SeqAn-1.1/seqan/index/index_generated_forwards.h

   1  /*==========================================================================
   2                 SeqAn - The Library for Sequence Analysis
   3                           http://www.seqan.de
   4  ============================================================================
   5   Copyright (C) 2007
   6
   7   This library is free software; you can redistribute it and/or
   8   modify it under the terms of the GNU Lesser General Public
   9   License as published by the Free Software Foundation; either
  10   version 3 of the License, or (at your option) any later version.
  11
  12   This library is distributed in the hope that it will be useful,
  13   but WITHOUT ANY WARRANTY; without even the implied warranty of
  14   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  15   Lesser General Public License for more details.
  16
  17  ==========================================================================*/
  18
  19 #ifndef SEQAN_HEADER_INDEX_GENERATED_FORWARDS_H
  20 #define SEQAN_HEADER_INDEX_GENERATED_FORWARDS_H
  21
  22 //////////////////////////////////////////////////////////////////////////////
  23 // NOTE: This file is automatically generated by build_forwards.py
  24 //       Do not edit this file manually!
  25 //////////////////////////////////////////////////////////////////////////////
  26
  27
  28 //////////////////////////////////////////////////////////////////////////////
  29 // CLASSES
  30 //////////////////////////////////////////////////////////////////////////////
  31
  32 namespace SEQAN_NAMESPACE_MAIN {
  33 namespace impl {
  34
  35 //____________________________________________________________________________
  36 // substringHelperPizzaChili
  37
  38 template <typename TValue, typename TSpec, typename TPos> struct substringHelperPizzaChili;             // "projects/library/seqan/index/index_pizzachili_string.h"(520)
  39
  40 } //namespace impl
  41 } //namespace SEQAN_NAMESPACE_MAIN
  42 //////////////////////////////////////////////////////////////////////////////
  43
  44 namespace SEQAN_NAMESPACE_MAIN {
  45
  46 //____________________________________________________________________________
  47 // Align
  48
  49 template <typename TSource, typename TSpec> class Align;        // "projects/library/seqan/index/index_esa_base.h"(189)
  50
  51 //____________________________________________________________________________
  52 // ArrayGaps
  53
  54 struct ArrayGaps;               // "projects/library/seqan/index/index_esa_base.h"(186)
  55
  56 //____________________________________________________________________________
  57 // BTree
  58
  59 template <unsigned BlockSize > struct BTree;            // "projects/library/seqan/index/index_esa_find.h"(70)
  60
  61 //____________________________________________________________________________
  62 // BWT
  63
  64 struct BWT;             // "projects/library/seqan/index/index_base.h"(46)
  65 struct BWT;             // "projects/library/seqan/index/index_bwt.h"(30)
  66
  67 //____________________________________________________________________________
  68 // BottomUp
  69
  70 template <typename TSpec > struct BottomUp;             // "projects/library/seqan/index/index_esa_base.h"(125)
  71
  72 //____________________________________________________________________________
  73 // ChildTab
  74
  75 struct ChildTab;        // "projects/library/seqan/index/index_childtab.h"(30)
  76 struct ChildTab;        // "projects/library/seqan/index/index_base.h"(45)
  77
  78 //____________________________________________________________________________
  79 // CompareSkewDCStream
  80
  81 template <typename TValue> struct CompareSkewDCStream;          // "projects/library/seqan/index/pipe_merger7.h"(95)
  82
  83 //____________________________________________________________________________
  84 // DeepShallow
  85
  86 struct DeepShallow;             // "projects/library/seqan/index/index_shawarma.h"(42)
  87
  88 //____________________________________________________________________________
  89 // DefaultIndexCreator
  90
  91 template <typename TIndex, typename TFibre > struct DefaultIndexCreator;        // "projects/library/seqan/index/index_base.h"(177)
  92
  93 //____________________________________________________________________________
  94 // DefaultIndexSpec
  95
  96 template <typename TObject > struct DefaultIndexSpec;           // "projects/library/seqan/index/index_base.h"(63)
  97
  98 //____________________________________________________________________________
  99 // DefaultIndexStringSpec
 100
 101 template <typename TIndex > struct DefaultIndexStringSpec;              // "projects/library/seqan/index/index_base.h"(78)
 102
 103 //____________________________________________________________________________
 104 // DivSufSort
 105
 106 struct DivSufSort;              // "projects/library/seqan/index/index_shawarma.h"(41)
 107
 108 //____________________________________________________________________________
 109 // EmptyEdges
 110
 111 struct EmptyEdges;              // "projects/library/seqan/index/index_esa_base.h"(102)
 112
 113 //____________________________________________________________________________
 114 // Extender3
 115
 116 struct Extender3;               // "projects/library/seqan/index/pump_extender3.h"(30)
 117
 118 //____________________________________________________________________________
 119 // Extender7
 120
 121 template <typename TCompression > struct Extender7;             // "projects/library/seqan/index/pump_extender7.h"(33)
 122
 123 //____________________________________________________________________________
 124 // Extender7Multi
 125
 126 template <typename TPair, typename TCompression > struct Extender7Multi;        // "projects/library/seqan/index/pump_extender7.h"(228)
 127
 128 //____________________________________________________________________________
 129 // Fibre
 130
 131 template <typename TIndex, typename TSpec > struct Fibre;               // "projects/library/seqan/index/index_base.h"(141)
 132
 133 //____________________________________________________________________________
 134 // FibreLess
 135
 136 struct FibreLess;               // "projects/library/seqan/index/index_base.h"(158)
 137
 138 //____________________________________________________________________________
 139 // FibreRecord
 140
 141 struct FibreRecord;             // "projects/library/seqan/index/index_base.h"(150)
 142
 143 //____________________________________________________________________________
 144 // FixedGappedShape
 145
 146 template <typename TSpec> struct FixedGappedShape;              // "projects/library/seqan/index/shape_base.h"(32)
 147
 148 //____________________________________________________________________________
 149 // FixedShape
 150
 151 template <unsigned q> struct FixedShape;        // "projects/library/seqan/index/shape_base.h"(28)
 152
 153 //____________________________________________________________________________
 154 // FunctorGlobalize
 155
 156 template <typename InType, typename TLimitsString, typename Result > struct FunctorGlobalize;           // "projects/library/seqan/index/index_base.h"(386)
 157
 158 //____________________________________________________________________________
 159 // GetVSTreeIteratorTraits
 160
 161 template <typename TIterator> struct GetVSTreeIteratorTraits;           // "projects/library/seqan/index/index_esa_base.h"(148)
 162
 163 //____________________________________________________________________________
 164 // HardwiredShape
 165
 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)
 167
 168 //____________________________________________________________________________
 169 // HideEmptyEdges
 170
 171 struct HideEmptyEdges;          // "projects/library/seqan/index/index_esa_base.h"(101)
 172
 173 //____________________________________________________________________________
 174 // Index
 175
 176 template <typename TObject, typename TSpec > class Index;               // "projects/library/seqan/index/index_base.h"(114)
 177
 178 //____________________________________________________________________________
 179 // Index_ESA
 180
 181 template <typename TSpec > struct Index_ESA;            // "projects/library/seqan/index/index_base.h"(49)
 182
 183 //____________________________________________________________________________
 184 // Index_QGram
 185
 186 template <typename TShapeSpec, typename TSpec > struct Index_QGram;             // "projects/library/seqan/index/index_qgram.h"(100)
 187
 188 //____________________________________________________________________________
 189 // Index_Wotd
 190
 191 template <typename TSpec > struct Index_Wotd;           // "projects/library/seqan/index/index_wotd.h"(56)
 192
 193 //____________________________________________________________________________
 194 // InvalidPizzaChiliSpec
 195
 196 struct InvalidPizzaChiliSpec;           // "projects/library/seqan/index/pizzachili_api.h"(37)
 197
 198 //____________________________________________________________________________
 199 // Kasai
 200
 201 struct Kasai;           // "projects/library/seqan/index/index_base.h"(41)
 202 struct Kasai;           // "projects/library/seqan/index/index_lcp.h"(30)
 203
 204 //____________________________________________________________________________
 205 // KasaiOriginal
 206
 207 struct KasaiOriginal;           // "projects/library/seqan/index/index_base.h"(42)
 208 struct KasaiOriginal;           // "projects/library/seqan/index/index_lcp.h"(31)
 209
 210 //____________________________________________________________________________
 211 // LarssonSadakane
 212
 213 struct LarssonSadakane;         // "projects/library/seqan/index/index_sa_lss.h"(336)
 214 struct LarssonSadakane;         // "projects/library/seqan/index/index_base.h"(35)
 215
 216 //____________________________________________________________________________
 217 // LcpConfig
 218
 219 struct LcpConfig;               // "projects/library/seqan/index/pump_lcp_core.h"(31)
 220
 221 //____________________________________________________________________________
 222 // LeftCompleteTree
 223
 224 struct LeftCompleteTree;        // "projects/library/seqan/index/index_esa_find.h"(67)
 225
 226 //____________________________________________________________________________
 227 // MSufSort
 228
 229 struct MSufSort;        // "projects/library/seqan/index/index_shawarma.h"(40)
 230
 231 //____________________________________________________________________________
 232 // MUMs
 233
 234 struct MUMs;            // "projects/library/seqan/index/index_esa_base.h"(129)
 235
 236 //____________________________________________________________________________
 237 // ManberMyers
 238
 239 struct ManberMyers;             // "projects/library/seqan/index/index_sa_mm.h"(27)
 240 struct ManberMyers;             // "projects/library/seqan/index/index_base.h"(36)
 241
 242 //____________________________________________________________________________
 243 // MaxRepeat
 244
 245 template <typename TSTree> struct MaxRepeat;            // "projects/library/seqan/index/index_esa_algs.h"(602)
 246
 247 //____________________________________________________________________________
 248 // MaxRepeatOccurrences
 249
 250 struct MaxRepeatOccurrences;            // "projects/library/seqan/index/index_esa_base.h"(132)
 251
 252 //____________________________________________________________________________
 253 // Merger3
 254
 255 struct Merger3;         // "projects/library/seqan/index/pipe_merger3.h"(30)
 256
 257 //____________________________________________________________________________
 258 // Merger7
 259
 260 struct Merger7;         // "projects/library/seqan/index/pipe_merger7.h"(178)
 261
 262 //____________________________________________________________________________
 263 // Merger7Multi
 264
