/index_base.h"(386) //____________________________________________________________________________ // GetVSTreeIteratorTraits template struct GetVSTreeIteratorTraits; // "projects/library/seqan/index/index_esa_base.h"(148) //____________________________________________________________________________ // HardwiredShape template struct HardwiredShape; // "projects/library/seqan/index/shape_gapped.h"(50) //____________________________________________________________________________ // HideEmptyEdges struct HideEmptyEdges; // "projects/library/seqan/index/index_esa_base.h"(101) //____________________________________________________________________________ // Index template class Index; // "projects/library/seqan/index/index_base.h"(114) //____________________________________________________________________________ // Index_ESA template struct Index_ESA; // "projects/library/seqan/index/index_base.h"(49) //____________________________________________________________________________ // Index_QGram template struct Index_QGram; // "projects/library/seqan/index/index_qgram.h"(100) //____________________________________________________________________________ // Index_Wotd template struct Index_Wotd; // "projects/library/seqan/index/index_wotd.h"(56) //____________________________________________________________________________ // InvalidPizzaChiliSpec struct InvalidPizzaChiliSpec; // "projects/library/seqan/index/pizzachili_api.h"(37) //____________________________________________________________________________ // Kasai struct Kasai; // "projects/library/seqan/index/index_base.h"(41) struct Kasai; // "projects/library/seqan/index/index_lcp.h"(30) //____________________________________________________________________________ // KasaiOriginal struct KasaiOriginal; // "projects/library/seqan/index/index_base.h"(42) struct KasaiOriginal; // "projects/library/seqan/index/index_lcp.h"(31) //____________________________________________________________________________ // LarssonSadakane struct LarssonSadakane; // "projects/library/seqan/index/index_sa_lss.h"(336) struct LarssonSadakane; // "projects/library/seqan/index/index_base.h"(35) //____________________________________________________________________________ // LcpConfig struct LcpConfig; // "projects/library/seqan/index/pump_lcp_core.h"(31) //____________________________________________________________________________ // LeftCompleteTree struct LeftCompleteTree; // "projects/library/seqan/index/index_esa_find.h"(67) //____________________________________________________________________________ // MSufSort struct MSufSort; // "projects/library/seqan/index/index_shawarma.h"(40) //____________________________________________________________________________ // MUMs struct MUMs; // "projects/library/seqan/index/index_esa_base.h"(129) //____________________________________________________________________________ // ManberMyers struct ManberMyers; // "projects/library/seqan/index/index_sa_mm.h"(27) struct ManberMyers; // "projects/library/seqan/index/index_base.h"(36) //____________________________________________________________________________ // MaxRepeat template struct MaxRepeat; // "projects/library/seqan/index/index_esa_algs.h"(602) //____________________________________________________________________________ // MaxRepeatOccurrences struct MaxRepeatOccurrences; // "projects/library/seqan/index/index_esa_base.h"(132) //____________________________________________________________________________ // Merger3 struct Merger3; // "projects/library/seqan/index/pipe_merger3.h"(30) //____________________________________________________________________________ // Merger7 struct Merger7; // "projects/library/seqan/index/pipe_merger7.h"(178) //____________________________________________________________________________ // Merger7Multi template struct Merger7Multi; // "projects/library/seqan/index/pipe_merger7.h"(187) //____________________________________________________________________________ // MultiMEM template struct MultiMEM; // "projects/library/seqan/index/index_esa_algs_multi.h"(385) //____________________________________________________________________________ // MultiMEMOccurences struct MultiMEMOccurences; // "projects/library/seqan/index/index_esa_base.h"(134) //____________________________________________________________________________ // ParentLinks template struct ParentLinks; // "projects/library/seqan/index/index_esa_base.h"(121) //____________________________________________________________________________ // PizzaChili template struct PizzaChili; // "projects/library/seqan/index/index_pizzachili_string.h"(47) //____________________________________________________________________________ // PizzaChiliCodeProvider template struct PizzaChiliCodeProvider; // "projects/library/seqan/index/pizzachili_api.h"(40) //____________________________________________________________________________ // Postorder struct Postorder; // "projects/library/seqan/index/index_esa_base.h"(96) //____________________________________________________________________________ // PostorderEmptyEdges struct PostorderEmptyEdges; // "projects/library/seqan/index/index_esa_base.h"(98) //____________________________________________________________________________ // Preorder struct Preorder; // "projects/library/seqan/index/index_esa_base.h"(95) //____________________________________________________________________________ // PreorderEmptyEdges struct PreorderEmptyEdges; // "projects/library/seqan/index/index_esa_base.h"(97) //____________________________________________________________________________ // QGram_Alg struct QGram_Alg; // "projects/library/seqan/index/index_base.h"(38) //____________________________________________________________________________ // QSufSort struct QSufSort; // "projects/library/seqan/index/index_shawarma.h"(43) //____________________________________________________________________________ // Repeat template struct Repeat; // "projects/library/seqan/index/repeat_base.h"(28) //____________________________________________________________________________ // RepeatFinderParams template struct RepeatFinderParams; // "projects/library/seqan/index/repeat_base.h"(47) //____________________________________________________________________________ // SAQSort struct SAQSort; // "projects/library/seqan/index/index_base.h"(37) struct SAQSort; // "projects/library/seqan/index/index_sa_qsort.h"(27) //____________________________________________________________________________ // SAValue template struct SAValue; // "projects/library/seqan/index/index_base.h"(288) //____________________________________________________________________________ // SearchTreeIterator template class SearchTreeIterator; // "projects/library/seqan/index/index_esa_find.h"(73) //____________________________________________________________________________ // Shape template class Shape; // "projects/library/seqan/index/shape_base.h"(54) //____________________________________________________________________________ // Shawarma template struct Shawarma; // "projects/library/seqan/index/index_shawarma.h"(38) //____________________________________________________________________________ // Skew3 struct Skew3; // "projects/library/seqan/index/index_base.h"(33) struct Skew3; // "projects/library/seqan/index/index_skew3.h"(30) //____________________________________________________________________________ // Skew7 struct Skew7; // "projects/library/seqan/index/index_base.h"(34) struct Skew7; // "projects/library/seqan/index/index_skew7.h"(30) //____________________________________________________________________________ // SkewDCStream template struct SkewDCStream; // "projects/library/seqan/index/pipe_merger7.h"(71) //____________________________________________________________________________ // SortedList struct