/dports/biology/fastx-toolkit/fastx_toolkit-0.0.14/src/libfastx/ |
H A D | sequence_alignment.h | 76 typedef float score_type; typedef 86 std::vector < score_type > query_border ; 87 std::vector < score_type > target_border ; 89 std::vector< std::vector< score_type > > score_matrix ; 93 score_type _gap_panelty ; 94 score_type _match_panelty ; 95 score_type _mismatch_panelty ; 96 score_type _neutral_panelty ; 111 score_type gap_panelty() const { return _gap_panelty ; } in gap_panelty() 112 score_type match_panelty() const { return _match_panelty ; } in match_panelty() [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/align/ |
H A D | test_local_align.h | 61 Score<int> score_type = Score<int>(2,-1,-2,0) ; in SEQAN_DEFINE_TEST() local 66 int score = _smithWaterman(ali,sw_finder,score_type,cutoff); in SEQAN_DEFINE_TEST() 75 score = _smithWatermanGetNext(ali,sw_finder,score_type,cutoff); in SEQAN_DEFINE_TEST() 215 Score<int> score_type = Score<int>(2,-1,-2,0) ; in SEQAN_DEFINE_TEST() local 218 int score = localAlignment(ali, sw_finder, score_type, 5); in SEQAN_DEFINE_TEST() 223 score = localAlignment(ali, sw_finder, score_type, 5); in SEQAN_DEFINE_TEST() 228 score = localAlignment(ali, sw_finder, score_type, 5, WatermanEggert()); in SEQAN_DEFINE_TEST() 238 Score<int> score_type = Score<int>(2,-1,-2,-2); in SEQAN_DEFINE_TEST() local 252 score = localAlignment(align, finder, score_type, 5, -6, 6, BandedWatermanEggert()); in SEQAN_DEFINE_TEST() 257 score = localAlignment(align, finder, score_type, 5, -6, 6, BandedWatermanEggert()); in SEQAN_DEFINE_TEST() [all …]
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/dports/biology/seqan1/seqan-1.3.1/seqan/refinement/ |
H A D | graph_algorithm_refine_aligngraph.h | 182 _getRefinedMatchScore(Score<TScoreValue,TScoreSpec> & score_type, in _getRefinedMatchScore() argument 228 ret_score += rest * scoreGapExtend(score_type); in _getRefinedMatchScore() 231 ret_score += len * scoreGapExtend(score_type); in _getRefinedMatchScore() 237 ret_score += len * scoreGapExtend(score_type); in _getRefinedMatchScore() 251 ret_score += (next_pos_j-pos_j) * scoreGapExtend(score_type); in _getRefinedMatchScore() 258 …ret_score += score(score_type,getValueById(seqs,seq_i_id)[pos_i++],getValueById(seqs,seq_j_id)[pos… in _getRefinedMatchScore() 267 ret_score += (last_pos_j-pos_j) * scoreGapExtend(score_type); in _getRefinedMatchScore() 275 ret_score += rest * scoreGapExtend(score_type); in _getRefinedMatchScore() 278 ret_score += len * scoreGapExtend(score_type); in _getRefinedMatchScore()
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H A D | graph_algorithm_refine_fragment.h | 163 _getRefinedMatchScore(Score<TScoreValue,TScoreSpec> & score_type, in _getRefinedMatchScore() argument 181 ret_score += score(score_type,*label_it0,*label_it1); in _getRefinedMatchScore() 194 _getRefinedMatchScore(Score<TScoreValue, Simple> & score_type, in _getRefinedMatchScore() argument 203 return len*scoreMatch(score_type); in _getRefinedMatchScore()