 265 template <typename TLimitsString> struct Merger7Multi;          // "projects/library/seqan/index/pipe_merger7.h"(187)
 266
 267 //____________________________________________________________________________
 268 // MultiMEM
 269
 270 template <typename TSTree> struct MultiMEM;             // "projects/library/seqan/index/index_esa_algs_multi.h"(385)
 271
 272 //____________________________________________________________________________
 273 // MultiMEMOccurences
 274
 275 struct MultiMEMOccurences;              // "projects/library/seqan/index/index_esa_base.h"(134)
 276
 277 //____________________________________________________________________________
 278 // ParentLinks
 279
 280 template <typename TSpec > struct ParentLinks;          // "projects/library/seqan/index/index_esa_base.h"(121)
 281
 282 //____________________________________________________________________________
 283 // PizzaChili
 284
 285 template <typename TSpec> struct PizzaChili;            // "projects/library/seqan/index/index_pizzachili_string.h"(47)
 286
 287 //____________________________________________________________________________
 288 // PizzaChiliCodeProvider
 289
 290 template <typename TSpec> struct PizzaChiliCodeProvider;        // "projects/library/seqan/index/pizzachili_api.h"(40)
 291
 292 //____________________________________________________________________________
 293 // Postorder
 294
 295 struct Postorder;               // "projects/library/seqan/index/index_esa_base.h"(96)
 296
 297 //____________________________________________________________________________
 298 // PostorderEmptyEdges
 299
 300 struct PostorderEmptyEdges;             // "projects/library/seqan/index/index_esa_base.h"(98)
 301
 302 //____________________________________________________________________________
 303 // Preorder
 304
 305 struct Preorder;        // "projects/library/seqan/index/index_esa_base.h"(95)
 306
 307 //____________________________________________________________________________
 308 // PreorderEmptyEdges
 309
 310 struct PreorderEmptyEdges;              // "projects/library/seqan/index/index_esa_base.h"(97)
 311
 312 //____________________________________________________________________________
 313 // QGram_Alg
 314
 315 struct QGram_Alg;               // "projects/library/seqan/index/index_base.h"(38)
 316
 317 //____________________________________________________________________________
 318 // QSufSort
 319
 320 struct QSufSort;        // "projects/library/seqan/index/index_shawarma.h"(43)
 321
 322 //____________________________________________________________________________
 323 // Repeat
 324
 325 template <typename TPos, typename TPeriod> struct Repeat;               // "projects/library/seqan/index/repeat_base.h"(28)
 326
 327 //____________________________________________________________________________
 328 // RepeatFinderParams
 329
 330 template <typename TSize> struct RepeatFinderParams;            // "projects/library/seqan/index/repeat_base.h"(47)
 331
 332 //____________________________________________________________________________
 333 // SAQSort
 334
 335 struct SAQSort;         // "projects/library/seqan/index/index_base.h"(37)
 336 struct SAQSort;         // "projects/library/seqan/index/index_sa_qsort.h"(27)
 337
 338 //____________________________________________________________________________
 339 // SAValue
 340
 341 template <typename TObject> struct SAValue;             // "projects/library/seqan/index/index_base.h"(288)
 342
 343 //____________________________________________________________________________
 344 // SearchTreeIterator
 345
 346 template <typename TString, typename TSpec > class SearchTreeIterator;          // "projects/library/seqan/index/index_esa_find.h"(73)
 347
 348 //____________________________________________________________________________
 349 // Shape
 350
 351 template <typename TValue , typename TSpec > class Shape;               // "projects/library/seqan/index/shape_base.h"(54)
 352
 353 //____________________________________________________________________________
 354 // Shawarma
 355
 356 template <typename TSpec> struct Shawarma;              // "projects/library/seqan/index/index_shawarma.h"(38)
 357
 358 //____________________________________________________________________________
 359 // Skew3
 360
 361 struct Skew3;           // "projects/library/seqan/index/index_base.h"(33)
 362 struct Skew3;           // "projects/library/seqan/index/index_skew3.h"(30)
 363
 364 //____________________________________________________________________________
 365 // Skew7
 366
 367 struct Skew7;           // "projects/library/seqan/index/index_base.h"(34)
 368 struct Skew7;           // "projects/library/seqan/index/index_skew7.h"(30)
 369
 370 //____________________________________________________________________________
 371 // SkewDCStream
 372
 373 template <typename TValue> struct SkewDCStream;         // "projects/library/seqan/index/pipe_merger7.h"(71)
 374
 375 //____________________________________________________________________________
 376 // SortedList
 377
 378 struct SortedList;              // "projects/library/seqan/index/index_esa_find.h"(66)
 379
 380 //____________________________________________________________________________
 381 // SuperMaxRepeats
 382
 383 struct SuperMaxRepeats;         // "projects/library/seqan/index/index_esa_base.h"(127)
 384
 385 //____________________________________________________________________________
 386 // SuperMaxRepeatsFast
 387
 388 struct SuperMaxRepeatsFast;             // "projects/library/seqan/index/index_esa_base.h"(128)
 389
 390 //____________________________________________________________________________
 391 // TRepeatFinder
 392
 393 struct TRepeatFinder;           // "projects/library/seqan/index/repeat_base.h"(53)
 394
 395 //____________________________________________________________________________
 396 // TopDown
 397
 398 template <typename TSpec > struct TopDown;              // "projects/library/seqan/index/index_esa_base.h"(117)
 399
 400 //____________________________________________________________________________
 401 // VSTree
 402
 403 template <typename TSpec > struct VSTree;               // "projects/library/seqan/index/index_esa_base.h"(113)
 404
 405 //____________________________________________________________________________
 406 // VSTreeIteratorTraits
 407
 408 template <typename TDFSOrder , typename THideEmptyEdges > struct VSTreeIteratorTraits;          // "projects/library/seqan/index/index_esa_base.h"(32)
 409
 410 //____________________________________________________________________________
 411 // VertexESA
 412
 413 template <typename TSize> struct VertexESA;             // "projects/library/seqan/index/index_esa_base.h"(153)
 414
 415 //____________________________________________________________________________
 416 // WotdDFI
 417
 418 template <typename TPredHull , typename TPred > struct WotdDFI;         // "projects/library/seqan/index/index_dfi.h"(74)
 419
 420 //____________________________________________________________________________
 421 // WotdOriginal_
 422
 423 struct WotdOriginal_;           // "projects/library/seqan/index/index_wotd.h"(52)
 424
 425 //____________________________________________________________________________
 426 // _AllocHelper
 427
 428 template <typename TValue, typename TSpec> struct _AllocHelper;         // "projects/library/seqan/index/index_pizzachili_string.h"(283)
 429
 430 //____________________________________________________________________________
 431 // _Context_LSS
 432
 433 template <typename TValue> struct _Context_LSS;         // "projects/library/seqan/index/index_sa_lss.h"(40)
 434
 435 //____________________________________________________________________________
 436 // _DFIEntry
 437
 438 struct _DFIEntry;               // "projects/library/seqan/index/index_dfi.h"(32)
 439
 440 //____________________________________________________________________________
 441 // _DFIPredDefault
 442
 443 template <bool RESULT> struct _DFIPredDefault;          // "projects/library/seqan/index/index_dfi.h"(44)
 444
 445 //____________________________________________________________________________
 446 // _Fibre_BWT
 447
 448 struct _Fibre_BWT;              // "projects/library/seqan/index/index_base.h"(245)
 449
 450 //____________________________________________________________________________
 451 // _Fibre_ChildTab
 452
 453 struct _Fibre_ChildTab;         // "projects/library/seqan/index/index_base.h"(244)
 454
 455 //____________________________________________________________________________
 456 // _Fibre_Counts
 457
 458 struct _Fibre_Counts;           // "projects/library/seqan/index/index_qgram.h"(64)
 459
 460 //____________________________________________________________________________
 461 // _Fibre_CountsDir
 462
 463 struct _Fibre_CountsDir;        // "projects/library/seqan/index/index_qgram.h"(65)
 464
 465 //____________________________________________________________________________
 466 // _Fibre_Dir
 467
 468 struct _Fibre_Dir;              // "projects/library/seqan/index/index_qgram.h"(61)
 469
 470 //____________________________________________________________________________
 471 // _Fibre_LCP
 472
 473 struct _Fibre_LCP;              // "projects/library/seqan/index/index_base.h"(242)
 474
 475 //____________________________________________________________________________
 476 // _Fibre_LCPE
 477
 478 struct _Fibre_LCPE;             // "projects/library/seqan/index/index_base.h"(243)
 479
 480 //____________________________________________________________________________
 481 // _Fibre_PizzaChili_Compressed
 482
 483 struct _Fibre_PizzaChili_Compressed;            // "projects/library/seqan/index/index_pizzachili.h"(41)
 484
 485 //____________________________________________________________________________
 486 // _Fibre_RawSA
 487
 488 struct _Fibre_RawSA;            // "projects/library/seqan/index/index_base.h"(240)
 489
 490 //____________________________________________________________________________
 491 // _Fibre_RawText
 492
 493 struct _Fibre_RawText;          // "projects/library/seqan/index/index_base.h"(238)
 494
 495 //____________________________________________________________________________
 496 // _Fibre_SA
 497
 498 struct _Fibre_SA;               // "projects/library/seqan/index/index_base.h"(239)
 499
 500 //____________________________________________________________________________
 501 // _Fibre_SADir
 502
 503 struct _Fibre_SADir;            // "projects/library/seqan/index/index_qgram.h"(62)
 504
 505 //____________________________________________________________________________
 506 // _Fibre_SAE
 507
 508 struct _Fibre_SAE;              // "projects/library/seqan/index/index_base.h"(241)
 509
 510 //____________________________________________________________________________
 511 // _Fibre_Shape
 512
 513 struct _Fibre_Shape;            // "projects/library/seqan/index/index_qgram.h"(63)
 514
 515 //____________________________________________________________________________
 516 // _Fibre_Text
 517
 518 struct _Fibre_Text;             // "projects/library/seqan/index/index_base.h"(237)
 519
 520 //____________________________________________________________________________
 521 // _Finder_LCPE
 522
 523 struct _Finder_LCPE;            // "projects/library/seqan/index/index_esa_find.h"(49)
 524
 525 //____________________________________________________________________________
 526 // _Finder_MLR
 527
 528 struct _Finder_MLR;             // "projects/library/seqan/index/index_esa_find.h"(48)
 529
 530 //____________________________________________________________________________
 531 // _Finder_QGramLookup
 532
 533 struct _Finder_QGramLookup;             // "projects/library/seqan/index/index_qgram_find.h"(30)
 534
 535 //____________________________________________________________________________
 536 // _FractionCompound
 537