SortedList; // "projects/library/seqan/index/index_esa_find.h"(66) //____________________________________________________________________________ // SuperMaxRepeats struct SuperMaxRepeats; // "projects/library/seqan/index/index_esa_base.h"(127) //____________________________________________________________________________ // SuperMaxRepeatsFast struct SuperMaxRepeatsFast; // "projects/library/seqan/index/index_esa_base.h"(128) //____________________________________________________________________________ // TRepeatFinder struct TRepeatFinder; // "projects/library/seqan/index/repeat_base.h"(53) //____________________________________________________________________________ // TopDown template struct TopDown; // "projects/library/seqan/index/index_esa_base.h"(117) //____________________________________________________________________________ // VSTree template struct VSTree; // "projects/library/seqan/index/index_esa_base.h"(113) //____________________________________________________________________________ // VSTreeIteratorTraits template struct VSTreeIteratorTraits; // "projects/library/seqan/index/index_esa_base.h"(32) //____________________________________________________________________________ // VertexESA template struct VertexESA; // "projects/library/seqan/index/index_esa_base.h"(153) //____________________________________________________________________________ // WotdDFI template struct WotdDFI; // "projects/library/seqan/index/index_dfi.h"(74) //____________________________________________________________________________ // WotdOriginal_ struct WotdOriginal_; // "projects/library/seqan/index/index_wotd.h"(52) //____________________________________________________________________________ // _AllocHelper template struct _AllocHelper; // "projects/library/seqan/index/index_pizzachili_string.h"(283) //____________________________________________________________________________ // _Context_LSS template struct _Context_LSS; // "projects/library/seqan/index/index_sa_lss.h"(40) //____________________________________________________________________________ // _DFIEntry struct _DFIEntry; // "projects/library/seqan/index/index_dfi.h"(32) //____________________________________________________________________________ // _DFIPredDefault template struct _DFIPredDefault; // "projects/library/seqan/index/index_dfi.h"(44) //____________________________________________________________________________ // _Fibre_BWT struct _Fibre_BWT; // "projects/library/seqan/index/index_base.h"(245) //____________________________________________________________________________ // _Fibre_ChildTab struct _Fibre_ChildTab; // "projects/library/seqan/index/index_base.h"(244) //____________________________________________________________________________ // _Fibre_Counts struct _Fibre_Counts; // "projects/library/seqan/index/index_qgram.h"(64) //____________________________________________________________________________ // _Fibre_CountsDir struct _Fibre_CountsDir; // "projects/library/seqan/index/index_qgram.h"(65) //____________________________________________________________________________ // _Fibre_Dir struct _Fibre_Dir; // "projects/library/seqan/index/index_qgram.h"(61) //____________________________________________________________________________ // _Fibre_LCP struct _Fibre_LCP; // "projects/library/seqan/index/index_base.h"(242) //____________________________________________________________________________ // _Fibre_LCPE struct _Fibre_LCPE; // "projects/library/seqan/index/index_base.h"(243) //____________________________________________________________________________ // _Fibre_PizzaChili_Compressed struct _Fibre_PizzaChili_Compressed; // "projects/library/seqan/index/index_pizzachili.h"(41) //____________________________________________________________________________ // _Fibre_RawSA struct _Fibre_RawSA; // "projects/library/seqan/index/index_base.h"(240) //____________________________________________________________________________ // _Fibre_RawText struct _Fibre_RawText; // "projects/library/seqan/index/index_base.h"(238) //____________________________________________________________________________ // _Fibre_SA struct _Fibre_SA; // "projects/library/seqan/index/index_base.h"(239) //____________________________________________________________________________ // _Fibre_SADir struct _Fibre_SADir; // "projects/library/seqan/index/index_qgram.h"(62) //____________________________________________________________________________ // _Fibre_SAE struct _Fibre_SAE; // "projects/library/seqan/index/index_base.h"(241) //____________________________________________________________________________ // _Fibre_Shape struct _Fibre_Shape; // "projects/library/seqan/index/index_qgram.h"(63) //____________________________________________________________________________ // _Fibre_Text struct _Fibre_Text; // "projects/library/seqan/index/index_base.h"(237) //____________________________________________________________________________ // _Finder_LCPE struct _Finder_LCPE; // "projects/library/seqan/index/index_esa_find.h"(49) //____________________________________________________________________________ // _Finder_MLR struct _Finder_MLR; // "projects/library/seqan/index/index_esa_find.h"(48) //____________________________________________________________________________ // _Finder_QGramLookup struct _Finder_QGramLookup; // "projects/library/seqan/index/index_qgram_find.h"(30) //____________________________________________________________________________ // _FractionCompound template struct _FractionCompound; // "projects/library/seqan/index/index_esa_algs.h"(250) //____________________________________________________________________________ // _FractionHeader template struct _FractionHeader; // "projects/library/seqan/index/index_esa_algs.h"(239) //____________________________________________________________________________ // _FractionMultiCompound template struct _FractionMultiCompound; // "projects/library/seqan/index/index_esa_algs_multi.h"(132) //____________________________________________________________________________ // _HistoryStackEntry template struct _HistoryStackEntry; // "projects/library/seqan/index/index_esa_stree.h"(125) //____________________________________________________________________________ // _HistoryStackWotdModified template struct _HistoryStackWotdModified; // "projects/library/seqan/index/index_wotd.h"(209) //____________________________________________________________________________ // _HistoryStackWotdOriginal template struct _HistoryStackWotdOriginal; // "projects/library/seqan/index/index_wotd.h"(202) //____________________________________________________________________________ // _MaxRepeats template struct _MaxRepeats; // "projects/library/seqan/index/index_esa_base.h"(106) //____________________________________________________________________________ // _MultiMEMs struct _MultiMEMs; // "projects/library/seqan/index/index_esa_base.h"(107) //____________________________________________________________________________ // _PizzaChiliFinder struct _PizzaChiliFinder; // "projects/library/seqan/index/index_pizzachili_find.h"(26) //____________________________________________________________________________ // _PizzaChili_AF struct _PizzaChili_AF; // "projects/library/seqan/index/pizzachili_api.h"(67) //____________________________________________________________________________ // _PizzaChili_CCSA struct _PizzaChili_CCSA; // "projects/library/seqan/index/pizzachili_api.h"(70) //____________________________________________________________________________ // _PizzaChili_FM struct _PizzaChili_FM; // "projects/library/seqan/index/pizzachili_api.h"(73) //____________________________________________________________________________ // _PizzaChili_LZ struct _PizzaChili_LZ; // "projects/library/seqan/index/pizzachili_api.h"(76) //____________________________________________________________________________ // _PizzaChili_RLFM