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H A D | graph_algorithm_refine_exact.h | 285 TScore & score_type, in _makeRefinedGraphEdges() argument 320 …typename Value<TScore>::Type score = _getRefinedMatchScore(score_type,seqs,*ali_it,act_pos,pos_j,f… in _makeRefinedGraphEdges() 322 score *= _getRefinedAnnoScore(ali_g,pm,vd,act_knot,score_type); in _makeRefinedGraphEdges() 359 TScore & score_type, in _makeAlignmentGraphFromRefinedSegments() argument 377 _makeRefinedGraphEdges(alis,pm,seqs,seq_map,score_type,ali_g,tag); in _makeAlignmentGraphFromRefinedSegments() 391 TScore & score_type, in _makeAlignmentGraphFromRefinedSegments() argument 415 _makeRefinedGraphEdges(alis,pm,seqs,seq_map,score_type,ali_g,tag); in _makeAlignmentGraphFromRefinedSegments() 435 TScore & score_type, in matchRefinement() argument 531 …_makeAlignmentGraphFromRefinedSegments(all_nodes,alis,score_type,seq,seq_map,ali_graph,tag,annotat… in matchRefinement() 542 Score<TScoreValue,TScoreSpec> & score_type, in matchRefinement() argument [all …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/graph_align/ |
H A D | graph_algorithm_refine_aligngraph.h | 181 _getRefinedMatchScore(Score<TScoreValue,TScoreSpec> & score_type, in _getRefinedMatchScore() argument 225 ret_score += rest * scoreGapExtend(score_type); in _getRefinedMatchScore() 228 ret_score += len * scoreGapExtend(score_type); in _getRefinedMatchScore() 234 ret_score += len * scoreGapExtend(score_type); in _getRefinedMatchScore() 248 ret_score += (next_pos_j-pos_j) * scoreGapExtend(score_type); in _getRefinedMatchScore() 255 …ret_score += score(score_type,getValueById(seqs,seq_i_id)[pos_i++],getValueById(seqs,seq_j_id)[pos… in _getRefinedMatchScore() 264 ret_score += (last_pos_j-pos_j) * scoreGapExtend(score_type); in _getRefinedMatchScore() 272 ret_score += rest * scoreGapExtend(score_type); in _getRefinedMatchScore() 275 ret_score += len * scoreGapExtend(score_type); in _getRefinedMatchScore()
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H A D | graph_algorithm_refine_fragment.h | 157 _getRefinedMatchScore(Score<TScoreValue,TScoreSpec> & score_type, in _getRefinedMatchScore() argument 174 ret_score += score(score_type,*label_it0,*label_it1); in _getRefinedMatchScore() 187 _getRefinedMatchScore(Score<TScoreValue, Simple> & score_type, in _getRefinedMatchScore() argument 195 return len*scoreMatch(score_type); in _getRefinedMatchScore()
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H A D | graph_algorithm_refine_exact.h | 279 TScore & score_type, in _makeRefinedGraphEdges() argument 313 …typename Value<TScore>::Type score = _getRefinedMatchScore(score_type,seqs,*ali_it,act_pos,pos_j,f… in _makeRefinedGraphEdges() 315 score *= _getRefinedAnnoScore(ali_g,pm,vd,act_knot,score_type); in _makeRefinedGraphEdges() 352 TScore & score_type, in _makeAlignmentGraphFromRefinedSegments() argument 369 _makeRefinedGraphEdges(alis,pm,seqs,seq_map,score_type,ali_g,tag); in _makeAlignmentGraphFromRefinedSegments() 383 TScore & score_type, in _makeAlignmentGraphFromRefinedSegments() argument 406 _makeRefinedGraphEdges(alis,pm,seqs,seq_map,score_type,ali_g,tag); in _makeAlignmentGraphFromRefinedSegments() 426 TScore & score_type, in matchRefinement() argument 521 …_makeAlignmentGraphFromRefinedSegments(all_nodes,alis,score_type,seq,seq_map,ali_graph,tag,annotat… in matchRefinement() 532 Score<TScoreValue,TScoreSpec> & score_type, in matchRefinement() argument [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/graph_align/ |
H A D | graph_algorithm_refine_aligngraph.h | 181 _getRefinedMatchScore(Score<TScoreValue,TScoreSpec> & score_type, in _getRefinedMatchScore() argument 225 ret_score += rest * scoreGapExtend(score_type); in _getRefinedMatchScore() 228 ret_score += len * scoreGapExtend(score_type); in _getRefinedMatchScore() 234 ret_score += len * scoreGapExtend(score_type); in _getRefinedMatchScore() 248 ret_score += (next_pos_j-pos_j) * scoreGapExtend(score_type); in _getRefinedMatchScore() 255 …ret_score += score(score_type,getValueById(seqs,seq_i_id)[pos_i++],getValueById(seqs,seq_j_id)[pos… in _getRefinedMatchScore() 264 ret_score += (last_pos_j-pos_j) * scoreGapExtend(score_type); in _getRefinedMatchScore() 272 ret_score += rest * scoreGapExtend(score_type); in _getRefinedMatchScore() 275 ret_score += len * scoreGapExtend(score_type); in _getRefinedMatchScore()