 538 template <typename TValue, typename TSize> struct _FractionCompound;            // "projects/library/seqan/index/index_esa_algs.h"(250)
 539
 540 //____________________________________________________________________________
 541 // _FractionHeader
 542
 543 template <typename TSize> struct _FractionHeader;               // "projects/library/seqan/index/index_esa_algs.h"(239)
 544
 545 //____________________________________________________________________________
 546 // _FractionMultiCompound
 547
 548 template <typename TValue, typename TSize> struct _FractionMultiCompound;               // "projects/library/seqan/index/index_esa_algs_multi.h"(132)
 549
 550 //____________________________________________________________________________
 551 // _HistoryStackEntry
 552
 553 template <typename TVSTreeIter > struct _HistoryStackEntry;             // "projects/library/seqan/index/index_esa_stree.h"(125)
 554
 555 //____________________________________________________________________________
 556 // _HistoryStackWotdModified
 557
 558 template <typename TSize> struct _HistoryStackWotdModified;             // "projects/library/seqan/index/index_wotd.h"(209)
 559
 560 //____________________________________________________________________________
 561 // _HistoryStackWotdOriginal
 562
 563 template <typename TSize> struct _HistoryStackWotdOriginal;             // "projects/library/seqan/index/index_wotd.h"(202)
 564
 565 //____________________________________________________________________________
 566 // _MaxRepeats
 567
 568 template <typename TSpec > struct _MaxRepeats;          // "projects/library/seqan/index/index_esa_base.h"(106)
 569
 570 //____________________________________________________________________________
 571 // _MultiMEMs
 572
 573 struct _MultiMEMs;              // "projects/library/seqan/index/index_esa_base.h"(107)
 574
 575 //____________________________________________________________________________
 576 // _PizzaChiliFinder
 577
 578 struct _PizzaChiliFinder;               // "projects/library/seqan/index/index_pizzachili_find.h"(26)
 579
 580 //____________________________________________________________________________
 581 // _PizzaChili_AF
 582
 583 struct _PizzaChili_AF;          // "projects/library/seqan/index/pizzachili_api.h"(67)
 584
 585 //____________________________________________________________________________
 586 // _PizzaChili_CCSA
 587
 588 struct _PizzaChili_CCSA;        // "projects/library/seqan/index/pizzachili_api.h"(70)
 589
 590 //____________________________________________________________________________
 591 // _PizzaChili_FM
 592
 593 struct _PizzaChili_FM;          // "projects/library/seqan/index/pizzachili_api.h"(73)
 594
 595 //____________________________________________________________________________
 596 // _PizzaChili_LZ
 597
 598 struct _PizzaChili_LZ;          // "projects/library/seqan/index/pizzachili_api.h"(76)
 599
 600 //____________________________________________________________________________
 601 // _PizzaChili_RLFM
 602
 603 struct _PizzaChili_RLFM;        // "projects/library/seqan/index/pizzachili_api.h"(82)
 604
 605 //____________________________________________________________________________
 606 // _PizzaChili_RSA
 607
 608 struct _PizzaChili_RSA;         // "projects/library/seqan/index/pizzachili_api.h"(79)
 609
 610 //____________________________________________________________________________
 611 // _PizzaChili_SA
 612
 613 struct _PizzaChili_SA;          // "projects/library/seqan/index/pizzachili_api.h"(85)
 614
 615 //____________________________________________________________________________
 616 // _PizzaChili_SADA
 617
 618 struct _PizzaChili_SADA;        // "projects/library/seqan/index/pizzachili_api.h"(88)
 619
 620 //____________________________________________________________________________
 621 // _PizzaChili_SSA
 622
 623 struct _PizzaChili_SSA;         // "projects/library/seqan/index/pizzachili_api.h"(91)
 624
 625 //____________________________________________________________________________
 626 // _PizzaChili_Test
 627
 628 struct _PizzaChili_Test;        // "projects/library/seqan/index/pizzachili_api.h"(94)
 629
 630 //____________________________________________________________________________
 631 // _Postorder
 632
 633 struct _Postorder;              // "projects/library/seqan/index/index_esa_base.h"(29)
 634
 635 //____________________________________________________________________________
 636 // _Preorder
 637
 638 struct _Preorder;               // "projects/library/seqan/index/index_esa_base.h"(28)
 639
 640 //____________________________________________________________________________
 641 // _QGramLess
 642
 643 template <typename TSAValue, typename TText > struct _QGramLess;        // "projects/library/seqan/index/index_qgram.h"(347)
 644
 645 //____________________________________________________________________________
 646 // _QGramLessNoCheck
 647
 648 template <typename TSAValue, typename TText > struct _QGramLessNoCheck;         // "projects/library/seqan/index/index_qgram.h"(506)
 649
 650 //____________________________________________________________________________
 651 // _QGramLessNoCheckOffset
 652
 653 template <typename TSAValue, typename TText > struct _QGramLessNoCheckOffset;           // "projects/library/seqan/index/index_qgram.h"(588)
 654
 655 //____________________________________________________________________________
 656 // _QGramLessOffset
 657
 658 template <typename TSAValue, typename TText > struct _QGramLessOffset;          // "projects/library/seqan/index/index_qgram.h"(442)
 659
 660 //____________________________________________________________________________
 661 // _RepeatLess
 662
 663 template <typename TPos> struct _RepeatLess;            // "projects/library/seqan/index/repeat_base.h"(82)
 664
 665 //____________________________________________________________________________
 666 // _SAValueLess
 667
 668 template <typename TOccValue> struct _SAValueLess;              // "projects/library/seqan/index/index_shims.h"(449)
 669
 670 //____________________________________________________________________________
 671 // _SkewNIndx
 672
 673 template <int I, typename T > struct _SkewNIndx;        // "projects/library/seqan/index/pipe_merger7.h"(34)
 674
 675 //____________________________________________________________________________
 676 // _SkewShift
 677
 678 template <int I, typename T > struct _SkewShift;        // "projects/library/seqan/index/pipe_merger7.h"(31)
 679
 680 //____________________________________________________________________________
 681 // _SuffixLess
 682
 683 template <typename TSAValue, typename TText > struct _SuffixLess;               // "projects/library/seqan/index/index_sa_qsort.h"(33)
 684
 685 //____________________________________________________________________________
 686 // _SuffixLessOffset
 687
 688 template <typename TSAValue, typename TText > struct _SuffixLessOffset;         // "projects/library/seqan/index/index_sa_qsort.h"(71)
 689
 690 //____________________________________________________________________________
 691 // _VertexWotdModified
 692
 693 template <typename TSize> struct _VertexWotdModified;           // "projects/library/seqan/index/index_wotd.h"(163)
 694
 695 //____________________________________________________________________________
 696 // _VertexWotdOriginal
 697
 698 template <typename TSize> struct _VertexWotdOriginal;           // "projects/library/seqan/index/index_wotd.h"(148)
 699
 700 //____________________________________________________________________________
 701 // _qgram_comp
 702
 703 template <typename InType, typename Result > struct _qgram_comp;        // "projects/library/seqan/index/index_qgram.h"(1227)
 704
 705 //____________________________________________________________________________
 706 // _qgram_hash
 707
 708 template <typename TValue, typename TResult > struct _qgram_hash;               // "projects/library/seqan/index/index_qgram.h"(1262)
 709
 710 //____________________________________________________________________________
 711 // filter_globalizer
 712
 713 template <typename InType, typename TLimitsString, typename Result > struct filter_globalizer;          // "projects/library/seqan/index/index_bwt.h"(130)
 714
 715 //____________________________________________________________________________
 716 // map_inverse
 717
 718 template <typename InType, typename Result > struct map_inverse;        // "projects/library/seqan/index/index_lcp.h"(45)
 719
 720 //____________________________________________________________________________
 721 // map_inverse_multi
 722
 723 template <typename InType, typename TLimitsString, typename Result > struct map_inverse_multi;          // "projects/library/seqan/index/index_lcp.h"(148)
 724
 725 //____________________________________________________________________________
 726 // skew3_extend_comp
 727
 728 template <typename InType, typename Result > struct skew3_extend_comp;          // "projects/library/seqan/index/index_skew3.h"(107)
 729
 730 //____________________________________________________________________________
 731 // skew3_ncomp
 732
 733 template <typename InType, typename Result > struct skew3_ncomp;        // "projects/library/seqan/index/index_skew3.h"(49)
 734
 735 //____________________________________________________________________________
 736 // skew3_nmap_extended
 737
 738 template <typename InType, typename Result > struct skew3_nmap_extended;        // "projects/library/seqan/index/index_skew3.h"(101)
 739
 740 //____________________________________________________________________________
 741 // skew3_nmap_linear
 742
 743 template <typename InType, typename Result > struct skew3_nmap_linear;          // "projects/library/seqan/index/index_skew3.h"(72)
 744
 745 //____________________________________________________________________________
 746 // skew3_nmap_sliced
 747
 748 template <typename InType, typename Result > struct skew3_nmap_sliced;          // "projects/library/seqan/index/index_skew3.h"(80)
 749
 750 //____________________________________________________________________________
 751 // skew3_unslicer_func
 752
 753 template <typename InType, typename Result > struct skew3_unslicer_func;        // "projects/library/seqan/index/index_skew3.h"(89)
 754
 755 //____________________________________________________________________________
 756 // skew7_extend_comp
 757
 758 template <typename InType, const int EXT_LENGTH, typename Result > struct skew7_extend_comp;            // "projects/library/seqan/index/index_skew7.h"(137)
 759
 760 //____________________________________________________________________________
 761 // skew7_global_sliced_multi
 762
 763 template <typename InType, typename TLimitsString, typename TResultSize , typename Result > struct skew7_global_sliced_multi;           // "projects/library/seqan/index/index_skew7_multi.h"(109)
 764
 765 //____________________________________________________________________________
 766 // skew7_ncomp
 767
 768 template <typename InType, typename Result > struct skew7_ncomp;        // "projects/library/seqan/index/index_skew7.h"(49)
 769
 770 //____________________________________________________________________________
 771 // skew7_ncomp_multi
 772
 773 template <typename InType, typename Result > struct skew7_ncomp_multi;          // "projects/library/seqan/index/index_skew7_multi.h"(42)
 774
 775 //____________________________________________________________________________
 776 // skew7_nmap_extended
 777
 778 template <typename InType, typename Result > struct skew7_nmap_extended;        // "projects/library/seqan/index/index_skew7.h"(131)
 779
 780 //____________________________________________________________________________
 781 // skew7_nmap_linear
 782
 783 template <typename InType, typename Result > struct skew7_nmap_linear;          // "projects/library/seqan/index/index_skew7.h"(91)
