1 // ========================================================================== 2 // SeqAn - The Library for Sequence Analysis 3 // ========================================================================== 4 // Copyright (c) 2006-2010, Knut Reinert, FU Berlin 5 // All rights reserved. 6 // 7 // Redistribution and use in source and binary forms, with or without 8 // modification, are permitted provided that the following conditions are met: 9 // 10 // * Redistributions of source code must retain the above copyright 11 // notice, this list of conditions and the following disclaimer. 12 // * Redistributions in binary form must reproduce the above copyright 13 // notice, this list of conditions and the following disclaimer in the 14 // documentation and/or other materials provided with the distribution. 15 // * Neither the name of Knut Reinert or the FU Berlin nor the names of 16 // its contributors may be used to endorse or promote products derived 17 // from this software without specific prior written permission. 18 // 19 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 20 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 21 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 22 // ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE 23 // FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 24 // DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 25 // SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 26 // CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT 27 // LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY 28 // OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH 29 // DAMAGE. 30 // 31 // ========================================================================== 32 33 34 #ifndef SEQAN_HEADER_GRAPH_MSA_GENERATED_FORWARDS_H 35 #define SEQAN_HEADER_GRAPH_MSA_GENERATED_FORWARDS_H 36 37 ////////////////////////////////////////////////////////////////////////////// 38 // NOTE: This file is automatically generated by build_forwards.py 39 // Do not edit this file manually! 40 ////////////////////////////////////////////////////////////////////////////// 41 42 43 ////////////////////////////////////////////////////////////////////////////// 44 // CLASSES 45 ////////////////////////////////////////////////////////////////////////////// 46 47 namespace SEQAN_NAMESPACE_MAIN { 48 49 //____________________________________________________________________________ 50 // BlastLib_ 51 52 struct BlastLib_; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(68) 53 54 //____________________________________________________________________________ 55 // FractionalScore_ 56 57 struct FractionalScore_; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(64) 58 59 //____________________________________________________________________________ 60 // FrequencyCounting_ 61 62 struct FrequencyCounting_; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(73) 63 64 //____________________________________________________________________________ 65 // GlobalPairwiseLibrary_ 66 67 struct GlobalPairwiseLibrary_; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(64) 68 69 //____________________________________________________________________________ 70 // KmerDistance_ 71 72 struct KmerDistance_; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_distance.h"(63) 73 74 //____________________________________________________________________________ 75 // KmerLibrary_ 76 77 struct KmerLibrary_; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(83) 78 79 //____________________________________________________________________________ 80 // LcsLibrary_ 81 82 struct LcsLibrary_; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(93) 83 84 //____________________________________________________________________________ 85 // LessMsaEdgeCargo_ 86 87 template <typename TVertexDescriptor, typename TCargo> struct LessMsaEdgeCargo_; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(279) 88 89 //____________________________________________________________________________ 90 // LibraryDistance_ 91 92 struct LibraryDistance_; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_distance.h"(54) 93 94 //____________________________________________________________________________ 95 // LocalPairwiseLibrary_ 96 97 struct LocalPairwiseLibrary_; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(74) 98 99 //____________________________________________________________________________ 100 // MsaEdgeCargo_ 101 102 template <typename TVertexDescriptor, typename TCargo> struct MsaEdgeCargo_; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(261) 103 104 //____________________________________________________________________________ 105 // MsaOptions 106 107 template <typename TAlphabet, typename TScore> struct MsaOptions; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_msa.h"(40) 108 109 //____________________________________________________________________________ 110 // MummerLib_ 111 112 struct MummerLib_; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(79) 113 114 //____________________________________________________________________________ 115 // NewickFormat_ 116 117 struct NewickFormat_; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(91) 118 119 //____________________________________________________________________________ 120 // ProfileProfileScore 121 122 template <typename T> struct ProfileProfileScore; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_refinement.h"(84) 123 124 //____________________________________________________________________________ 125 // ReScore_ 126 127 struct ReScore_; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(81) 128 129 //____________________________________________________________________________ 130 // TCoffeeLib_ 131 132 struct TCoffeeLib_; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(57) 133 134 //____________________________________________________________________________ 135 // UpgmaAvg_ 136 137 struct UpgmaAvg_; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_guidetree.h"(314) 138 139 //____________________________________________________________________________ 140 // UpgmaMax_ 141 142 struct UpgmaMax_; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_guidetree.h"(303) 143 144 //____________________________________________________________________________ 145 // UpgmaMin_ 146 147 struct UpgmaMin_; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_guidetree.h"(292) 148 149 //____________________________________________________________________________ 150 // UpgmaWeightAvg_ 151 152 struct UpgmaWeightAvg_; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_guidetree.h"(325) 153 154 } //namespace SEQAN_NAMESPACE_MAIN 155 156 157 ////////////////////////////////////////////////////////////////////////////// 158 // TYPEDEFS 159 ////////////////////////////////////////////////////////////////////////////// 160 161 namespace SEQAN_NAMESPACE_MAIN { 162 163 //____________________________________________________________________________ 164 // BlastLib 165 166 typedef Tag<BlastLib_> const BlastLib; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(69) 167 168 //____________________________________________________________________________ 169 // FractionalScore 170 171 typedef Tag<FractionalScore_> const FractionalScore; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(65) 172 173 //____________________________________________________________________________ 174 // FrequencyCounting 175 176 typedef Tag<FrequencyCounting_> const FrequencyCounting; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(74) 177 178 //____________________________________________________________________________ 179 // GlobalPairwiseLibrary 180 181 typedef Tag<GlobalPairwiseLibrary_> const GlobalPairwiseLibrary; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(65) 182 183 //____________________________________________________________________________ 184 // KmerDistance 185 186 typedef Tag<KmerDistance_> const KmerDistance; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_distance.h"(64) 187 188 //____________________________________________________________________________ 189 // KmerLibrary 190 191 typedef Tag<KmerLibrary_> const KmerLibrary; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(84) 192 193 //____________________________________________________________________________ 194 // LcsLibrary 195 196 typedef Tag<LcsLibrary_> const LcsLibrary; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(94) 197 198 //____________________________________________________________________________ 199 // LibraryDistance 200 201 typedef Tag<LibraryDistance_> const LibraryDistance; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_distance.h"(55) 202 203 //____________________________________________________________________________ 204 // LocalPairwiseLibrary 205 206 typedef Tag<LocalPairwiseLibrary_> const LocalPairwiseLibrary; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(75) 207 208 //____________________________________________________________________________ 209 // MummerLib 210 211 typedef Tag<MummerLib_> const MummerLib; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(80) 212 213 //____________________________________________________________________________ 214 // NewickFormat 215 216 typedef Tag<NewickFormat_> const NewickFormat; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(92) 217 218 //____________________________________________________________________________ 219 // ReScore 220 221 typedef Tag<ReScore_> const ReScore; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(82) 222 223 //____________________________________________________________________________ 224 // TCoffeeLib 225 226 typedef Tag<TCoffeeLib_> const TCoffeeLib; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(58) 227 228 //____________________________________________________________________________ 229 // UpgmaAvg 230 231 typedef Tag<UpgmaAvg_> const UpgmaAvg; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_guidetree.h"(315) 232 233 //____________________________________________________________________________ 234 // UpgmaMax 235 236 typedef Tag<UpgmaMax_> const UpgmaMax; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_guidetree.h"(304) 237 238 //____________________________________________________________________________ 239 // UpgmaMin 240 241 typedef Tag<UpgmaMin_> const UpgmaMin; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_guidetree.h"(293) 242 243 //____________________________________________________________________________ 244 // UpgmaWeightAvg 245 246 typedef Tag<UpgmaWeightAvg_> const UpgmaWeightAvg; // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_guidetree.h"(326) 247 248 } //namespace SEQAN_NAMESPACE_MAIN 249 250 251 ////////////////////////////////////////////////////////////////////////////// 252 // FUNCTIONS 253 ////////////////////////////////////////////////////////////////////////////// 254 255 