struct _PizzaChili_RLFM; // "projects/library/seqan/index/pizzachili_api.h"(82) //____________________________________________________________________________ // _PizzaChili_RSA struct _PizzaChili_RSA; // "projects/library/seqan/index/pizzachili_api.h"(79) //____________________________________________________________________________ // _PizzaChili_SA struct _PizzaChili_SA; // "projects/library/seqan/index/pizzachili_api.h"(85) //____________________________________________________________________________ // _PizzaChili_SADA struct _PizzaChili_SADA; // "projects/library/seqan/index/pizzachili_api.h"(88) //____________________________________________________________________________ // _PizzaChili_SSA struct _PizzaChili_SSA; // "projects/library/seqan/index/pizzachili_api.h"(91) //____________________________________________________________________________ // _PizzaChili_Test struct _PizzaChili_Test; // "projects/library/seqan/index/pizzachili_api.h"(94) //____________________________________________________________________________ // _Postorder struct _Postorder; // "projects/library/seqan/index/index_esa_base.h"(29) //____________________________________________________________________________ // _Preorder struct _Preorder; // "projects/library/seqan/index/index_esa_base.h"(28) //____________________________________________________________________________ // _QGramLess template struct _QGramLess; // "projects/library/seqan/index/index_qgram.h"(347) //____________________________________________________________________________ // _QGramLessNoCheck template struct _QGramLessNoCheck; // "projects/library/seqan/index/index_qgram.h"(506) //____________________________________________________________________________ // _QGramLessNoCheckOffset template struct _QGramLessNoCheckOffset; // "projects/library/seqan/index/index_qgram.h"(588) //____________________________________________________________________________ // _QGramLessOffset template struct _QGramLessOffset; // "projects/library/seqan/index/index_qgram.h"(442) //____________________________________________________________________________ // _RepeatLess template struct _RepeatLess; // "projects/library/seqan/index/repeat_base.h"(82) //____________________________________________________________________________ // _SAValueLess template struct _SAValueLess; // "projects/library/seqan/index/index_shims.h"(449) //____________________________________________________________________________ // _SkewNIndx template struct _SkewNIndx; // "projects/library/seqan/index/pipe_merger7.h"(34) //____________________________________________________________________________ // _SkewShift template struct _SkewShift; // "projects/library/seqan/index/pipe_merger7.h"(31) //____________________________________________________________________________ // _SuffixLess template struct _SuffixLess; // "projects/library/seqan/index/index_sa_qsort.h"(33) //____________________________________________________________________________ // _SuffixLessOffset template struct _SuffixLessOffset; // "projects/library/seqan/index/index_sa_qsort.h"(71) //____________________________________________________________________________ // _VertexWotdModified template struct _VertexWotdModified; // "projects/library/seqan/index/index_wotd.h"(163) //____________________________________________________________________________ // _VertexWotdOriginal template struct _VertexWotdOriginal; // "projects/library/seqan/index/index_wotd.h"(148) //____________________________________________________________________________ // _qgram_comp template struct _qgram_comp; // "projects/library/seqan/index/index_qgram.h"(1227) //____________________________________________________________________________ // _qgram_hash template struct _qgram_hash; // "projects/library/seqan/index/index_qgram.h"(1262) //____________________________________________________________________________ // filter_globalizer template struct filter_globalizer; // "projects/library/seqan/index/index_bwt.h"(130) //____________________________________________________________________________ // map_inverse template struct map_inverse; // "projects/library/seqan/index/index_lcp.h"(45) //____________________________________________________________________________ // map_inverse_multi template struct map_inverse_multi; // "projects/library/seqan/index/index_lcp.h"(148) //____________________________________________________________________________ // skew3_extend_comp template struct skew3_extend_comp; // "projects/library/seqan/index/index_skew3.h"(107) //____________________________________________________________________________ // skew3_ncomp template struct skew3_ncomp; // "projects/library/seqan/index/index_skew3.h"(49) //____________________________________________________________________________ // skew3_nmap_extended template struct skew3_nmap_extended; // "projects/library/seqan/index/index_skew3.h"(101) //____________________________________________________________________________ // skew3_nmap_linear template struct skew3_nmap_linear; // "projects/library/seqan/index/index_skew3.h"(72) //____________________________________________________________________________ // skew3_nmap_sliced template struct skew3_nmap_sliced; // "projects/library/seqan/index/index_skew3.h"(80) //____________________________________________________________________________ // skew3_unslicer_func template struct skew3_unslicer_func; // "projects/library/seqan/index/index_skew3.h"(89) //____________________________________________________________________________ // skew7_extend_comp template struct skew7_extend_comp; // "projects/library/seqan/index/index_skew7.h"(137) //____________________________________________________________________________ // skew7_global_sliced_multi template struct skew7_global_sliced_multi; // "projects/library/seqan/index/index_skew7_multi.h"(109) //____________________________________________________________________________ // skew7_ncomp template struct skew7_ncomp; // "projects/library/seqan/index/index_skew7.h"(49) //____________________________________________________________________________ // skew7_ncomp_multi template struct skew7_ncomp_multi; // "projects/library/seqan/index/index_skew7_multi.h"(42) //____________________________________________________________________________ // skew7_nmap_extended template struct skew7_nmap_extended; // "projects/library/seqan/index/index_skew7.h"(131) //____________________________________________________________________________ // skew7_nmap_linear template struct skew7_nmap_linear; // "projects/library/seqan/index/index_skew7.h"(91) //____________________________________________________________________________ // skew7_nmap_sliced template struct skew7_nmap_sliced; // "projects/library/seqan/index/index_skew7.h"(99) //____________________________________________________________________________ // skew7_unslicer_func template struct skew7_unslicer_func; // "projects/library/seqan/index/index_skew7.h"(115) } //namespace SEQAN_NAMESPACE_MAIN ////////////////////////////////////////////////////////////////////////////// // TYPEDEFS ////////////////////////////////////////////////////////////////////////////// namespace SEQAN_NAMESPACE_MAIN { namespace impl { //____________________________________________________________________________ // error_t typedef int error_t; // "projects/library/seqan/index/pizzachili_api.h"(34) //____________________________________________________________________________ // index_t typedef void* index_t; // "projects/library/seqan/index/pizzachili_api.h"(33) //____________________________________________________________________________ // uchar_t typedef unsigned char uchar_t; // "projects/library/seqan/index/pizzachili_api.h"(31) //____________________________________________________________________________ // ulong_t typedef unsigned