 784
 785 //____________________________________________________________________________
 786 // skew7_nmap_sliced
 787
 788 template <typename InType, typename Result > struct skew7_nmap_sliced;          // "projects/library/seqan/index/index_skew7.h"(99)
 789
 790 //____________________________________________________________________________
 791 // skew7_unslicer_func
 792
 793 template <typename InType, typename Result > struct skew7_unslicer_func;        // "projects/library/seqan/index/index_skew7.h"(115)
 794
 795 } //namespace SEQAN_NAMESPACE_MAIN
 796
 797
 798 //////////////////////////////////////////////////////////////////////////////
 799 // TYPEDEFS
 800 //////////////////////////////////////////////////////////////////////////////
 801
 802 namespace SEQAN_NAMESPACE_MAIN {
 803 namespace impl {
 804
 805 //____________________________________________________________________________
 806 // error_t
 807
 808 typedef int error_t;            // "projects/library/seqan/index/pizzachili_api.h"(34)
 809
 810 //____________________________________________________________________________
 811 // index_t
 812
 813 typedef void* index_t;          // "projects/library/seqan/index/pizzachili_api.h"(33)
 814
 815 //____________________________________________________________________________
 816 // uchar_t
 817
 818 typedef unsigned char uchar_t;          // "projects/library/seqan/index/pizzachili_api.h"(31)
 819
 820 //____________________________________________________________________________
 821 // ulong_t
 822
 823 typedef unsigned long ulong_t;          // "projects/library/seqan/index/pizzachili_api.h"(32)
 824
 825 } //namespace impl
 826 } //namespace SEQAN_NAMESPACE_MAIN
 827 //////////////////////////////////////////////////////////////////////////////
 828
 829 namespace SEQAN_NAMESPACE_MAIN {
 830
 831 //____________________________________________________________________________
 832 // ESA_BWT
 833
 834 typedef Fibre_BWT ESA_BWT;              // "projects/library/seqan/index/index_esa_base.h"(239)
 835
 836 //____________________________________________________________________________
 837 // ESA_ChildTab
 838
 839 typedef Fibre_ChildTab ESA_ChildTab;            // "projects/library/seqan/index/index_esa_base.h"(238)
 840
 841 //____________________________________________________________________________
 842 // ESA_FIND_LCPE
 843
 844 typedef Tag<_Finder_LCPE> const ESA_FIND_LCPE;          // "projects/library/seqan/index/index_esa_find.h"(52)
 845
 846 //____________________________________________________________________________
 847 // ESA_FIND_MLR
 848
 849 typedef Tag<_Finder_MLR> const ESA_FIND_MLR;            // "projects/library/seqan/index/index_esa_find.h"(51)
 850
 851 //____________________________________________________________________________
 852 // ESA_LCP
 853
 854 typedef Fibre_LCP ESA_LCP;              // "projects/library/seqan/index/index_esa_base.h"(236)
 855
 856 //____________________________________________________________________________
 857 // ESA_LCPE
 858
 859 typedef Fibre_LCPE ESA_LCPE;            // "projects/library/seqan/index/index_esa_base.h"(237)
 860
 861 //____________________________________________________________________________
 862 // ESA_RawSA
 863
 864 typedef Fibre_RawSA ESA_RawSA;          // "projects/library/seqan/index/index_esa_base.h"(234)
 865
 866 //____________________________________________________________________________
 867 // ESA_RawText
 868
 869 typedef Fibre_RawText ESA_RawText;              // "projects/library/seqan/index/index_esa_base.h"(232)
 870
 871 //____________________________________________________________________________
 872 // ESA_SA
 873
 874 typedef Fibre_SA ESA_SA;        // "projects/library/seqan/index/index_esa_base.h"(233)
 875
 876 //____________________________________________________________________________
 877 // ESA_SAE
 878
 879 typedef Fibre_SAE ESA_SAE;              // "projects/library/seqan/index/index_esa_base.h"(235)
 880
 881 //____________________________________________________________________________
 882 // ESA_Text
 883
 884 typedef Fibre_Text ESA_Text;            // "projects/library/seqan/index/index_esa_base.h"(231)
 885
 886 //____________________________________________________________________________
 887 // Fibre_BWT
 888
 889 typedef Tag<_Fibre_BWT> const Fibre_BWT;        // "projects/library/seqan/index/index_base.h"(255)
 890
 891 //____________________________________________________________________________
 892 // Fibre_ChildTab
 893
 894 typedef Tag<_Fibre_ChildTab> const Fibre_ChildTab;              // "projects/library/seqan/index/index_base.h"(254)
 895
 896 //____________________________________________________________________________
 897 // Fibre_Counts
 898
 899 typedef Tag<_Fibre_Counts> const Fibre_Counts;          // "projects/library/seqan/index/index_qgram.h"(70)
 900
 901 //____________________________________________________________________________
 902 // Fibre_CountsDir
 903
 904 typedef Tag<_Fibre_CountsDir> const Fibre_CountsDir;            // "projects/library/seqan/index/index_qgram.h"(71)
 905
 906 //____________________________________________________________________________
 907 // Fibre_Dir
 908
 909 typedef Tag<_Fibre_Dir> const Fibre_Dir;        // "projects/library/seqan/index/index_qgram.h"(67)
 910
 911 //____________________________________________________________________________
 912 // Fibre_LCP
 913
 914 typedef Tag<_Fibre_LCP> const Fibre_LCP;        // "projects/library/seqan/index/index_base.h"(252)
 915
 916 //____________________________________________________________________________
 917 // Fibre_LCPE
 918
 919 typedef Tag<_Fibre_LCPE> const Fibre_LCPE;              // "projects/library/seqan/index/index_base.h"(253)
 920
 921 //____________________________________________________________________________
 922 // Fibre_PizzaChili_Compressed
 923
 924 typedef Tag<_Fibre_PizzaChili_Compressed> const Fibre_PizzaChili_Compressed;            // "projects/library/seqan/index/index_pizzachili.h"(44)
 925
 926 //____________________________________________________________________________
 927 // Fibre_PizzaChili_Text
 928
 929 typedef Tag<_Fibre_Text> const Fibre_PizzaChili_Text;           // "projects/library/seqan/index/index_pizzachili.h"(43)
 930
 931 //____________________________________________________________________________
 932 // Fibre_RawSA
 933
 934 typedef Tag<_Fibre_RawSA> const Fibre_RawSA;            // "projects/library/seqan/index/index_base.h"(250)
 935
 936 //____________________________________________________________________________
 937 // Fibre_RawText
 938
 939 typedef Tag<_Fibre_RawText> const Fibre_RawText;        // "projects/library/seqan/index/index_base.h"(248)
 940
 941 //____________________________________________________________________________
 942 // Fibre_SA
 943
 944 typedef Tag<_Fibre_SA> const Fibre_SA;          // "projects/library/seqan/index/index_base.h"(249)
 945
 946 //____________________________________________________________________________
 947 // Fibre_SADir
 948
 949 typedef Tag<_Fibre_SADir> const Fibre_SADir;            // "projects/library/seqan/index/index_qgram.h"(68)
 950
 951 //____________________________________________________________________________
 952 // Fibre_SAE
 953
 954 typedef Tag<_Fibre_SAE> const Fibre_SAE;        // "projects/library/seqan/index/index_base.h"(251)
 955
 956 //____________________________________________________________________________
 957 // Fibre_Shape
 958
 959 typedef Tag<_Fibre_Shape> const Fibre_Shape;            // "projects/library/seqan/index/index_qgram.h"(69)
 960
 961 //____________________________________________________________________________
 962 // Fibre_Text
 963
 964 typedef Tag<_Fibre_Text> const Fibre_Text;              // "projects/library/seqan/index/index_base.h"(247)
 965
 966 //____________________________________________________________________________
 967 // GappedShape
 968
 969 typedef FixedGappedShape<Default> GappedShape;          // "projects/library/seqan/index/shape_base.h"(33)
 970
 971 //____________________________________________________________________________
 972 // MaxRepeats
 973
 974 typedef _MaxRepeats<void> MaxRepeats;           // "projects/library/seqan/index/index_esa_base.h"(131)
 975
 976 //____________________________________________________________________________
 977 // MultiMEMs
 978
 979 typedef _MaxRepeats<_MultiMEMs> MultiMEMs;              // "projects/library/seqan/index/index_esa_base.h"(133)
 980
 981 //____________________________________________________________________________
 982 // PizzaChiliFinder
 983
 984 typedef Tag<_PizzaChiliFinder> const PizzaChiliFinder;          // "projects/library/seqan/index/index_pizzachili_find.h"(36)
 985
 986 //____________________________________________________________________________
 987 // PizzaChili_AF
 988
 989 typedef Tag<_PizzaChili_AF> const PizzaChili_AF;        // "projects/library/seqan/index/pizzachili_api.h"(68)
 990
 991 //____________________________________________________________________________
 992 // PizzaChili_CCSA
 993
 994 typedef Tag<_PizzaChili_CCSA> const PizzaChili_CCSA;            // "projects/library/seqan/index/pizzachili_api.h"(71)
 995
 996 //____________________________________________________________________________
 997 // PizzaChili_Compressed
 998
 999 typedef Fibre_PizzaChili_Compressed PizzaChili_Compressed;              // "projects/library/seqan/index/index_pizzachili.h"(47)
1000
1001 //____________________________________________________________________________
1002 // PizzaChili_FM
1003
1004 typedef Tag<_PizzaChili_FM> const PizzaChili_FM;        // "projects/library/seqan/index/pizzachili_api.h"(74)
1005
1006 //____________________________________________________________________________
1007 // PizzaChili_LZ
1008
1009 typedef Tag<_PizzaChili_LZ> const PizzaChili_LZ;        // "projects/library/seqan/index/pizzachili_api.h"(77)
1010
1011 //____________________________________________________________________________
1012 // PizzaChili_RLFM
1013
1014 typedef Tag<_PizzaChili_RLFM> const PizzaChili_RLFM;            // "projects/library/seqan/index/pizzachili_api.h"(83)
1015
1016 //____________________________________________________________________________
1017 // PizzaChili_RSA
1018
1019 typedef Tag<_PizzaChili_RSA> const PizzaChili_RSA;              // "projects/library/seqan/index/pizzachili_api.h"(80)
1020
1021 //____________________________________________________________________________
1022 // PizzaChili_SA
1023
1024 typedef Tag<_PizzaChili_SA> const PizzaChili_SA;        // "projects/library/seqan/index/pizzachili_api.h"(86)
1025
1026 //____________________________________________________________________________
1027 // PizzaChili_SADA
1028
1029 typedef Tag<_PizzaChili_SADA> const PizzaChili_SADA;            // "projects/library/seqan/index/pizzachili_api.h"(89)
1030
1031 //____________________________________________________________________________
1032 // PizzaChili_SSA
1033
1034 typedef Tag<_PizzaChili_SSA> const PizzaChili_SSA;              // "projects/library/seqan/index/pizzachili_api.h"(92)
1035
1036 //____________________________________________________________________________
1037 // PizzaChili_Test
1038
1039 typedef Tag<_PizzaChili_Test> const PizzaChili_Test;            // "projects/library/seqan/index/pizzachili_api.h"(95)
1040
1041 //____________________________________________________________________________
1042 // PizzaChili_Text
1043
1044 typedef Fibre_PizzaChili_Text PizzaChili_Text;          // "projects/library/seqan/index/index_pizzachili.h"(46)
1045
1046 //____________________________________________________________________________
1047 // QGram_Counts
1048
1049 typedef Fibre_Counts QGram_Counts;              // "projects/library/seqan/index/index_qgram.h"(82)
1050