namespace SEQAN_NAMESPACE_MAIN { 256 257 //____________________________________________________________________________ 258 // _appendFragment 259 260 template <typename TSizeSpec, typename TSpec1, typename TSpec2, typename TSize> inline void _appendFragment(String<Fragment<TSizeSpec, ExactReversableFragment<TSpec1> >, TSpec2>& matches, TSize seq1Id, TSize beg1, TSize seq2Id, TSize beg2, TSize len, bool reversed); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(525) 261 template <typename TSizeSpec, typename TSpec1, typename TSpec2, typename TSize> inline void _appendFragment(String<Fragment<TSizeSpec, ExactFragment<TSpec1> >, TSpec2>& matches, TSize seq1Id, TSize beg1, TSize seq2Id, TSize beg2, TSize len, bool reversed); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(542) 262 263 //____________________________________________________________________________ 264 // _appendNewMatch 265 266 template <typename TPos, typename TSpec2, typename TSpec1, typename TScores, typename TId, typename TSize> inline void _appendNewMatch(String<Fragment<TPos, ExactReversableFragment<TSpec2> >, TSpec1>& matches, TScores& scores, TId seq1Id, TId seq2Id, TSize beg1, TSize beg2, TSize len, bool); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(725) 267 template <typename TPos, typename TSpec2, typename TSpec1, typename TScores, typename TId, typename TSize> inline void _appendNewMatch(String<Fragment<TPos, ExactFragment<TSpec2> >, TSpec1>& matches, TScores& scores, TId seq1Id, TId seq2Id, TSize beg1, TSize beg2, TSize len, bool reversed); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(743) 268 269 //____________________________________________________________________________ 270 // _appendSegmentMatches 271 272 template <typename TStrSpec, typename TSpec, typename TList, typename TScore, typename TSegmentMatches, typename TScores> inline void _appendSegmentMatches(StringSet<String<AminoAcid, TStrSpec>, Dependent<TSpec> > const& str, TList const& pList, TScore const&, TSegmentMatches& matches, TScores& scores); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_msa.h"(183) 273 template <typename TValue, typename TStrSpec, typename TSpec, typename TList, typename TScore, typename TSegmentMatches, typename TScores> inline void _appendSegmentMatches(StringSet<String<TValue, TStrSpec>, Dependent<TSpec> > const& str, TList const& pList, TScore const& score_type, TSegmentMatches& matches, TScores& scores); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_msa.h"(197) 274 275 //____________________________________________________________________________ 276 // _buildLeafString 277 278 template <typename TStringSet, typename TCargo, typename TSpec, typename TPosition, typename TSequence> inline void _buildLeafString(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g, TPosition const pos, TSequence& alignSeq); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_progressive.h"(50) 279 280 //____________________________________________________________________________ 281 // _buildNewickString 282 283 template <typename TCargo, typename TSpec, typename TNames, typename TNewickString, typename TVertexDescriptor> void _buildNewickString(Graph<Tree<TCargo, TSpec> >& guideTree, TNames& names, TNewickString& str, TVertexDescriptor v, bool collapseRoot); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(942) 284 285 //____________________________________________________________________________ 286 // _collectSegmentMatches 287 288 template <typename TValue, typename TSpec2, typename TFragment, typename TSpec, typename TScores, typename TSize> void _collectSegmentMatches(String<TValue, TSpec2> const& mat, String<TFragment, TSpec>& matches, TScores& scores, TSize nseq); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(395) 289 290 //____________________________________________________________________________ 291 // _createAlignmentGraph 292 293 template <typename TStringSet, typename TCargo, typename TSpec, typename TSegmentString, typename TOutGraph> inline void _createAlignmentGraph(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g, TSegmentString& alignSeq, TOutGraph& gOut); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_progressive.h"(84) 294 295 //____________________________________________________________________________ 296 // _createMatchingGraph 297 298 template <typename TStringSet, typename TCargo, typename TSpec, typename TSegmentString, typename TEdgeMap, typename TOutGraph> inline void _createMatchingGraph(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g, TSegmentString& alignSeq, TEdgeMap& edgeMap, TOutGraph& gOut, TEdgeMap& edgeMapOut); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_progressive.h"(202) 299 300 //____________________________________________________________________________ 301 // _debugMatches 302 303 template <typename TStringSet, typename TMatches> void _debugMatches(TStringSet& str, TMatches& matches); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_msa.h"(416) 304 305 //____________________________________________________________________________ 306 // _debugRefinedMatches 307 308 template <typename TGraph> void _debugRefinedMatches(TGraph& g); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_msa.h"(453) 309 310 //____________________________________________________________________________ 311 // _getTupelString 312 313 template <typename TString, typename TTupelString, typename TKTup, typename TAlphabet> inline void _getTupelString(TString