long ulong_t; // "projects/library/seqan/index/pizzachili_api.h"(32) } //namespace impl } //namespace SEQAN_NAMESPACE_MAIN ////////////////////////////////////////////////////////////////////////////// namespace SEQAN_NAMESPACE_MAIN { //____________________________________________________________________________ // ESA_BWT typedef Fibre_BWT ESA_BWT; // "projects/library/seqan/index/index_esa_base.h"(239) //____________________________________________________________________________ // ESA_ChildTab typedef Fibre_ChildTab ESA_ChildTab; // "projects/library/seqan/index/index_esa_base.h"(238) //____________________________________________________________________________ // ESA_FIND_LCPE typedef Tag<_Finder_LCPE> const ESA_FIND_LCPE; // "projects/library/seqan/index/index_esa_find.h"(52) //____________________________________________________________________________ // ESA_FIND_MLR typedef Tag<_Finder_MLR> const ESA_FIND_MLR; // "projects/library/seqan/index/index_esa_find.h"(51) //____________________________________________________________________________ // ESA_LCP typedef Fibre_LCP ESA_LCP; // "projects/library/seqan/index/index_esa_base.h"(236) //____________________________________________________________________________ // ESA_LCPE typedef Fibre_LCPE ESA_LCPE; // "projects/library/seqan/index/index_esa_base.h"(237) //____________________________________________________________________________ // ESA_RawSA typedef Fibre_RawSA ESA_RawSA; // "projects/library/seqan/index/index_esa_base.h"(234) //____________________________________________________________________________ // ESA_RawText typedef Fibre_RawText ESA_RawText; // "projects/library/seqan/index/index_esa_base.h"(232) //____________________________________________________________________________ // ESA_SA typedef Fibre_SA ESA_SA; // "projects/library/seqan/index/index_esa_base.h"(233) //____________________________________________________________________________ // ESA_SAE typedef Fibre_SAE ESA_SAE; // "projects/library/seqan/index/index_esa_base.h"(235) //____________________________________________________________________________ // ESA_Text typedef Fibre_Text ESA_Text; // "projects/library/seqan/index/index_esa_base.h"(231) //____________________________________________________________________________ // Fibre_BWT typedef Tag<_Fibre_BWT> const Fibre_BWT; // "projects/library/seqan/index/index_base.h"(255) //____________________________________________________________________________ // Fibre_ChildTab typedef Tag<_Fibre_ChildTab> const Fibre_ChildTab; // "projects/library/seqan/index/index_base.h"(254) //____________________________________________________________________________ // Fibre_Counts typedef Tag<_Fibre_Counts> const Fibre_Counts; // "projects/library/seqan/index/index_qgram.h"(70) //____________________________________________________________________________ // Fibre_CountsDir typedef Tag<_Fibre_CountsDir> const Fibre_CountsDir; // "projects/library/seqan/index/index_qgram.h"(71) //____________________________________________________________________________ // Fibre_Dir typedef Tag<_Fibre_Dir> const Fibre_Dir; // "projects/library/seqan/index/index_qgram.h"(67) //____________________________________________________________________________ // Fibre_LCP typedef Tag<_Fibre_LCP> const Fibre_LCP; // "projects/library/seqan/index/index_base.h"(252) //____________________________________________________________________________ // Fibre_LCPE typedef Tag<_Fibre_LCPE> const Fibre_LCPE; // "projects/library/seqan/index/index_base.h"(253) //____________________________________________________________________________ // Fibre_PizzaChili_Compressed typedef Tag<_Fibre_PizzaChili_Compressed> const Fibre_PizzaChili_Compressed; // "projects/library/seqan/index/index_pizzachili.h"(44) //____________________________________________________________________________ // Fibre_PizzaChili_Text typedef Tag<_Fibre_Text> const Fibre_PizzaChili_Text; // "projects/library/seqan/index/index_pizzachili.h"(43) //____________________________________________________________________________ // Fibre_RawSA typedef Tag<_Fibre_RawSA> const Fibre_RawSA; // "projects/library/seqan/index/index_base.h"(250) //____________________________________________________________________________ // Fibre_RawText typedef Tag<_Fibre_RawText> const Fibre_RawText; // "projects/library/seqan/index/index_base.h"(248) //____________________________________________________________________________ // Fibre_SA typedef Tag<_Fibre_SA> const Fibre_SA; // "projects/library/seqan/index/index_base.h"(249) //____________________________________________________________________________ // Fibre_SADir typedef Tag<_Fibre_SADir> const Fibre_SADir; // "projects/library/seqan/index/index_qgram.h"(68) //____________________________________________________________________________ // Fibre_SAE typedef Tag<_Fibre_SAE> const Fibre_SAE; // "projects/library/seqan/index/index_base.h"(251) //____________________________________________________________________________ // Fibre_Shape typedef Tag<_Fibre_Shape> const Fibre_Shape; // "projects/library/seqan/index/index_qgram.h"(69) //____________________________________________________________________________ // Fibre_Text typedef Tag<_Fibre_Text> const Fibre_Text; // "projects/library/seqan/index/index_base.h"(247) //____________________________________________________________________________ // GappedShape typedef FixedGappedShape GappedShape; // "projects/library/seqan/index/shape_base.h"(33) //____________________________________________________________________________ // MaxRepeats typedef _MaxRepeats MaxRepeats; // "projects/library/seqan/index/index_esa_base.h"(131) //____________________________________________________________________________ // MultiMEMs typedef _MaxRepeats<_MultiMEMs> MultiMEMs; // "projects/library/seqan/index/index_esa_base.h"(133) //____________________________________________________________________________ // PizzaChiliFinder typedef Tag<_PizzaChiliFinder> const PizzaChiliFinder; // "projects/library/seqan/index/index_pizzachili_find.h"(36) //____________________________________________________________________________ // PizzaChili_AF typedef Tag<_PizzaChili_AF> const PizzaChili_AF; // "projects/library/seqan/index/pizzachili_api.h"(68) //____________________________________________________________________________ // PizzaChili_CCSA typedef Tag<_PizzaChili_CCSA> const PizzaChili_CCSA; // "projects/library/seqan/index/pizzachili_api.h"(71) //____________________________________________________________________________ // PizzaChili_Compressed typedef Fibre_PizzaChili_Compressed PizzaChili_Compressed; // "projects/library/seqan/index/index_pizzachili.h"(47) //____________________________________________________________________________ // PizzaChili_FM typedef Tag<_PizzaChili_FM> const PizzaChili_FM; // "projects/library/seqan/index/pizzachili_api.h"(74) //____________________________________________________________________________ // PizzaChili_LZ typedef Tag<_PizzaChili_LZ> const PizzaChili_LZ; // "projects/library/seqan/index/pizzachili_api.h"(77) //____________________________________________________________________________ // PizzaChili_RLFM typedef Tag<_PizzaChili_RLFM> const PizzaChili_RLFM; // "projects/library/seqan/index/pizzachili_api.h"(83) //____________________________________________________________________________ // PizzaChili_RSA typedef Tag<_PizzaChili_RSA> const PizzaChili_RSA; // "projects/library/seqan/index/pizzachili_api.h"(80) //____________________________________________________________________________ // PizzaChili_SA typedef Tag<_PizzaChili_SA> const PizzaChili_SA; // "projects/library/seqan/index/pizzachili_api.h"(86) //____________________________________________________________________________ // PizzaChili_SADA typedef Tag<_PizzaChili_SADA> const