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H A D | graph_algorithm_refine_fragment.h | 157 _getRefinedMatchScore(Score<TScoreValue,TScoreSpec> & score_type, in _getRefinedMatchScore() argument 174 ret_score += score(score_type,*label_it0,*label_it1); in _getRefinedMatchScore() 187 _getRefinedMatchScore(Score<TScoreValue, Simple> & score_type, in _getRefinedMatchScore() argument 195 return len*scoreMatch(score_type); in _getRefinedMatchScore()
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/graph_align/ |
H A D | graph_algorithm_refine_aligngraph.h | 183 _getRefinedMatchScore(Score<TScoreValue,TScoreSpec> & score_type, in _getRefinedMatchScore() argument 228 ret_score += rest * scoreGapExtend(score_type); in _getRefinedMatchScore() 231 ret_score += len * scoreGapExtend(score_type); in _getRefinedMatchScore() 237 ret_score += len * scoreGapExtend(score_type); in _getRefinedMatchScore() 251 ret_score += (next_pos_j-pos_j) * scoreGapExtend(score_type); in _getRefinedMatchScore() 258 …ret_score += score(score_type,getValueById(seqs,seq_i_id)[pos_i++],getValueById(seqs,seq_j_id)[pos… in _getRefinedMatchScore() 267 ret_score += (last_pos_j-pos_j) * scoreGapExtend(score_type); in _getRefinedMatchScore() 275 ret_score += rest * scoreGapExtend(score_type); in _getRefinedMatchScore() 278 ret_score += len * scoreGapExtend(score_type); in _getRefinedMatchScore()
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H A D | graph_algorithm_refine_fragment.h | 161 _getRefinedMatchScore(Score<TScoreValue,TScoreSpec> & score_type, in _getRefinedMatchScore() argument 179 ret_score += score(score_type,*label_it0,*label_it1); in _getRefinedMatchScore() 192 _getRefinedMatchScore(Score<TScoreValue, Simple> & score_type, in _getRefinedMatchScore() argument 201 return len*scoreMatch(score_type); in _getRefinedMatchScore()
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/dports/games/neverball/neverball-1.6.0/ball/ |
H A D | util.c | 153 static int score_type = GUI_SCORE_COIN; variable 165 while (!(types & score_type)) in gui_score_board() 166 score_type = GUI_SCORE_NEXT(score_type); in gui_score_board() 181 gui_set_hilite(coin_btn_id, score_type == GUI_SCORE_COIN); in gui_score_board() 188 gui_set_hilite(time_btn_id, score_type == GUI_SCORE_TIME); in gui_score_board() 225 switch (score_type) in set_score_board() 244 gui_set_hilite(coin_btn_id, (score_type == GUI_SCORE_COIN)); in set_score_board() 245 gui_set_hilite(time_btn_id, (score_type == GUI_SCORE_TIME)); in set_score_board() 246 gui_set_hilite(goal_btn_id, (score_type == GUI_SCORE_GOAL)); in set_score_board() 251 score_type = t; in gui_score_set() [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/graph_msa/ |