const& str, TTupelString& tupelString, TKTup const ktup, TAlphabet); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_kmer.h"(51) 314 315 //____________________________________________________________________________ 316 // _matchScore 317 318 template <typename TScore, typename TSc> inline void _matchScore(TScore&, TSc); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_refinement.h"(45) 319 template <typename TValue, typename TSc> inline void _matchScore(Score<TValue, Simple>& sc, TSc msc); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_refinement.h"(65) 320 321 //____________________________________________________________________________ 322 // _mismatchScore 323 324 template <typename TScore, typename TSc> inline void _mismatchScore(TScore&, TSc); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_refinement.h"(55) 325 template <typename TValue, typename TSc> inline void _mismatchScore(Score<TValue, Simple>& sc, TSc mmsc); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_refinement.h"(75) 326 327 //____________________________________________________________________________ 328 // _msaRefinement 329 330 template <typename TValue, typename TSpec, typename TSize, typename TAlphabet, typename TScore> inline void _msaRefinement(String<TValue, TSpec>& mat, TSize nseq, TSize splitPos, TScore& sc, TAlphabet); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_refinement.h"(286) 331 332 //____________________________________________________________________________ 333 // _recursiveProgressiveMatching 334 335 template <typename TStringSet, typename TCargo, typename TSpec, typename TGuideTree, typename TVertexDescriptor, typename TSequence> inline void _recursiveProgressiveMatching(Graph<Alignment<TStringSet, TCargo, TSpec> >& g, TGuideTree& tree, TVertexDescriptor const root, TSequence& alignSeq); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_progressive.h"(429) 336 337 //____________________________________________________________________________ 338 // _resizeWithRespectToDistance 339 340 template <typename TValue, typename TSpec, typename TSize> inline void _resizeWithRespectToDistance(String<TValue, TSpec>& dist, TSize nseq); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(375) 341 template <typename TCargo, typename TSpec, typename TSize> inline void _resizeWithRespectToDistance(Graph<Undirected<TCargo, TSpec> >& dist, TSize nseq); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(385) 342 template <typename TSize> inline void _resizeWithRespectToDistance(Nothing&, TSize); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(397) 343 344 //____________________________________________________________________________ 345 // _scoreMatches 346 347 template <typename TString, typename TSpec, typename TScoreType, typename TSize, typename TSpec2, typename TScoreString, typename TScoreValue> inline void _scoreMatches(StringSet<TString, TSpec> const& seqSet, TScoreType const& scType, String<Fragment<TSize, ExactFragment<> >, TSpec2> const& matches, TScoreString& scores, TScoreValue offset); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(187) 348 template <typename TString, typename TSpec, typename TScoreType, typename TFragment, typename TSpec2, typename TScoreString> inline void _scoreMatches(StringSet<TString, TSpec> const& seqSet, TScoreType const& scType, String<TFragment, TSpec2> const& matches, TScoreString& scores); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(226) 349 350 //____________________________________________________________________________ 351 // _setDistanceValue 352 353 template <typename TFragment, typename TSpec1, typename TString, typename TSpec2, typename TValue, typename TSpec, typename TSize> inline void _setDistanceValue(String<TFragment, TSpec1>& matches, StringSet<TString, TSpec2>& pairSet, String<TValue, TSpec>& dist, TSize i, TSize j, TSize nseq, TSize from); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(412) 354 template <typename TFragment, typename TSpec1, typename TString, typename TSpec2, typename TCargo, typename TSpec, typename TSize> inline void _setDistanceValue(String<TFragment, TSpec1>& matches, StringSet<TString, TSpec2>& pairSet, Graph<Undirected<TCargo, TSpec> >& dist, TSize i, TSize j, TSize, TSize from); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(441) 355 template <typename TFragment, typename TSpec, typename TString, typename TSpec2, typename TSize> inline void _setDistanceValue(String<TFragment, TSpec>&, StringSet<TString, TSpec2>&, Nothing&, TSize, TSize, TSize, TSize); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(468) 356 357 //____________________________________________________________________________ 358 // _subTreeSearch 359 360 template <typename TGuideTree, typename TSeqGroups, typename TGroupRoot, typename TSize> inline void _subTreeSearch(TGuideTree& guideTree, TSeqGroups& seqGroups, TGroupRoot& groupRoot, TSize minMembers); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(370) 361 362 //____________________________________________________________________________ 363 // _upgmaTreeMerge 364 365 template <typename TMatrix, typename TActive, typename TSize> inline void _upgmaTreeMerge(TMatrix& mat, TActive& active, TSize index_i, TSize index_j, TSize nseq, UpgmaWeightAvg); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_guidetree.h"(340) 366 template <typename TMatrix, typename TActive, typename TSize> inline void _upgmaTreeMerge(TMatrix& mat, TActive& active, TSize index_i, TSize