1051 //____________________________________________________________________________
1052 // QGram_CountsDir
1053
1054 typedef Fibre_CountsDir QGram_CountsDir;        // "projects/library/seqan/index/index_qgram.h"(83)
1055
1056 //____________________________________________________________________________
1057 // QGram_Dir
1058
1059 typedef Fibre_Dir QGram_Dir;            // "projects/library/seqan/index/index_qgram.h"(79)
1060
1061 //____________________________________________________________________________
1062 // QGram_FIND_Lookup
1063
1064 typedef Tag<_Finder_QGramLookup> const QGram_FIND_Lookup;               // "projects/library/seqan/index/index_qgram_find.h"(38)
1065
1066 //____________________________________________________________________________
1067 // QGram_RawSA
1068
1069 typedef Fibre_RawSA QGram_RawSA;        // "projects/library/seqan/index/index_qgram.h"(78)
1070
1071 //____________________________________________________________________________
1072 // QGram_RawText
1073
1074 typedef Fibre_RawText QGram_RawText;            // "projects/library/seqan/index/index_qgram.h"(76)
1075
1076 //____________________________________________________________________________
1077 // QGram_SA
1078
1079 typedef Fibre_SA QGram_SA;              // "projects/library/seqan/index/index_qgram.h"(77)
1080
1081 //____________________________________________________________________________
1082 // QGram_SADir
1083
1084 typedef Fibre_SADir QGram_SADir;        // "projects/library/seqan/index/index_qgram.h"(80)
1085
1086 //____________________________________________________________________________
1087 // QGram_Shape
1088
1089 typedef Fibre_Shape QGram_Shape;        // "projects/library/seqan/index/index_qgram.h"(81)
1090
1091 //____________________________________________________________________________
1092 // QGram_Text
1093
1094 typedef Fibre_Text QGram_Text;          // "projects/library/seqan/index/index_qgram.h"(75)
1095
1096 //____________________________________________________________________________
1097 // SimpleShape
1098
1099 typedef FixedShape<0> SimpleShape;              // "projects/library/seqan/index/shape_base.h"(29)
1100
1101 //____________________________________________________________________________
1102 // WotdOriginal
1103
1104 typedef Tag<WotdOriginal_> const WotdOriginal;          // "projects/library/seqan/index/index_wotd.h"(53)
1105
1106 //____________________________________________________________________________
1107 // Wotd_Dir
1108
1109 typedef Fibre_Dir Wotd_Dir;             // "projects/library/seqan/index/index_wotd.h"(35)
1110
1111 //____________________________________________________________________________
1112 // Wotd_RawSA
1113
1114 typedef Fibre_RawSA Wotd_RawSA;         // "projects/library/seqan/index/index_wotd.h"(34)
1115
1116 //____________________________________________________________________________
1117 // Wotd_RawText
1118
1119 typedef Fibre_RawText Wotd_RawText;             // "projects/library/seqan/index/index_wotd.h"(32)
1120
1121 //____________________________________________________________________________
1122 // Wotd_SA
1123
1124 typedef Fibre_SA Wotd_SA;               // "projects/library/seqan/index/index_wotd.h"(33)
1125
1126 //____________________________________________________________________________
1127 // Wotd_Text
1128
1129 typedef Fibre_Text Wotd_Text;           // "projects/library/seqan/index/index_wotd.h"(31)
1130
1131 } //namespace SEQAN_NAMESPACE_MAIN
1132
1133
1134 //////////////////////////////////////////////////////////////////////////////
1135 // FUNCTIONS
1136 //////////////////////////////////////////////////////////////////////////////
1137
1138 namespace SEQAN_NAMESPACE_MAIN {
1139 namespace impl {
1140
1141 //____________________________________________________________________________
1142 // clearIndex
1143
1144 template <typename TText, typename TSpec> inline void clearIndex(Index<TText, PizzaChili<TSpec> >& me);         // "projects/library/seqan/index/index_pizzachili.h"(132)
1145
1146 //____________________________________________________________________________
1147 // createPizzaChiliIndex
1148
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)
1150
1151 //____________________________________________________________________________
1152 // getOptionsString
1153
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)
1158
1159 //____________________________________________________________________________
1160 // getPizzaChiliString
1161
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)
1164
1165 //____________________________________________________________________________
1166 // queryText
1167
1168 template <typename TValue, typename TSpec> inline void queryText(String<TValue, PizzaChili<TSpec> > const& me);         // "projects/library/seqan/index/index_pizzachili_string.h"(419)
1169
1170 } //namespace impl
1171 } //namespace SEQAN_NAMESPACE_MAIN
1172 //////////////////////////////////////////////////////////////////////////////
1173
1174 namespace SEQAN_NAMESPACE_MAIN {
1175
1176 //____________________________________________________________________________
1177 // __cp_
1178
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)
1180
1181 //____________________________________________________________________________
1182 // _adjustRightBorder
1183
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)
1186
1187 //____________________________________________________________________________
1188 // _bucketLCP
1189
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)
1193
1194 //____________________________________________________________________________
1195 // _createBWTableWrapper
1196
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)
1199
1200 //____________________________________________________________________________
1201 // _dataHost
1202
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)
1205
1206 //____________________________________________________________________________
1207 // _deallocateStorage
1208
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)
1210
1211 //____________________________________________________________________________
1212 // _dfsClear
1213
1214 template <typename TIndex, class TSpec > inline void _dfsClear(Iter<TIndex, VSTree<TSpec> > &it);               // "projects/library/seqan/index/index_esa_stree.h"(1393)
1215
1216 //____________________________________________________________________________
1217 // _dfsLCP
1218
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)
1221
1222 //____________________________________________________________________________
1223 // _dfsOnLeaf
1224
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)
1228
1229 //____________________________________________________________________________
1230 // _dfsOnPop
1231
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)
1233
1234 //____________________________________________________________________________
1235 // _dfsOnPush
1236
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)
1239
1240 //____________________________________________________________________________
1241 // _dfsRange
1242
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)
1245
1246 //____________________________________________________________________________
1247 // _dfsReversedOrder
1248
1249 template <typename TIndex, typename TSpec > inline bool _dfsReversedOrder(Iter<TIndex, VSTree< BottomUp<TSpec> > > &it);        // "projects/library/seqan/index/index_esa_stree.h"(256)
1250
1251 //____________________________________________________________________________
1252 // _dump
1253
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)
1257
1258 //____________________________________________________________________________
1259 // _dumpFreq
1260
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)
1262
1263 //____________________________________________________________________________
1264 // _dumpHistoryStack
1265
1266 template <typename TIndex, typename TSpec > inline void _dumpHistoryStack(Iter<TIndex, VSTree<TSpec> > &it);            // "projects/library/seqan/index/index_esa_stree.h"(229)
1267
1268 //____________________________________________________________________________
1269 // _equalRangeLCPE
1270
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)
1273
1274 //____________________________________________________________________________
1275 // _equalRangeSA
1276
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)
1278
1279 //____________________________________________________________________________
1280 // _findFirstIndex
1281
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)
1286
1287 //____________________________________________________________________________
1288 // _fractionMerge
1289
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)
1292
1293 //____________________________________________________________________________
1294 // _fullDir2Length
1295
1296 template <typename TIndex> inline int _fullDir2Length(TIndex const &index);             // "projects/library/seqan/index/index_qgram.h"(330)
1297
1298 //____________________________________________________________________________
1299 // _fullDirLength
1300
1301 template <typename TIndex> inline int _fullDirLength(TIndex const &index);              // "projects/library/seqan/index/index_qgram.h"(322)
1302
1303 //____________________________________________________________________________
1304 // _getDown
1305
1306 template <typename TSize, typename TIndex > inline TSize _getDown(TSize i, TIndex const &index);        // "projects/library/seqan/index/index_esa_stree.h"(1836)
1307
1308 //____________________________________________________________________________
1309 // _getNextl
1310
1311 template <typename TSize, typename TIndex > inline TSize _getNextl(TSize i, TIndex const &index);               // "projects/library/seqan/index/index_esa_stree.h"(1821)
1312
1313 //____________________________________________________________________________
1314 // _getNodeByChar
1315
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)
1317
1318 //____________________________________________________________________________
1319 // _getNodeLP
1320
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)
1322
1323 //____________________________________________________________________________
1324 // _getUp
1325
1326 template <typename TSize, typename TIndex > inline TSize _getUp(TSize i, TIndex const &index);          // "projects/library/seqan/index/index_esa_stree.h"(1827)
1327
1328 //____________________________________________________________________________
1329 // _goDown
1330
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)
1335
1336 //____________________________________________________________________________
1337 // _goDownChar
1338
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)
1342
1343 //____________________________________________________________________________
1344 // _goDownObject
1345
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)
1348
1349 //____________________________________________________________________________
1350 // _goDownString
1351
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)
1353
1354 //____________________________________________________________________________
1355 // _goRight
1356
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)
1360
1361 //____________________________________________________________________________
1362 // _goUp
1363
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)
1369
1370 //____________________________________________________________________________
1371 // _hashFixedShape
1372
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)
1375
1376 //____________________________________________________________________________
1377 // _hashHardwiredShape
1378
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)
1382
1383 //____________________________________________________________________________