H A D | test_graph_tcoffee.h | 68 Blosum62 score_type(-1,-11); in Test_Distances() 72 … appendSegmentMatches(strSet, pList, score_type, matches, scores, dist, GlobalPairwiseLibrary() ); in Test_Distances() 121 Blosum62 score_type(-1,-11); in Test_Libraries() 134 appendSegmentMatches(strSet, pList, score_type, matches, scores, LocalPairwiseLibrary() ); in Test_Libraries() 140 … appendSegmentMatches(strSet, pList, score_type, matches, scores, noth, GlobalPairwiseLibrary() ); in Test_Libraries() 178 Blosum62 score_type(-1,-11); in Test_ExternalLibraries() 313 Score<int> score_type = Score<int>(5,-4,-2,-10); in Test_SumOfPairsScore() local 326 SEQAN_ASSERT(sumOfPairsScore(gOut, score_type) == -8); in Test_SumOfPairsScore() 327 SEQAN_ASSERT(sumOfPairsScoreInd(gOut, score_type) == 16); in Test_SumOfPairsScore() 425 Blosum62 score_type(-1,-11); in Test_Progressive() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/ |
H A D | seqalign_set_convert.cpp | 71 const string score_type = (*s)->GetId().GetStr(); in SetScores() local 72 if (score_type == "score") { in SetScores() 74 } else if (score_type == "e_value") { in SetScores() 76 } else if (score_type == "bit_score") { in SetScores() 78 } else if (score_type == "num_ident") { in SetScores()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/ |
H A D | seqalign_set_convert.cpp | 71 const string score_type = (*s)->GetId().GetStr(); in SetScores() local 72 if (score_type == "score") { in SetScores() 74 } else if (score_type == "e_value") { in SetScores() 76 } else if (score_type == "bit_score") { in SetScores() 78 } else if (score_type == "num_ident") { in SetScores()
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/dports/lang/gcc9/gcc-9.4.0/gcc/testsuite/g++.dg/lto/ |
H A D | pr96591_0.C | 26 using score_type = typename builtin_simd<int, 1>::type; variable 27 score_type data[1]{fill<score_type>(8)};
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/dports/lang/gcc11-devel/gcc-11-20211009/gcc/testsuite/g++.dg/lto/ |
H A D | pr96591_0.C | 26 using score_type = typename builtin_simd<int, 1>::type; variable 27 score_type data[1]{fill<score_type>(8)};
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/dports/lang/gcc11/gcc-11.2.0/gcc/testsuite/g++.dg/lto/ |
H A D | pr96591_0.C | 26 using score_type = typename builtin_simd<int, 1>::type; variable 27 score_type data[1]{fill<score_type>(8)};
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/dports/misc/cxx_atomics_pic/gcc-11.2.0/gcc/testsuite/g++.dg/lto/ |
H A D | pr96591_0.C | 26 using score_type = typename builtin_simd<int, 1>::type; variable 27 score_type data[1]{fill<score_type>(8)};
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/dports/lang/gcc10/gcc-10.3.0/gcc/testsuite/g++.dg/lto/ |
H A D | pr96591_0.C | 26 using score_type = typename builtin_simd<int, 1>::type; variable 27 score_type data[1]{fill<score_type>(8)};
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/dports/lang/gcc9-devel/gcc-9-20211007/gcc/testsuite/g++.dg/lto/ |
H A D | pr96591_0.C | 26 using score_type = typename builtin_simd<int, 1>::type; variable 27 score_type data[1]{fill<score_type>(8)};
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/dports/lang/gcc8/gcc-8.5.0/gcc/testsuite/g++.dg/lto/ |
H A D | pr96591_0.C | 26 using score_type = typename builtin_simd<int, 1>::type; variable 27 score_type data[1]{fill<score_type>(8)};
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/dports/lang/gcc10-devel/gcc-10-20211008/gcc/testsuite/g++.dg/lto/ |
H A D | pr96591_0.C | 26 using score_type = typename builtin_simd<int, 1>::type; variable 27 score_type data[1]{fill<score_type>(8)};
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/dports/lang/gcc12-devel/gcc-12-20211205/gcc/testsuite/g++.dg/lto/ |
H A D | pr96591_0.C | 26 using score_type = typename builtin_simd<int, 1>::type; variable 27 score_type data[1]{fill<score_type>(8)};
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