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/dports/biology/fastx-toolkit/fastx_toolkit-0.0.14/src/libfastx/
H A Dsequence_alignment.h76 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/align/
H A Dtest_local_align.h61 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()
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/dports/biology/seqan1/seqan-1.3.1/seqan/refinement/
H A Dgraph_algorithm_refine_aligngraph.h182 _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()
H A Dgraph_algorithm_refine_fragment.h163 _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()
H A Dgraph_algorithm_refine_exact.h285 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
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/graph_align/
H A Dgraph_algorithm_refine_aligngraph.h181 _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()
H A Dgraph_algorithm_refine_fragment.h157 _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()
H A Dgraph_algorithm_refine_exact.h279 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
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/graph_align/
H A Dgraph_algorithm_refine_aligngraph.h181 _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()
H A Dgraph_algorithm_refine_fragment.h157 _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()
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/graph_align/
H A Dgraph_algorithm_refine_aligngraph.h183 _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()
H A Dgraph_algorithm_refine_fragment.h161 _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()
/dports/games/neverball/neverball-1.6.0/ball/
H A Dutil.c153 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/graph_msa/
H A Dtest_graph_tcoffee.h68 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/
H A Dseqalign_set_convert.cpp71 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/
H A Dseqalign_set_convert.cpp71 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()
/dports/lang/gcc9/gcc-9.4.0/gcc/testsuite/g++.dg/lto/
H A Dpr96591_0.C26 using score_type = typename builtin_simd<int, 1>::type; variable
27 score_type data[1]{fill<score_type>(8)};
/dports/lang/gcc11-devel/gcc-11-20211009/gcc/testsuite/g++.dg/lto/
H A Dpr96591_0.C26 using score_type = typename builtin_simd<int, 1>::type; variable
27 score_type data[1]{fill<score_type>(8)};
/dports/lang/gcc11/gcc-11.2.0/gcc/testsuite/g++.dg/lto/
H A Dpr96591_0.C26 using score_type = typename builtin_simd<int, 1>::type; variable
27 score_type data[1]{fill<score_type>(8)};
/dports/misc/cxx_atomics_pic/gcc-11.2.0/gcc/testsuite/g++.dg/lto/
H A Dpr96591_0.C26 using score_type = typename builtin_simd<int, 1>::type; variable
27 score_type data[1]{fill<score_type>(8)};
/dports/lang/gcc10/gcc-10.3.0/gcc/testsuite/g++.dg/lto/
H A Dpr96591_0.C26 using score_type = typename builtin_simd<int, 1>::type; variable
27 score_type data[1]{fill<score_type>(8)};
/dports/lang/gcc9-devel/gcc-9-20211007/gcc/testsuite/g++.dg/lto/
H A Dpr96591_0.C26 using score_type = typename builtin_simd<int, 1>::type; variable
27 score_type data[1]{fill<score_type>(8)};
/dports/lang/gcc8/gcc-8.5.0/gcc/testsuite/g++.dg/lto/
H A Dpr96591_0.C26 using score_type = typename builtin_simd<int, 1>::type; variable
27 score_type data[1]{fill<score_type>(8)};
/dports/lang/gcc10-devel/gcc-10-20211008/gcc/testsuite/g++.dg/lto/
H A Dpr96591_0.C26 using score_type = typename builtin_simd<int, 1>::type; variable
27 score_type data[1]{fill<score_type>(8)};
/dports/lang/gcc12-devel/gcc-12-20211205/gcc/testsuite/g++.dg/lto/
H A Dpr96591_0.C26 using score_type = typename builtin_simd<int, 1>::type; variable
27 score_type data[1]{fill<score_type>(8)};

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