1384 // _hashTuple2FixedShape
1385
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)
1388
1389 //____________________________________________________________________________
1390 // _haveMaximalRepeats
1391
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)
1394
1395 //____________________________________________________________________________
1396 // _historyClear
1397
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)
1400
1401 //____________________________________________________________________________
1402 // _historyPush
1403
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)
1409
1410 //____________________________________________________________________________
1411 // _indexRequireBottomUpIteration
1412
1413 template <typename TText, typename TSpec > void _indexRequireBottomUpIteration(Index<TText, Index_ESA<TSpec> > &index);         // "projects/library/seqan/index/index_esa_base.h"(298)
1414
1415 //____________________________________________________________________________
1416 // _indexRequireTopDownIteration
1417
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)
1420
1421 //____________________________________________________________________________
1422 // _isLeaf
1423
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)
1429
1430 //____________________________________________________________________________
1431 // _isNextl
1432
1433 template <typename TSize, typename TIndex > inline bool _isNextl(TSize i, TIndex const &index);         // "projects/library/seqan/index/index_esa_stree.h"(1805)
1434
1435 //____________________________________________________________________________
1436 // _isRoot
1437
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)
1441
1442 //____________________________________________________________________________
1443 // _isSizeInval
1444
1445 template <typename TValue> inline bool _isSizeInval(TValue const &v);           // "projects/library/seqan/index/index_base.h"(794)
1446
1447 //____________________________________________________________________________
1448 // _isUp
1449
1450 template <typename TSize, typename TIndex > inline bool _isUp(TSize i, TIndex const &index);            // "projects/library/seqan/index/index_esa_stree.h"(1813)
1451
1452 //____________________________________________________________________________
1453 // _leqSkew3
1454
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)
1457
1458 //____________________________________________________________________________
1459 // _leqSkew7
1460
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)
1464
1465 //____________________________________________________________________________
1466 // _lowerBoundLCPE
1467
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)
1470
1471 //____________________________________________________________________________
1472 // _lowerBoundSA
1473
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)
1475
1476 //____________________________________________________________________________
1477 // _onGoDown
1478
1479 template <typename TIndex, typename TSpec > inline void _onGoDown(Iter<TIndex, VSTree< TopDown<TSpec> > > &);           // "projects/library/seqan/index/index_esa_stree.h"(1018)
1480
1481 //____________________________________________________________________________
1482 // _onGoRight
1483
1484 template <typename TIndex, typename TSpec > inline void _onGoRight(Iter<TIndex, VSTree< TopDown<TSpec> > > &);          // "projects/library/seqan/index/index_esa_stree.h"(1021)
1485
1486 //____________________________________________________________________________
1487 // _onGoUp
1488
1489 template <typename TIndex, typename TSpec > inline void _onGoUp(Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &);              // "projects/library/seqan/index/index_esa_stree.h"(1024)
1490
1491 //____________________________________________________________________________
1492 // _pizzaChiliDeallocate
1493
1494 template <typename TValue> inline void _pizzaChiliDeallocate(TValue* begin);            // "projects/library/seqan/index/index_pizzachili_string.h"(276)
1495
1496 //____________________________________________________________________________
1497 // _pizzaChiliReallocate
1498
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)
1500
1501 //____________________________________________________________________________
1502 // _qgramCountQGrams
1503
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)
1506
1507 //____________________________________________________________________________
1508 // _qgramCummulativeSum
1509
1510 template <typename TDir, typename TWithConstraints > inline typename Value<TDir>::Type _qgramCummulativeSum(TDir &dir, TWithConstraints);               // "projects/library/seqan/index/index_qgram.h"(690)
1511
1512 //____________________________________________________________________________
1513 // _qgramCummulativeSumAlt
1514
1515 template <typename TDir, typename TWithConstraints > inline typename Value<TDir>::Type _qgramCummulativeSumAlt(TDir &dir, TWithConstraints const);              // "projects/library/seqan/index/index_qgram.h"(722)
1516
1517 //____________________________________________________________________________
1518 // _qgramDisableBuckets
1519
1520 template <typename TIndex > inline bool _qgramDisableBuckets(TIndex &);         // "projects/library/seqan/index/index_qgram.h"(863)
1521
1522 //____________________________________________________________________________
1523 // _qgramFillSuffixArray
1524
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)
1527
1528 //____________________________________________________________________________
1529 // _qgramPostprocessBuckets
1530
1531 template <typename TDir > inline void _qgramPostprocessBuckets(TDir &dir);              // "projects/library/seqan/index/index_qgram.h"(831)
1532
1533 //____________________________________________________________________________
1534 // _reallocateStorage
1535
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)
1537
1538 //____________________________________________________________________________
1539 // _refineQGramIndex
1540
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)
1542
1543 //____________________________________________________________________________
1544 // _setLength
1545
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)
1547
1548 //____________________________________________________________________________
1549 // _setSizeInval
1550
1551 template <typename TValue> inline void _setSizeInval(TValue &v);        // "projects/library/seqan/index/index_base.h"(789)
1552
1553 //____________________________________________________________________________
1554 // _sortBucketQuickSort
1555
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)
1557
1558 //____________________________________________________________________________
1559 // _sortFirstWotdBucket
1560
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)
1564
1565 //____________________________________________________________________________
1566 // _sortWotdBucket
1567
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)
1572
1573 //____________________________________________________________________________
1574 // _storeWotdChildren
1575
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)
1579
1580 //____________________________________________________________________________
1581 // _treeLevels
1582
1583 template <typename TSize > inline unsigned _treeLevels(TSize lcpSize);          // "projects/library/seqan/index/index_lcp_tree.h"(146)
1584
1585 //____________________________________________________________________________
1586 // _upperBoundLCPE
1587
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)
1590
1591 //____________________________________________________________________________
1592 // _upperBoundSA
1593
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)
1595
1596 //____________________________________________________________________________
1597 // _wotdCountChars
1598
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)
1603
1604 //____________________________________________________________________________
1605 // _wotdCountCharsWotdOriginal
1606
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)
1608
1609 //____________________________________________________________________________
1610 // _wotdCreateFirstLevel
1611
1612 template <typename TText, typename TSpec> inline void _wotdCreateFirstLevel(Index<TText, Index_Wotd<TSpec> > &index);           // "projects/library/seqan/index/index_wotd.h"(1681)
1613
1614 //____________________________________________________________________________
1615 // _wotdCummulativeSum
1616
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)
1619
1620 //____________________________________________________________________________
1621 // _wotdEvaluate
1622
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)
1625
1626 //____________________________________________________________________________
1627 // alignment
1628
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)
1631
1632 //____________________________________________________________________________
1633 // assign
1634
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)
1638
1639 //____________________________________________________________________________
1640 // atBegin
1641
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)
1643
1644 //____________________________________________________________________________
1645 // atEnd
1646
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)
1656
1657 //____________________________________________________________________________
1658 // begin
1659
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)
1664
1665 //____________________________________________________________________________
1666 // bwtAt
1667
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)
1670
1671 //____________________________________________________________________________
1672 // cargo
1673
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)
1676
1677 //____________________________________________________________________________
1678 // childAt
1679
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)
1682
1683 //____________________________________________________________________________
1684 // childrenAreLeaves
1685
1686 template <typename TIndex, class TSpec > inline bool childrenAreLeaves(Iter<TIndex, VSTree<TSpec> > const &it);         // "projects/library/seqan/index/index_esa_stree.h"(1734)
1687
1688 //____________________________________________________________________________
1689 // childtab_process
1690
1691 template <typename TLCPInput, typename TDest > inline void childtab_process(TLCPInput &lcpIn, TDest &dest);             // "projects/library/seqan/index/index_childtab.h"(44)
1692
1693 //____________________________________________________________________________
1694 // clear
1695
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)
1701
1702 //____________________________________________________________________________
1703 // container
1704
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)
1709
1710 //____________________________________________________________________________
1711 // control
1712
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)
1721
1722 //____________________________________________________________________________
1723 // countChildren
1724
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)
1726
1727 //____________________________________________________________________________
1728 // countOccurrences
1729
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)
1731
1732 //____________________________________________________________________________
1733 // countSequences
1734
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)
1736
1737 //____________________________________________________________________________
1738 // createBWTable
1739