index_j, TSize nseq, UpgmaAvg); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_guidetree.h"(370) 367 template <typename TMatrix, typename TActive, typename TSize> inline void _upgmaTreeMerge(TMatrix& mat, TActive& active, TSize index_i, TSize index_j, TSize nseq, UpgmaMin); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_guidetree.h"(396) 368 template <typename TMatrix, typename TActive, typename TSize> inline void _upgmaTreeMerge(TMatrix& mat, TActive& active, TSize index_i, TSize index_j, TSize nseq, UpgmaMax); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_guidetree.h"(421) 369 template <typename TCargo, typename TSpec, typename TActive, typename TEdgeDescriptor> inline void _upgmaTreeMerge(Graph<Undirected<TCargo, TSpec> >& pairGraph, TActive const&, TEdgeDescriptor best, UpgmaMax); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_guidetree.h"(444) 370 template <typename TCargo, typename TSpec, typename TActive, typename TEdgeDescriptor> inline void _upgmaTreeMerge(Graph<Undirected<TCargo, TSpec> >& pairGraph, TActive const&, TEdgeDescriptor best, UpgmaMin); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_guidetree.h"(478) 371 template <typename TCargo, typename TSpec, typename TActive, typename TEdgeDescriptor> inline void _upgmaTreeMerge(Graph<Undirected<TCargo, TSpec> >& pairGraph, TActive const& active, TEdgeDescriptor best, UpgmaWeightAvg); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_guidetree.h"(511) 372 template <typename TCargo, typename TSpec, typename TActive, typename TEdgeDescriptor> inline void _upgmaTreeMerge(Graph<Undirected<TCargo, TSpec> >& pairGraph, TActive const&, TEdgeDescriptor best, UpgmaAvg); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_guidetree.h"(547) 373 374 //____________________________________________________________________________ 375 // alignmentEvaluation 376 377 template <typename TStringSet, typename TCargo, typename TSpec, typename TScore, typename TSize> inline typename Value<TScore>::Type alignmentEvaluation(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g, TScore const& score_type, TSize& gapExCount, TSize& gapCount, TSize& pairCount, String<TSize>& numPairs, TSize& len); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(881) 378 379 //____________________________________________________________________________ 380 // appendSegmentMatches 381 382 template <typename TString, typename TSpec, typename TSize2, typename TSpec2, typename TSegmentMatches, typename TScores> inline void appendSegmentMatches(StringSet<TString, Dependent<TSpec> > const& str, String<TSize2, TSpec2> const& pList, TSegmentMatches& matches, TScores& scores, LcsLibrary); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(209) 383 template <typename TString, typename TSpec, typename TSegmentMatches, typename TScores, typename TAlphabet, typename TSize> inline void appendSegmentMatches(StringSet<TString, Dependent<TSpec> > const& str, TSegmentMatches& matches, TScores& scores, TSize ktup, TAlphabet, KmerLibrary); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(258) 384 template <typename TString, typename TSpec, typename TSegmentMatches, typename TScores, typename TSize> inline void appendSegmentMatches(StringSet<TString, Dependent<TSpec> > const& str, TSegmentMatches& matches, TScores& scores, TSize ktup, KmerLibrary); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(317) 385 template <typename TString, typename TSpec, typename TSegmentMatches, typename TScores> inline void appendSegmentMatches(StringSet<TString, Dependent<TSpec> > const& str, TSegmentMatches& matches, TScores& scores, KmerLibrary); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(330) 386 template <typename TString, typename TSpec, typename TSize2, typename TSpec2, typename TScore, typename TSegmentMatches, typename TScores> inline void appendSegmentMatches(StringSet<TString, Dependent<TSpec> > const& str, String<TSize2, TSpec2> const& pList, TScore const& score_type, TSegmentMatches& matches, TScores& scores, LocalPairwiseLibrary); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(346) 387 template <typename TString, typename TSpec, typename TSize2, typename TSpec2, typename TScore, typename TSegmentMatches, typename TScoreValues, typename TDistance, typename TAlignConfig> inline void appendSegmentMatches(StringSet<TString, Dependent<TSpec> > const& str, String<TSize2, TSpec2> const& pList, TScore const& score_type, TSegmentMatches& matches, TScoreValues& scores, TDistance& dist, TAlignConfig const& ac, GlobalPairwiseLibrary); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(484) 388 template <typename TString, typename TSpec, typename TSize2, typename TSpec2, typename TScore, typename TSegmentMatches, typename TScoreValues, typename TDistance> inline void appendSegmentMatches(StringSet<TString, Dependent<TSpec> > const& str, String<TSize2, TSpec2> const& pList, TScore const& score_type, TSegmentMatches& matches, TScoreValues& scores, TDistance& dist, GlobalPairwiseLibrary); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(537) 389 390 //____________________________________________________________________________ 391 // buildAlignmentGraph 392 393 template <typename TFragment, typename TSpec1, typename TScoreValue, typename TSpec2, typename TStringSet, typename TCargo, typename TSpec> inline void buildAlignmentGraph(String<TFragment, TSpec1>& matches, String<TScoreValue, TSpec2>& scores, Graph<Alignment<TStringSet, TCargo, TSpec> >& outGraph, FractionalScore); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(98) 