PizzaChili_SADA; // "projects/library/seqan/index/pizzachili_api.h"(89) //____________________________________________________________________________ // PizzaChili_SSA typedef Tag<_PizzaChili_SSA> const PizzaChili_SSA; // "projects/library/seqan/index/pizzachili_api.h"(92) //____________________________________________________________________________ // PizzaChili_Test typedef Tag<_PizzaChili_Test> const PizzaChili_Test; // "projects/library/seqan/index/pizzachili_api.h"(95) //____________________________________________________________________________ // PizzaChili_Text typedef Fibre_PizzaChili_Text PizzaChili_Text; // "projects/library/seqan/index/index_pizzachili.h"(46) //____________________________________________________________________________ // QGram_Counts typedef Fibre_Counts QGram_Counts; // "projects/library/seqan/index/index_qgram.h"(82) //____________________________________________________________________________ // QGram_CountsDir typedef Fibre_CountsDir QGram_CountsDir; // "projects/library/seqan/index/index_qgram.h"(83) //____________________________________________________________________________ // QGram_Dir typedef Fibre_Dir QGram_Dir; // "projects/library/seqan/index/index_qgram.h"(79) //____________________________________________________________________________ // QGram_FIND_Lookup typedef Tag<_Finder_QGramLookup> const QGram_FIND_Lookup; // "projects/library/seqan/index/index_qgram_find.h"(38) //____________________________________________________________________________ // QGram_RawSA typedef Fibre_RawSA QGram_RawSA; // "projects/library/seqan/index/index_qgram.h"(78) //____________________________________________________________________________ // QGram_RawText typedef Fibre_RawText QGram_RawText; // "projects/library/seqan/index/index_qgram.h"(76) //____________________________________________________________________________ // QGram_SA typedef Fibre_SA QGram_SA; // "projects/library/seqan/index/index_qgram.h"(77) //____________________________________________________________________________ // QGram_SADir typedef Fibre_SADir QGram_SADir; // "projects/library/seqan/index/index_qgram.h"(80) //____________________________________________________________________________ // QGram_Shape typedef Fibre_Shape QGram_Shape; // "projects/library/seqan/index/index_qgram.h"(81) //____________________________________________________________________________ // QGram_Text typedef Fibre_Text QGram_Text; // "projects/library/seqan/index/index_qgram.h"(75) //____________________________________________________________________________ // SimpleShape typedef FixedShape<0> SimpleShape; // "projects/library/seqan/index/shape_base.h"(29) //____________________________________________________________________________ // WotdOriginal typedef Tag const WotdOriginal; // "projects/library/seqan/index/index_wotd.h"(53) //____________________________________________________________________________ // Wotd_Dir typedef Fibre_Dir Wotd_Dir; // "projects/library/seqan/index/index_wotd.h"(35) //____________________________________________________________________________ // Wotd_RawSA typedef Fibre_RawSA Wotd_RawSA; // "projects/library/seqan/index/index_wotd.h"(34) //____________________________________________________________________________ // Wotd_RawText typedef Fibre_RawText Wotd_RawText; // "projects/library/seqan/index/index_wotd.h"(32) //____________________________________________________________________________ // Wotd_SA typedef Fibre_SA Wotd_SA; // "projects/library/seqan/index/index_wotd.h"(33) //____________________________________________________________________________ // Wotd_Text typedef Fibre_Text Wotd_Text; // "projects/library/seqan/index/index_wotd.h"(31) } //namespace SEQAN_NAMESPACE_MAIN ////////////////////////////////////////////////////////////////////////////// // FUNCTIONS ////////////////////////////////////////////////////////////////////////////// namespace SEQAN_NAMESPACE_MAIN { namespace impl { //____________________________________________________________________________ // clearIndex template inline void clearIndex(Index >& me); // "projects/library/seqan/index/index_pizzachili.h"(132) //____________________________________________________________________________ // createPizzaChiliIndex template inline bool createPizzaChiliIndex( Index >& me, uchar_t* textstart, ulong_t textlength ); // "projects/library/seqan/index/index_pizzachili.h"(256) //____________________________________________________________________________ // getOptionsString template inline char const* getOptionsString(Index >& ); // "projects/library/seqan/index/index_pizzachili.h"(162) template inline char const* getOptionsString(Index >& ); // "projects/library/seqan/index/index_pizzachili.h"(169) template inline char const* getOptionsString(Index >& ); // "projects/library/seqan/index/index_pizzachili.h"(176) template inline char const* getOptionsString(Index >& ); // "projects/library/seqan/index/index_pizzachili.h"(183) //____________________________________________________________________________ // getPizzaChiliString template inline uchar_t* getPizzaChiliString(TPattern const& pattern); // "projects/library/seqan/index/index_pizzachili_find.h"(92) inline uchar_t* getPizzaChiliString(char const* pattern); // "projects/library/seqan/index/index_pizzachili_find.h"(110) //____________________________________________________________________________ // queryText template inline void queryText(String > const& me); // "projects/library/seqan/index/index_pizzachili_string.h"(419) } //namespace impl } //namespace SEQAN_NAMESPACE_MAIN ////////////////////////////////////////////////////////////////////////////// namespace SEQAN_NAMESPACE_MAIN { //____________________________________________________________________________ // __cp_ template static finline Src const __cp_(Dest &dst, Ofs const ofs, Src const src); // "projects/library/seqan/index/pump_extender7.h"(67) //____________________________________________________________________________ // _adjustRightBorder template inline void _adjustRightBorder( Iter< Index >, VSTree< TopDown > > &); // "projects/library/seqan/index/index_wotd.h"(493) template inline void _adjustRightBorder( Iter< Index >, VSTree< TopDown > > &it); // "projects/library/seqan/index/index_wotd.h"(499) //____________________________________________________________________________ // _bucketLCP template typename Size::Type _bucketLCP(TSA const &sa, TText const &text); // "projects/library/seqan/index/index_wotd.h"(1249) template typename Size::Type _bucketLCP(TSA const &sa, TText const &text, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(1283) template typename Size::Type _bucketLCP(TSA const &sa, StringSet const &stringSet, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(1315) //____________________________________________________________________________ // _createBWTableWrapper template inline void _createBWTableWrapper(TBWT &bwt, TText const &s, TSA const &sa, _TTextRandom const); // "projects/library/seqan/index/index_shims.h"(424) template inline void _createBWTableWrapper(TBWT &bwt, TText const &s, TSA const &sa, True const); // "projects/library/seqan/index/index_shims.h"(432) //____________________________________________________________________________ // _dataHost template inline Holder & _dataHost(Index &index); // "projects/library/seqan/index/index_base.h"(464) template inline Holder const & _dataHost(Index const &index); // "projects/library/seqan/index/index_base.h"(468) //____________________________________________________________________________ // _deallocateStorage template inline void _deallocateStorage( String >& , TValue* begin, typename Size > >::Type ); // "projects/library/seqan/index/index_pizzachili_string.h"(370) //____________________________________________________________________________ // _dfsClear template inline void _dfsClear(Iter > &it); // "projects/library/seqan/index/index_esa_stree.h"(1393) //____________________________________________________________________________ // _dfsLCP template inline typename Size::Type & _dfsLCP(Iter< TIndex, VSTree< BottomUp > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1860) template inline typename Size::Type _dfsLCP(Iter< TIndex, VSTree< BottomUp > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1866) //____________________________________________________________________________ // _dfsOnLeaf template inline void _dfsOnLeaf(Iter > > &it); // "projects/library/seqan/index/index_esa_stree.h"(274) template inline void _dfsOnLeaf(Iter > > > &it); // "projects/library/seqan/index/index_esa_algs.h"(496) template inline void _dfsOnLeaf(Iter > > &it); // "projects/library/seqan/index/index_esa_algs_multi.h"(338) //____________________________________________________________________________ // _dfsOnPop template inline void _dfsOnPop(Iter > > &it, TSize const); // "projects/library/seqan/index/index_esa_stree.h"(262) //____________________________________________________________________________ // _dfsOnPush template inline void _dfsOnPush(Iter > > &it, TElement const &e); // "projects/library/seqan/index/index_esa_stree.h"(269) template inline void _dfsOnPush(Iter > > > &it, TElement const &e); // "projects/library/seqan/index/index_esa_algs.h"(482) //____________________________________________________________________________ // _dfsRange template inline Pair::Type> & _dfsRange(Iter< TIndex, VSTree< BottomUp > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1847) template inline Pair::Type> const & _dfsRange(Iter< TIndex, VSTree< BottomUp > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1854) //____________________________________________________________________________ // _dfsReversedOrder template inline bool _dfsReversedOrder(Iter > > &it); // "projects/library/seqan/index/index_esa_stree.h"(256) //____________________________________________________________________________ // _dump template inline void _dump(Index > > &index); // "projects/library/seqan/index/index_dfi.h"(470) template inline void _dump(Index > &index); // "projects/library/seqan/index/index_wotd.h"(1580) template inline void _dump(Index > &index); // "projects/library/seqan/index/index_esa_stree.h"(238) //____________________________________________________________________________ // _dumpFreq template inline void _dumpFreq(Index > > &index); // "projects/library/seqan/index/index_dfi.h"(497) //____________________________________________________________________________ // _dumpHistoryStack template inline void _dumpHistoryStack(Iter > &it); // "projects/library/seqan/index/index_esa_stree.h"(229) //____________________________________________________________________________ // _equalRangeLCPE template inline Pair< typename Iterator::Type > _equalRangeLCPE( TText &text, TSA &sa, SearchTreeIterator< TLCP, TSpec > treeIter, TQuery &query); // "projects/library/seqan/index/index_esa_find.h"(1362) template inline Pair< typename Iterator::Type > _equalRangeLCPE( TText &text, TSA &sa, TLCP &lcp, TQuery &query); // "projects/library/seqan/index/index_esa_find.h"(1514) //____________________________________________________________________________ // _equalRangeSA template inline Pair< typename Iterator::Type > _equalRangeSA( TText &text, SearchTreeIterator< TSA, TSpec > treeIter, TQuery &query); // "projects/library/seqan/index/index_esa_find.h"(632) //____________________________________________________________________________ // _findFirstIndex template inline void _findFirstIndex( Finder >, TSpecFinder>& finder, TPattern const& pattern, PizzaChiliFinder const ); // "projects/library/seqan/index/index_pizzachili_find.h"(123) template inline void _findFirstIndex( Finder< Index, TSpecFinder > &finder, TPattern const &pattern, QGram_FIND_Lookup const); // "projects/library/seqan/index/index_qgram_find.h"(57) template inline void _findFirstIndex( Finder< Index, TSpecFinder > &finder, TPattern const &pattern, ESA_FIND_MLR const); // "projects/library/seqan/index/index_esa_find.h"(1742) template inline void _findFirstIndex( Finder< Index, TSpecFinder > &finder, TPattern const &pattern, ESA_FIND_LCPE const); // "projects/library/seqan/index/index_esa_find.h"(1754) //____________________________________________________________________________ // _fractionMerge template inline void _fractionMerge( Iter > > &it, _FractionCompound &parent, _FractionCompound &child); // "projects/library/seqan/index/index_esa_algs.h"(451) template inline void _fractionMerge( Iter > > &it, _FractionMultiCompound &parent, _FractionMultiCompound &child); // "projects/library/seqan/index/index_esa_algs_multi.h"(317) //____________________________________________________________________________ // _fullDir2Length template inline int _fullDir2Length(TIndex const &index); // "projects/library/seqan/index/index_qgram.h"(330) //____________________________________________________________________________ // _fullDirLength template inline int _fullDirLength(TIndex const &index); // "projects/library/seqan/index/index_qgram.h"(322) //____________________________________________________________________________ // _getDown template inline TSize _getDown(TSize i, TIndex const &index); // "projects/library/seqan/index/index_esa_stree.h"(1836) //____________________________________________________________________________ // _getNextl template inline TSize _getNextl(TSize i, TIndex const &index); // "projects/library/seqan/index/index_esa_stree.h"(1821) //____________________________________________________________________________ // _getNodeByChar template inline bool _getNodeByChar( Iter< Index >, VSTree > const &it, TValue c, typename VertexDescriptor< Index > >::Type &childDesc); // "projects/library/seqan/index/index_esa_stree.h"(787) //____________________________________________________________________________ // _getNodeLP template inline TPos _getNodeLP( Index > const &index, TPos pos); // "projects/library/seqan/index/index_wotd.h"(1366) //____________________________________________________________________________ // _getUp template inline TSize _getUp(TSize i, TIndex const &index); // "projects/library/seqan/index/index_esa_stree.h"(1827) //____________________________________________________________________________ // _goDown template inline bool _goDown( Iter< Index >, VSTree< TopDown > > &it, VSTreeIteratorTraits const); // "projects/library/seqan/index/index_wotd.h"(524) template inline bool _goDown( Iter< Index >, VSTree< TopDown > > &it, VSTreeIteratorTraits const); // "projects/library/seqan/index/index_wotd.h"(560) template inline bool _goDown( Iter< Index >, VSTree< TopDown > > &it, VSTreeIteratorTraits const); // "projects/library/seqan/index/index_esa_stree.h"(1035) template inline bool _goDown( Iter< Index >, VSTree< TopDown > > &it, VSTreeIteratorTraits const); // "projects/library/seqan/index/index_esa_stree.h"(1055) //____________________________________________________________________________ // _goDownChar template inline bool _goDownChar( Iter >, VSTree< TopDown > > &it, TValue c); // "projects/library/seqan/index/index_wotd.h"(1609) template inline bool _goDownChar( Iter >, VSTree< TopDown > > &it, TValue c); // "projects/library/seqan/index/index_wotd.h"(1631) template inline bool _goDownChar(Iter< TIndex, VSTree< TopDown > > &it, TValue c); // "projects/library/seqan/index/index_esa_stree.h"(1100) //____________________________________________________________________________ // _goDownObject template inline bool _goDownObject( Iter< TIndex, VSTree< TopDown > > &it, TObject const &obj, False); // "projects/library/seqan/index/index_esa_stree.h"(1168) template inline bool _goDownObject( Iter< TIndex, VSTree< TopDown > > &it, TObject const &obj, True); // "projects/library/seqan/index/index_esa_stree.h"(1178) //____________________________________________________________________________ // _goDownString template inline bool _goDownString( Iter< TIndex, VSTree< TopDown > > &node, TString const &pattern, TSize &lcp); // "projects/library/seqan/index/index_esa_stree.h"(1118) //____________________________________________________________________________ // _goRight template inline bool _goRight( Iter< Index >, VSTree< TopDown > > &it, VSTreeIteratorTraits const); // "projects/library/seqan/index/index_wotd.h"(596) template inline bool _goRight( Iter< Index >, VSTree< TopDown > > &it, VSTreeIteratorTraits const); // "projects/library/seqan/index/index_wotd.h"(620) template inline bool _goRight( Iter< Index >, VSTree< TopDown > > &it, VSTreeIteratorTraits const); // "projects/library/seqan/index/index_esa_stree.h"(1289) //____________________________________________________________________________ // _goUp template inline bool _goUp(Iter< Index >, VSTree< TopDown > > &it); // "projects/library/seqan/index/index_wotd.h"(645) template inline bool _goUp(Iter< Index >, VSTree< TopDown< ParentLinks > > > &it); // "projects/library/seqan/index/index_wotd.h"(657) template inline bool _goUp(Iter< Index >, VSTree< TopDown< ParentLinks > > > &it); // "projects/library/seqan/index/index_wotd.h"(674) template inline bool _goUp(Iter< TIndex, VSTree< TopDown > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1219) template inline bool _goUp(Iter< TIndex, VSTree< TopDown< ParentLinks > > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1231) //____________________________________________________________________________ // _hashFixedShape template inline THValue _hashFixedShape(THValue hash, TIter &, TValue const, FixedShape<1> const); // "projects/library/seqan/index/shape_base.h"(290) template inline THValue _hashFixedShape(THValue hash, TIter &it, TValue const, FixedShape const); // "projects/library/seqan/index/shape_base.h"(296) //____________________________________________________________________________ // _hashHardwiredShape template 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) template 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) template 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) //____________________________________________________________________________ // _hashTuple2FixedShape template inline THValue _hashTuple2FixedShape( THValue const, Tuple const &tuple, TValue const, FixedShape<1> const); // "projects/library/seqan/index/shape_base.h"(353) template inline THValue _hashTuple2FixedShape( THValue const, Tuple const &tuple, TValue const, FixedShape const); // "projects/library/seqan/index/shape_base.h"(364) //____________________________________________________________________________ // _haveMaximalRepeats template int _haveMaximalRepeats( _FractionCompound const &a, _FractionCompound const &b); // "projects/library/seqan/index/index_esa_algs.h"(268) template int _haveMaximalRepeats( _FractionCompound const &a, _FractionCompound const &b, TValue &equalKey); // "projects/library/seqan/index/index_esa_algs.h"(289) //____________________________________________________________________________ // _historyClear template inline void _historyClear(Iter< TIndex, VSTree > &); // "projects/library/seqan/index/index_esa_stree.h"(989) template inline void _historyClear(Iter< TIndex, VSTree< TopDown< ParentLinks > > > &it); // "projects/library/seqan/index/index_esa_stree.h"(993) //____________________________________________________________________________ // _historyPush template inline void _historyPush(Iter< Index >, VSTree< TopDown > > &it); // "projects/library/seqan/index/index_wotd.h"(235) template inline void _historyPush(Iter< Index >, VSTree< TopDown< ParentLinks > > > &it); // "projects/library/seqan/index/index_wotd.h"(244) template inline void _historyPush(Iter< Index >, VSTree< TopDown< ParentLinks > > > &it); // "projects/library/seqan/index/index_wotd.h"(255) template inline void _historyPush(Iter< Index >, VSTree< TopDown > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1004) template inline void _historyPush(Iter< Index >, VSTree< TopDown< ParentLinks > > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1010) //____________________________________________________________________________ // _indexRequireBottomUpIteration template void _indexRequireBottomUpIteration(Index > &index); // "projects/library/seqan/index/index_esa_base.h"(298) //____________________________________________________________________________ // _indexRequireTopDownIteration template void _indexRequireTopDownIteration(Index > &index); // "projects/library/seqan/index/index_esa_base.h"(290) template void _indexRequireTopDownIteration(Index > &index); // "projects/library/seqan/index/index_wotd.h"(193) //____________________________________________________________________________ // _isLeaf template inline bool _isLeaf( Iter< Index >, VSTree > const &it, VSTreeIteratorTraits const); // "projects/library/seqan/index/index_wotd.h"(281) template inline bool _isLeaf( Iter< Index >, VSTree > const &it, VSTreeIteratorTraits const); // "projects/library/seqan/index/index_wotd.h"(292) template inline bool _isLeaf(VertexESA const &vDesc); // "projects/library/seqan/index/index_esa_stree.h"(1750) template inline bool _isLeaf( Iter > const &it, VSTreeIteratorTraits const); // "projects/library/seqan/index/index_esa_stree.h"(1760) template inline bool _isLeaf( Iter > const &it, VSTreeIteratorTraits const); // "projects/library/seqan/index/index_esa_stree.h"(1769) //____________________________________________________________________________ // _isNextl template inline bool _isNextl(TSize i, TIndex const &index); // "projects/library/seqan/index/index_esa_stree.h"(1805) //____________________________________________________________________________ // _isRoot template inline bool _isRoot(_VertexWotdOriginal const &value); // "projects/library/seqan/index/index_wotd.h"(267) template inline bool _isRoot(_VertexWotdModified const &value); // "projects/library/seqan/index/index_wotd.h"(272) template inline bool _isRoot(VertexESA const &value); // "projects/library/seqan/index/index_esa_stree.h"(1501) //____________________________________________________________________________ // _isSizeInval template inline bool _isSizeInval(TValue const &v); // "projects/library/seqan/index/index_base.h"(794) //____________________________________________________________________________ // _isUp template inline bool _isUp(TSize i, TIndex const &index); // "projects/library/seqan/index/index_esa_stree.h"(1813) //____________________________________________________________________________ // _leqSkew3 template inline bool _leqSkew3(T a1, ST a2, T b1, ST b2); // "projects/library/seqan/index/index_skew3.h"(313) template inline bool _leqSkew3(T a1, T a2, ST a3, T b1, T b2, ST b3); // "projects/library/seqan/index/index_skew3.h"(319) //____________________________________________________________________________ // _leqSkew7 template inline bool _leqSkew7(TTextIter a1, TSize a2, TTextIter b1, TSize b2, TSize n); // "projects/library/seqan/index/index_skew7.h"(414) template inline bool _leqSkew7(TTextIter a, TTextIter b, TSize n); // "projects/library/seqan/index/index_skew7.h"(425) template 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) //____________________________________________________________________________ // _lowerBoundLCPE template inline typename Iterator::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) template inline typename Iterator::Type _lowerBoundLCPE( TText &text, TSA &sa, SearchTreeIterator< TLCP, TSpec > &treeIter, TQuery &query); // "projects/library/seqan/index/index_esa_find.h"(1169) //____________________________________________________________________________ // _lowerBoundSA template inline typename