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)
1741
1742 //____________________________________________________________________________
1743 // createBWTableExt
1744
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)
1746
1747 //____________________________________________________________________________
1748 // createBWTableInt
1749
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)
1752
1753 //____________________________________________________________________________
1754 // createChildTable
1755
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)
1758
1759 //____________________________________________________________________________
1760 // createChildTableExt
1761
1762 template <typename TLCPTable, typename TChildTable > void createChildTableExt( TChildTable &childtab, TLCPTable &lcp);          // "projects/library/seqan/index/index_childtab.h"(171)
1763
1764 //____________________________________________________________________________
1765 // createCountsArray
1766
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)
1768
1769 //____________________________________________________________________________
1770 // createLCPBinTree
1771
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)
1775
1776 //____________________________________________________________________________
1777 // createLCPETable
1778
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)
1782
1783 //____________________________________________________________________________
1784 // createLCPETableExt
1785
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)
1787
1788 //____________________________________________________________________________
1789 // createLCPTable
1790
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)
1794
1795 //____________________________________________________________________________
1796 // createLCPTableExt
1797
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)
1800
1801 //____________________________________________________________________________
1802 // createQGramIndex
1803
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)
1806
1807 //____________________________________________________________________________
1808 // createQGramIndexDirOnly
1809
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)
1812
1813 //____________________________________________________________________________
1814 // createQGramIndexExt
1815
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)
1818
1819 //____________________________________________________________________________
1820 // createQGramIndexSAOnly
1821
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)
1824
1825 //____________________________________________________________________________
1826 // createSABTree
1827
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)
1831
1832 //____________________________________________________________________________
1833 // createSuffixArray
1834
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)
1848
1849 //____________________________________________________________________________
1850 // createSuffixArrayExt
1851
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)
1854
1855 //____________________________________________________________________________
1856 // createSuffixArrayPart
1857
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)
1861
1862 //____________________________________________________________________________
1863 // dirAt
1864
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)
1867
1868 //____________________________________________________________________________
1869 // empty
1870
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)
1874
1875 //____________________________________________________________________________
1876 // emptyParentEdge
1877
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)
1881
1882 //____________________________________________________________________________
1883 // end
1884
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)
1889
1890 //____________________________________________________________________________
1891 // eof
1892
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)
1895
1896 //____________________________________________________________________________
1897 // equalRangeLCPE
1898
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)
1901
1902 //____________________________________________________________________________
1903 // equalRangeLCPEIterator
1904
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)
1907
1908 //____________________________________________________________________________
1909 // equalRangeSA
1910
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)
1915
1916 //____________________________________________________________________________
1917 // equalRangeSAIterator
1918
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)
1921
1922 //____________________________________________________________________________
1923 // find
1924
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)
1927
1928 //____________________________________________________________________________
1929 // findRepeats
1930
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)
1933
1934 //____________________________________________________________________________
1935 // getFibre
1936
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)
1963
1964 //____________________________________________________________________________
1965 // getFrequency
1966
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)
1969
1970 //____________________________________________________________________________
1971 // getKmerSimilarityMatrix
1972
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)
1975
1976 //____________________________________________________________________________
1977 // getOccurrence
1978
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)
1981
1982 //____________________________________________________________________________
1983 // getOccurrences
1984
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)
1986
1987 //____________________________________________________________________________
1988 // getOccurrencesBWT
1989
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)
1991
1992 //____________________________________________________________________________
1993 // goBegin
1994
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)
1999
2000 //____________________________________________________________________________
2001 // goDown
2002
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)
2006
2007 //____________________________________________________________________________
2008 // goEnd
2009
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)
2014
2015 //____________________________________________________________________________
2016 // goNext
2017
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)
2026
2027 //____________________________________________________________________________
2028 // goNextImpl
2029
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)
2033
2034 //____________________________________________________________________________
2035 // goRight
2036
2037 template <typename TIndex, class TSpec > inline bool goRight(Iter< TIndex, VSTree< TopDown<TSpec> > > &it);             // "projects/library/seqan/index/index_esa_stree.h"(1316)
2038
2039 //____________________________________________________________________________
2040 // goRoot
2041
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)
2045
2046 //____________________________________________________________________________
2047 // goUp
2048
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)
2050
2051 //____________________________________________________________________________
2052 // hash
2053
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)
2062
2063 //____________________________________________________________________________
2064 // hash2
2065
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)
2067
2068 //____________________________________________________________________________
2069 // hash2Next
2070
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)
2072
2073 //____________________________________________________________________________
2074 // hash2Upper
2075
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)
2077
2078 //____________________________________________________________________________
2079 // hashNext
2080
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)
2083
2084 //____________________________________________________________________________
2085 // hashUpper
2086
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)
2089
2090 //____________________________________________________________________________
2091 // host
2092
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)
2095
2096 //____________________________________________________________________________
2097 // hostIterator
2098
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)
2101
2102 //____________________________________________________________________________
2103 // indexBWT
2104
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)
2107
2108 //____________________________________________________________________________
2109 // indexChildTab
2110
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)
2113
2114 //____________________________________________________________________________
2115 // indexCounts
2116
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)
2119
2120 //____________________________________________________________________________
2121 // indexCountsDir
2122
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)
2125
2126 //____________________________________________________________________________
2127 // indexCreate
2128
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)
2141
2142 //____________________________________________________________________________
2143 // indexDir
2144
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)
2147
2148 //____________________________________________________________________________
2149 // indexLCP
2150
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)
2153
2154 //____________________________________________________________________________
2155 // indexLCPE
2156
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)
2159
2160 //____________________________________________________________________________
2161 // indexRawSA
2162
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)
2165
2166 //____________________________________________________________________________
2167 // indexRawText
2168
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)
2171
2172 //____________________________________________________________________________
2173 // indexRequire
2174
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)
2176
2177 //____________________________________________________________________________
2178 // indexSA
2179
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)
2182
2183 //____________________________________________________________________________
2184 // indexShape
2185
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)
2188
2189 //____________________________________________________________________________
2190 // indexSolveDependencies
2191
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)
2198
2199 //____________________________________________________________________________
2200 // indexSupplied
2201
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)
2206
2207 //____________________________________________________________________________
2208 // indexText
2209
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)
2214
2215 //____________________________________________________________________________
2216 // infix
2217
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)
2220
2221 //____________________________________________________________________________
2222 // isLeaf
2223