394 template <typename TFragment, typename TSpec1, typename TStringSet, typename TCargo, typename TSpec> inline void buildAlignmentGraph(String<TFragment, TSpec1>& matches, Graph<Alignment<TStringSet, TCargo, TSpec> >& outGraph, FrequencyCounting); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(152) 395 template <typename TFragment, typename TSpec1, typename TScoreValue, typename TSpec2, typename TStringSet, typename TCargo, typename TSpec> inline void buildAlignmentGraph(String<TFragment, TSpec1>& matches, String<TScoreValue, TSpec2>&, Graph<Alignment<TStringSet, TCargo, TSpec> >& outGraph, FrequencyCounting); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(174) 396 template <typename TFragment, typename TSpec1, typename TScoreValue, typename TSpec2, typename TStringSet, typename TCargo, typename TSpec, typename TScore> inline void buildAlignmentGraph(String<TFragment, TSpec1>& matches, String<TScoreValue, TSpec2>& scores, Graph<Alignment<TStringSet, TCargo, TSpec> >& outGraph, TScore const& scType, ReScore); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(241) 397 398 //____________________________________________________________________________ 399 // convertAlignment 400 401 template <typename TStringSet, typename TCargo, typename TSpec, typename TSource, typename TSpec2> inline bool convertAlignment(Graph<Alignment<TStringSet, TCargo, TSpec> > const& gAlign, Align<TSource, TSpec2>& align); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(952) 402 template <typename TSource, typename TSpec2, typename TStringSet, typename TCargo, typename TSpec> inline bool convertAlignment(Align<TSource, TSpec2> const& align, Graph<Alignment<TStringSet, TCargo, TSpec> >& gAlign); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(1002) 403 404 //____________________________________________________________________________ 405 // evaluateAlignment 406 407 template <typename TAlphabet, typename TScore> inline void evaluateAlignment(MsaOptions<TAlphabet, TScore> const& msaOpt); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_msa.h"(86) 408 409 //____________________________________________________________________________ 410 // getAlignmentStatistics 411 412 template <typename TFragment, typename TSpec1, typename TStringSet, typename TPos, typename TSize1> inline void getAlignmentStatistics(String<TFragment, TSpec1> const& matches, TStringSet& str, TPos const from, TPos const to, TSize1& matchLength, TSize1& overlapLength, TSize1& alignLength); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(144) 413 414 //____________________________________________________________________________ 415 // getDistanceMatrix 416 417 template <typename TStringSet, typename TCargo, typename TSpec, typename TMatrix> inline void getDistanceMatrix(Graph<Alignment<TStringSet, TCargo, TSpec> >& g, TMatrix& distanceMatrix, LibraryDistance); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_distance.h"(82) 418 template <typename TStringSet, typename TCargo, typename TSpec, typename TMatrix, typename TSize, typename TAlphabet> inline void getDistanceMatrix(Graph<Alignment<TStringSet, TCargo, TSpec> >& g, TMatrix& distanceMatrix, TSize ktup, TAlphabet, KmerDistance); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_distance.h"(144) 419 template <typename TStringSet, typename TCargo, typename TSpec, typename TMatrix, typename TSize> inline void getDistanceMatrix(Graph<Alignment<TStringSet, TCargo, TSpec> >& g, TMatrix& distanceMatrix, TSize ktup, KmerDistance); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_distance.h"(166) 420 template <typename TStringSet, typename TCargo, typename TSpec, typename TMatrix> inline void getDistanceMatrix(Graph<Alignment<TStringSet, TCargo, TSpec> >& g, TMatrix& distanceMatrix, KmerDistance); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_distance.h"(178) 421 template <typename TStringSet, typename TCargo, typename TSpec, typename TMatrix> inline void getDistanceMatrix(Graph<Alignment<TStringSet, TCargo, TSpec> >& g, TMatrix& distanceMatrix); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_distance.h"(213) 422 423 //____________________________________________________________________________ 424 // getKmerSimilarityMatrix 425 426 template <typename TString, typename TSpec, typename THitMatrix, typename TSize, typename TAlphabet> inline void getKmerSimilarityMatrix(StringSet<TString, TSpec> const& strSet, THitMatrix& mat, TSize ktup, TAlphabet); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_kmer.h"(93) 427 428 //____________________________________________________________________________ 429 // globalMsaAlignment 430 431 template <typename TStringSet, typename TCargo, typename TSpec, typename TStringSet1, typename TNames, typename TAlphabet, typename TScore> inline void globalMsaAlignment(Graph<Alignment<TStringSet, TCargo, TSpec> >& gAlign, TStringSet1& sequenceSet, TNames& sequenceNames, MsaOptions<TAlphabet, TScore> const& msaOpt); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_msa.h"(222) 432 template <typename TStringSet, typename TCargo, typename TSpec, typename TScore> inline void globalMsaAlignment(Graph<Alignment<TStringSet, TCargo, TSpec> >& gAlign, TScore const& scoreObject); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_msa.h"(377) 433 template <typename TSource, typename TSpec, typename TScore> inline void globalMsaAlignment(Align<TSource, TSpec>& align, TScore