Iterator::Type _lowerBoundSA( TText &text, SearchTreeIterator< TSA, TSpec > treeIter, TQuery &query); // "projects/library/seqan/index/index_esa_find.h"(524) //____________________________________________________________________________ // _onGoDown template inline void _onGoDown(Iter > > &); // "projects/library/seqan/index/index_esa_stree.h"(1018) //____________________________________________________________________________ // _onGoRight template inline void _onGoRight(Iter > > &); // "projects/library/seqan/index/index_esa_stree.h"(1021) //____________________________________________________________________________ // _onGoUp template inline void _onGoUp(Iter > > > &); // "projects/library/seqan/index/index_esa_stree.h"(1024) //____________________________________________________________________________ // _pizzaChiliDeallocate template inline void _pizzaChiliDeallocate(TValue* begin); // "projects/library/seqan/index/index_pizzachili_string.h"(276) //____________________________________________________________________________ // _pizzaChiliReallocate template inline typename Value > >::Type* _pizzaChiliReallocate( String >& me, typename Size > >::Type new_capacity ); // "projects/library/seqan/index/index_pizzachili_string.h"(259) //____________________________________________________________________________ // _qgramCountQGrams template inline void _qgramCountQGrams(TDir &dir, TText const &text, TShape &shape); // "projects/library/seqan/index/index_qgram.h"(640) template inline void _qgramCountQGrams(TDir &dir, StringSet const &stringSet, TShape &shape); // "projects/library/seqan/index/index_qgram.h"(660) //____________________________________________________________________________ // _qgramCummulativeSum template inline typename Value::Type _qgramCummulativeSum(TDir &dir, TWithConstraints); // "projects/library/seqan/index/index_qgram.h"(690) //____________________________________________________________________________ // _qgramCummulativeSumAlt template inline typename Value::Type _qgramCummulativeSumAlt(TDir &dir, TWithConstraints const); // "projects/library/seqan/index/index_qgram.h"(722) //____________________________________________________________________________ // _qgramDisableBuckets template inline bool _qgramDisableBuckets(TIndex &); // "projects/library/seqan/index/index_qgram.h"(863) //____________________________________________________________________________ // _qgramFillSuffixArray template inline void _qgramFillSuffixArray(TSA &sa, TText const &text, TShape &shape, TDir &dir, TWithConstraints const); // "projects/library/seqan/index/index_qgram.h"(748) template inline void _qgramFillSuffixArray( TSA &sa, StringSet const &stringSet, TShape &shape, TDir &dir, TWithConstraints const); // "projects/library/seqan/index/index_qgram.h"(790) //____________________________________________________________________________ // _qgramPostprocessBuckets template inline void _qgramPostprocessBuckets(TDir &dir); // "projects/library/seqan/index/index_qgram.h"(831) //____________________________________________________________________________ // _reallocateStorage template inline typename Value > >::Type* _reallocateStorage( String >& me, typename Size > >::Type new_capacity, Exact ); // "projects/library/seqan/index/index_pizzachili_string.h"(359) //____________________________________________________________________________ // _refineQGramIndex template void _refineQGramIndex( TSA &sa, TDir &dir, TText const &text, TSize1 oldQ, TSize2 newQ); // "projects/library/seqan/index/index_qgram.h"(1033) //____________________________________________________________________________ // _setLength template inline void _setLength( String >& me, size_t new_length ); // "projects/library/seqan/index/index_pizzachili_string.h"(409) //____________________________________________________________________________ // _setSizeInval template inline void _setSizeInval(TValue &v); // "projects/library/seqan/index/index_base.h"(789) //____________________________________________________________________________ // _sortBucketQuickSort template void _sortBucketQuickSort( TSA &sa, TText &text, TSize lcp); // "projects/library/seqan/index/index_sa_qsort.h"(87) //____________________________________________________________________________ // _sortFirstWotdBucket template typename Size< Index, Index_Wotd > > >::Type _sortFirstWotdBucket(Index, Index_Wotd > > &index); // "projects/library/seqan/index/index_dfi.h"(171) template typename Size::Type _sortFirstWotdBucket(TIndex &index); // "projects/library/seqan/index/index_wotd.h"(890) template typename Size< Index, TIndexSpec> >::Type _sortFirstWotdBucket(Index, TIndexSpec> &index); // "projects/library/seqan/index/index_wotd.h"(935) //____________________________________________________________________________ // _sortWotdBucket template TSize _sortWotdBucket( Index, Index_Wotd > > &index, TSize left, TSize right, TSize prefixLen); // "projects/library/seqan/index/index_dfi.h"(260) template TSize _sortWotdBucket( Index > &index, TSize left, TSize right, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(999) template TSize _sortWotdBucket( TIndex &index, TSize left, TSize right, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(1108) template TSize _sortWotdBucket( Index, TIndexSpec> &index, TSize left, TSize right, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(1171) //____________________________________________________________________________ // _storeWotdChildren template inline void _storeWotdChildren( Index > > &index, TSize dirOfs, TSize lcp); // "projects/library/seqan/index/index_dfi.h"(397) template inline void _storeWotdChildren( Index > &index, TPos dirOfs); // "projects/library/seqan/index/index_wotd.h"(1385) template inline void _storeWotdChildren( Index > &index, TSize dirOfs, TSize lcp); // "projects/library/seqan/index/index_wotd.h"(1441) //____________________________________________________________________________ // _treeLevels template inline unsigned _treeLevels(TSize lcpSize); // "projects/library/seqan/index/index_lcp_tree.h"(146) //____________________________________________________________________________ // _upperBoundLCPE template inline typename Iterator::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) template inline typename Iterator::Type _upperBoundLCPE( TText &text, TSA &sa, SearchTreeIterator< TLCP, TSpec > &treeIter, TQuery &query); // "projects/library/seqan/index/index_esa_find.h"(1342) //____________________________________________________________________________ // _upperBoundSA template inline typename Iterator::Type _upperBoundSA( TText &text, SearchTreeIterator< TSA, TSpec > treeIter, TQuery &query); // "projects/library/seqan/index/index_esa_find.h"(578) //____________________________________________________________________________ // _wotdCountChars template inline void _wotdCountChars(TBuckets &buckets, TText const &text); // "projects/library/seqan/index/index_wotd.h"(700) template inline void _wotdCountChars(TBuckets &buckets, StringSet const &stringSet); // "projects/library/seqan/index/index_wotd.h"(714) template inline typename Size::Type _wotdCountChars( TBuckets &buckets, TText const &text, TSA const &sa, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(767) template inline typename Size::Type _wotdCountChars( TBuckets &buckets, StringSet const &stringSet, TSA const &sa, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(803) //____________________________________________________________________________ // _wotdCountCharsWotdOriginal template inline typename Size::Type _wotdCountCharsWotdOriginal( TBuckets &buckets, TText const &text, TSA &sa, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(736) //____________________________________________________________________________ // _wotdCreateFirstLevel template inline void _wotdCreateFirstLevel(Index