2224 template <typename TIndex, class TSpec > inline bool isLeaf(Iter<TIndex, VSTree<TSpec> > const &it);            // "projects/library/seqan/index/index_esa_stree.h"(1795)
2225
2226 //____________________________________________________________________________
2227 // isLeftMaximal
2228
2229 template <typename TIndex, class TSpec > inline bool isLeftMaximal(Iter<TIndex, VSTree<TSpec> > const &it);             // "projects/library/seqan/index/index_esa_stree.h"(1541)
2230
2231 //____________________________________________________________________________
2232 // isPartiallyLeftExtensible
2233
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)
2236
2237 //____________________________________________________________________________
2238 // isRightTerminal
2239
2240 template <typename TIndex, class TSpec > inline bool isRightTerminal(Iter<TIndex, VSTree<TSpec> > const &it);           // "projects/library/seqan/index/index_esa_stree.h"(1518)
2241
2242 //____________________________________________________________________________
2243 // isRoot
2244
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)
2247
2248 //____________________________________________________________________________
2249 // isUnique
2250
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)
2253
2254 //____________________________________________________________________________
2255 // lca
2256
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)
2258
2259 //____________________________________________________________________________
2260 // lcp
2261
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)
2263
2264 //____________________________________________________________________________
2265 // lcpAt
2266
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)
2269
2270 //____________________________________________________________________________
2271 // lcp_process
2272
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)
2275
2276 //____________________________________________________________________________
2277 // lcp_process_multi
2278
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)
2281
2282 //____________________________________________________________________________
2283 // lcpeAt
2284
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)
2287
2288 //____________________________________________________________________________
2289 // length
2290
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)
2301
2302 //____________________________________________________________________________
2303 // lowerBoundLCPE
2304
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)
2307
2308 //____________________________________________________________________________
2309 // lowerBoundLCPEIterator
2310
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)
2312
2313 //____________________________________________________________________________
2314 // lowerBoundSA
2315
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)
2320
2321 //____________________________________________________________________________
2322 // lowerBoundSAIterator
2323
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)
2326
2327 //____________________________________________________________________________
2328 // nodeDepth
2329
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)
2331
2332 //____________________________________________________________________________
2333 // nodeHullPredicate
2334
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)
2338
2339 //____________________________________________________________________________
2340 // nodePredicate
2341
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)
2345
2346 //____________________________________________________________________________
2347 // nodeUp
2348
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)
2351
2352 //____________________________________________________________________________
2353 // open
2354
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)
2366
2367 //____________________________________________________________________________
2368 // operator!=
2369
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)
2371
2372 //____________________________________________________________________________
2373 // operator<<
2374
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)
2384
2385 //____________________________________________________________________________
2386 // operator==
2387
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)
2389
2390 //____________________________________________________________________________
2391 // orderOccurrences
2392
2393 template <typename TValue, typename TSpec> inline void orderOccurrences(String<TValue, TSpec> &occString);              // "projects/library/seqan/index/index_shims.h"(474)
2394
2395 //____________________________________________________________________________
2396 // parentEdgeFirstChar
2397
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)
2399
2400 //____________________________________________________________________________
2401 // parentEdgeLabel
2402
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)
2405
2406 //____________________________________________________________________________
2407 // parentEdgeLength
2408
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)
2413
2414 //____________________________________________________________________________
2415 // parentRepLength
2416
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)
2420
2421 //____________________________________________________________________________
2422 // position
2423
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)
2426
2427 //____________________________________________________________________________
2428 // prefix
2429
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)
2432
2433 //____________________________________________________________________________
2434 // radixExtend
2435
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)
2437
2438 //____________________________________________________________________________
2439 // radixExtendClip
2440
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)
2442
2443 //____________________________________________________________________________
2444 // radixPass
2445
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)
2448
2449 //____________________________________________________________________________
2450 // rawsaAt
2451
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)
2453
2454 //____________________________________________________________________________
2455 // rawtextAt
2456
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)
2459
2460 //____________________________________________________________________________
2461 // repLength
2462
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)
2468
2469 //____________________________________________________________________________
2470 // representative
2471
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)
2473
2474 //____________________________________________________________________________
2475 // resize
2476
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)
2478
2479 //____________________________________________________________________________
2480 // saAt
2481
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)
2484
2485 //____________________________________________________________________________
2486 // save
2487
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)
2499
2500 //____________________________________________________________________________
2501 // sequenceLength
2502
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)
2504
2505 //____________________________________________________________________________
2506 // setContainer
2507
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)
2509
2510 //____________________________________________________________________________
2511 // setHost
2512
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)
2514
2515 //____________________________________________________________________________
2516 // setIndexText
2517
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)
2519
2520 //____________________________________________________________________________
2521 // sizeofLCPE
2522
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)
2525
2526 //____________________________________________________________________________
2527 // sizeofLCPH
2528
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)
2531
2532 //____________________________________________________________________________
2533 // sizeofSAB
2534
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)
2537
2538 //____________________________________________________________________________
2539 // skew3_extend
2540
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)
2542
2543 //____________________________________________________________________________
2544 // skew7_extend
2545
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)
2547
2548 //____________________________________________________________________________
2549 // skew7_extend_multi
2550
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)
2552
2553 //____________________________________________________________________________
2554 // skew7_separate_slices
2555
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)
2557
2558 //____________________________________________________________________________
2559 // stringSetLimits
2560
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)
2565
2566 //____________________________________________________________________________
2567 // stringToShape
2568
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)
2570
2571 //____________________________________________________________________________
2572 // suffix
2573
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)
2576
2577 //____________________________________________________________________________
2578 // suffixLength
2579
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)
2581
2582 //____________________________________________________________________________
2583 // textAt
2584
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)
2588
2589 //____________________________________________________________________________
2590 // treeLevelsSAB
2591
2592 template <typename TSize > inline unsigned treeLevelsSAB(TSize saSize, unsigned BlockSize);             // "projects/library/seqan/index/index_sa_btree.h"(103)
2593
2594 //____________________________________________________________________________
2595 // unhash
2596
2597 template <typename TString, typename THash> inline void unhash(TString &result, THash hash, unsigned q);        // "projects/library/seqan/index/shape_base.h"(593)
2598
2599 //____________________________________________________________________________
2600 // upperBoundLCPE
2601
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)
2604
2605 //____________________________________________________________________________
2606 // upperBoundLCPEIterator
2607
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)
2609
2610 //____________________________________________________________________________
2611 // upperBoundSA
2612
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)
2617
2618 //____________________________________________________________________________
2619 // upperBoundSAIterator
2620
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)
2623
2624 //____________________________________________________________________________
2625 // value
2626
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)
2633
2634 //____________________________________________________________________________
2635 // weight
2636
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)
2639
2640 //____________________________________________________________________________
2641 // write
2642
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)
2644
2645 } //namespace SEQAN_NAMESPACE_MAIN
2646
2647 #endif
2648