const& scoreObject); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_msa.h"(397) 434 435 //____________________________________________________________________________ 436 // graphBasedTripletLibraryExtension 437 438 template <typename TStringSet, typename TCargo, typename TSpec> inline void graphBasedTripletLibraryExtension(Graph<Alignment<TStringSet, TCargo, TSpec> >& g); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(599) 439 440 //____________________________________________________________________________ 441 // heaviestMatching 442 443 template <typename TStringSet, typename TCargo, typename TSpec, typename TString, typename TOutString> inline TCargo heaviestMatching(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g, TString const& str1, TString const& str2, TOutString& align); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_progressive.h"(245) 444 445 //____________________________________________________________________________ 446 // msaRefinement 447 448 template <typename TStringSet, typename TCargo, typename TSpec, typename TScore> inline void msaRefinement(Graph<Alignment<TStringSet, TCargo, TSpec> >& gAlign, TScore& sc); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_refinement.h"(501) 449 450 //____________________________________________________________________________ 451 // njTree 452 453 template <typename TValue, typename TStringSpec, typename TCargo, typename TSpec> inline void njTree(String<TValue, TStringSpec>& mat, Graph<Tree<TCargo, TSpec> >& g); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_guidetree.h"(72) 454 455 //____________________________________________________________________________ 456 // progressiveAlignment 457 458 template <typename TStringSet, typename TCargo, typename TSpec, typename TGuideTree, typename TOutGraph> inline void progressiveAlignment(Graph<Alignment<TStringSet, TCargo, TSpec> >& g, TGuideTree& tree, TOutGraph& gOut); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_progressive.h"(136) 459 460 //____________________________________________________________________________ 461 // progressiveMatching 462 463 template <typename TStringSet, typename TCargo, typename TSpec, typename TGuideTree, typename TEdgeMap, typename TOutGraph> inline void progressiveMatching(Graph<Alignment<TStringSet, TCargo, TSpec> >& g, TGuideTree& tree, TEdgeMap& edgeMap, TOutGraph& gOut, TEdgeMap& edgeMapOut); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_progressive.h"(471) 464 465 //____________________________________________________________________________ 466 // read 467 468 template <typename TFile, typename TFragment, typename TSpec, typename TScoreValue, typename TSpec2, typename TNames> void read(TFile & file, String<TFragment, TSpec>& matches, String<TScoreValue, TSpec2>& scores, TNames const& names, TCoffeeLib); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(113) 469 template <typename TFile, typename TString, typename TSpec, typename TNames> void read(TFile & file, StringSet<TString, TSpec>& oriStr, TNames& names, TCoffeeLib); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(235) 470 template <typename TFile, typename TString, typename TSpec, typename TNames> void read(TFile & file, StringSet<TString, TSpec>& oriStr, TNames& names, FastaAlign); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(355) 471 template <typename TFile, typename TFragment, typename TSpec, typename TScoreValue, typename TSpec2, typename TNames> void read(TFile & file, String<TFragment, TSpec>& matches, String<TScoreValue, TSpec2>& scores, TNames const& origNames, FastaAlign); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(459) 472 template <typename TFile, typename TFragment, typename TSpec1, typename TScoreValue, typename TSpec2, typename TNames> inline void read(TFile & file, String<TFragment, TSpec1>& matches, String<TScoreValue, TSpec2>& scores, TNames& names, BlastLib); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(557) 473 template <typename TFile, typename TFragment, typename TSpec1, typename TScoreValue, typename TSpec2, typename TStringSet, typename TNames> inline void read(TFile & file, String<TFragment, TSpec1>& matches, String<TScoreValue, TSpec2>& scores, TStringSet const& strSet, TNames const& names, MummerLib); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(761) 474 template <typename TFile, typename TCargo, typename TSpec, typename TNames> void read(TFile & file, Graph<Tree<TCargo, TSpec> >& guideTree, TNames& names, NewickFormat); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(826) 475 476 //____________________________________________________________________________ 477 // score 478 479 template <typename TValue, typename TScoreMember, typename TPos1, typename TPos2, typename TSeq1, typename TSeq2> inline TValue score(Score<TValue, ProfileProfileScore<TScoreMember> > const & me, TPos1 pos1, TPos2 pos2, TSeq1 const &seq1, TSeq2 const &seq2); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_refinement.h"(242) 480 481 //____________________________________________________________________________ 482 // scoreGapExtendHorizontal 483 484 template <typename TValue, typename TScoreMember, typename TPos1, typename TPos2, typename TSeq1, typename TSeq2> inline TValue scoreGapExtendHorizontal( Score<TValue, ProfileProfileScore<TScoreMember> > const & me, TPos1 pos1, TPos2, TSeq1 const& seq1, TSeq2 const&); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_refinement.h"(135) 485 486 //____________________________________________________________________________ 487 // scoreGapExtendVertical 488 489 template <typename TValue, typename TScoreMember, typename TPos1, typename TPos2, typename TSeq1, typename TSeq2> inline TValue scoreGapExtendVertical( Score<TValue, ProfileProfileScore<TScoreMember> > const & me, TPos1, TPos2 pos2, TSeq1 const &, TSeq2 const & seq2); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_refinement.h"(189) 490 491 //____________________________________________________________________________ 492 // scoreGapOpenHorizontal 493 494 template <typename TValue, typename TScoreMember, typename TPos1, typename TPos2, typename TSeq1, typename TSeq2> inline TValue scoreGapOpenHorizontal( Score<TValue, ProfileProfileScore<TScoreMember> > const & me, TPos1 pos1, TPos2, TSeq1 const & seq1, TSeq2 const &); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_refinement.h"(161) 495 496 //____________________________________________________________________________ 497 // scoreGapOpenVertical 498 499 template <typename TValue, typename TScoreMember, typename TPos1, typename TPos2, typename TSeq1, typename TSeq2> inline TValue scoreGapOpenVertical( Score<TValue, ProfileProfileScore<TScoreMember> > const & me, TPos1, TPos2 pos2, TSeq1 const &, TSeq2 const & seq2); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_refinement.h"(215) 500 501 //____________________________________________________________________________ 502 // selectPairs 503 504 template <typename TString, typename TSpec, typename TSize2, typename TSpec2> inline void selectPairs(StringSet<TString, TSpec> const& str, String<TSize2, TSpec2>& pList); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_library.h"(111) 505 506 //____________________________________________________________________________ 507 // sumOfPairsScore 508 509 template <typename TStringSet, typename TCargo, typename TSpec, typename TScore> inline typename Value<TScore>::Type sumOfPairsScore(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g, TScore const& score_type); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(762) 510 511 //____________________________________________________________________________ 512 // sumOfPairsScoreInd 513 514 template <typename TStringSet, typename TCargo, typename TSpec, typename TScore> inline typename Value<TScore>::Type sumOfPairsScoreInd(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g, TScore const& score_type); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(818) 515 516 //____________________________________________________________________________ 517 // tripletLibraryExtension 518 519 template <typename TStringSet, typename TCargo, typename TSpec> inline void tripletLibraryExtension(Graph<Alignment<TStringSet, TCargo, TSpec> >& g); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(307) 520 template <typename TStringSet, typename TCargo, typename TSpec, typename TGuideTree, typename TSize> inline void tripletLibraryExtension(Graph<Alignment<TStringSet, TCargo, TSpec> >& g, TGuideTree& guideTree, TSize minMembers); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_base.h"(505) 521 522 //____________________________________________________________________________ 523 // upgmaTree 524 525 template <typename TStringValue, typename TStringSpec, typename TCargo, typename TSpec, typename TTag> inline void upgmaTree(String<TStringValue, TStringSpec>& mat, Graph<Tree<TCargo, TSpec> >& g, TTag); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_guidetree.h"(582) 526 template <typename TValue, typename TSpec1, typename TCargo, typename TSpec2, typename TTag> inline void upgmaTree(Graph<Undirected<TValue, TSpec1> >& pairGraph, Graph<Tree<TCargo, TSpec2> >& g, TTag); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_guidetree.h"(698) 527 template <typename TDistance, typename TCargo, typename TSpec> inline void upgmaTree(TDistance& dist, Graph<Tree<TCargo, TSpec> >& g); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_guidetree.h"(874) 528 529 //____________________________________________________________________________ 530 // write 531 532 template <typename TFile, typename TStringSet, typename TCargo, typename TSpec, typename TNames> void write(TFile & file, Graph<Alignment<TStringSet, TCargo, TSpec> > const& g, TNames& names, TCoffeeLib); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(271) 533 template <typename TFile, typename TStringSet, typename TCargo, typename TSpec, typename TNames, typename TEdgeMap> void write(TFile & file, Graph<Alignment<TStringSet, TCargo, TSpec> > const& g, TNames& names, TEdgeMap& edgeMap, BlastLib); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(632) 534 template <typename TFile, typename TStringSet, typename TCargo, typename TSpec, typename TNames> void write(TFile & file, Graph<Alignment<TStringSet, TCargo, TSpec> > const& g, TNames& names, BlastLib); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(699) 535 template <typename TFile, typename TCargo, typename TSpec, typename TNames> void write(TFile & file, Graph<Tree<TCargo, TSpec> >& guideTree, TNames& names, bool collapseRoot, NewickFormat); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(1016) 536 template <typename TFile, typename TCargo, typename TSpec, typename TNames> void write(TFile & file, Graph<Tree<TCargo, TSpec> >& guideTree, TNames& names, NewickFormat); // "seqan-1.3.1/seqan/graph_msa/graph_align_tcoffee_io.h"(1036) 537 538 } //namespace SEQAN_NAMESPACE_MAIN 539 540 #endif 541 542