/dports/biology/ncbi-toolkit/ncbi/algo/blast/composition_adjustment/ |
H A D | smith_waterman.c | 86 for (queryPos = 0; queryPos < queryLength; queryPos++) { in BLbasicSmithWatermanScoreOnly() 88 matrixRow = matrix[queryPos]; in BLbasicSmithWatermanScoreOnly() 122 bestQueryPos = queryPos; in BLbasicSmithWatermanScoreOnly() 180 for (queryPos = queryEnd; queryPos >= 0; queryPos--) { in BLSmithWatermanFindStart() 182 matrixRow = matrix[queryPos]; in BLSmithWatermanFindStart() 216 bestQueryPos = queryPos; in BLSmithWatermanFindStart() 281 for (queryPos = 0; queryPos < queryLength; queryPos++) { in BLspecialSmithWatermanScoreOnly() 283 matrixRow = matrix[queryPos]; in BLspecialSmithWatermanScoreOnly() 328 bestQueryPos = queryPos; in BLspecialSmithWatermanScoreOnly() 392 for (queryPos = queryEnd; queryPos >= 0; queryPos--) { in BLspecialSmithWatermanFindStart() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/composition_adjustment/ |
H A D | smith_waterman.c | 86 for (queryPos = 0; queryPos < queryLength; queryPos++) { in BLbasicSmithWatermanScoreOnly() 88 matrixRow = matrix[queryPos]; in BLbasicSmithWatermanScoreOnly() 122 bestQueryPos = queryPos; in BLbasicSmithWatermanScoreOnly() 180 for (queryPos = queryEnd; queryPos >= 0; queryPos--) { in BLSmithWatermanFindStart() 182 matrixRow = matrix[queryPos]; in BLSmithWatermanFindStart() 216 bestQueryPos = queryPos; in BLSmithWatermanFindStart() 281 for (queryPos = 0; queryPos < queryLength; queryPos++) { in BLspecialSmithWatermanScoreOnly() 283 matrixRow = matrix[queryPos]; in BLspecialSmithWatermanScoreOnly() 328 bestQueryPos = queryPos; in BLspecialSmithWatermanScoreOnly() 392 for (queryPos = queryEnd; queryPos >= 0; queryPos--) { in BLspecialSmithWatermanFindStart() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/composition_adjustment/ |
H A D | smith_waterman.c | 86 for (queryPos = 0; queryPos < queryLength; queryPos++) { in BLbasicSmithWatermanScoreOnly() 88 matrixRow = matrix[queryPos]; in BLbasicSmithWatermanScoreOnly() 122 bestQueryPos = queryPos; in BLbasicSmithWatermanScoreOnly() 180 for (queryPos = queryEnd; queryPos >= 0; queryPos--) { in BLSmithWatermanFindStart() 182 matrixRow = matrix[queryPos]; in BLSmithWatermanFindStart() 216 bestQueryPos = queryPos; in BLSmithWatermanFindStart() 281 for (queryPos = 0; queryPos < queryLength; queryPos++) { in BLspecialSmithWatermanScoreOnly() 283 matrixRow = matrix[queryPos]; in BLspecialSmithWatermanScoreOnly() 328 bestQueryPos = queryPos; in BLspecialSmithWatermanScoreOnly() 392 for (queryPos = queryEnd; queryPos >= 0; queryPos--) { in BLspecialSmithWatermanFindStart() [all …]
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/dports/biology/mmseqs2/MMseqs2-13-45111/src/alignment/ |
H A D | MultipleAlignment.cpp | 53 size_t queryPos = 0; in computeQueryGaps() local 56 queryPos = alignment.qStartPos; in computeQueryGaps() 62 ++queryPos; in computeQueryGaps() 67 ++queryPos; in computeQueryGaps() 83 for(int queryPos = 0; queryPos < centerSeq->L; queryPos++) { in updateGapsInCenterSequence() local 108 unsigned int queryPos = result.qStartPos; in updateGapsInSequenceSet() local 133 queryPos++; in updateGapsInSequenceSet() 150 queryPos++; in updateGapsInSequenceSet() 154 queryPos++; in updateGapsInSequenceSet() 171 queryPos++; in updateGapsInSequenceSet() [all …]
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H A D | Matcher.cpp | 96 int32_t targetPos = alignment.dbStartPos1, queryPos = alignment.qStartPos1; in getSWResult() local 104 … if (dbSeq->numSequence[targetPos] == currentQuery->numSequence[queryPos]){ in getSWResult() 107 ++queryPos; in getSWResult() 112 ++queryPos; in getSWResult() 387 int queryPos = result.qStartPos; in updateResultByRescoringBacktrace() local 395 … curr = subMat[static_cast<int>(querySeq[queryPos])][static_cast<int>(targetSeq[targetPos])]; in updateResultByRescoringBacktrace() 396 identicalAAs += (querySeq[queryPos] == targetSeq[targetPos]); in updateResultByRescoringBacktrace() 409 minQueryPos = (letter == 'D') ? queryPos - 1 : queryPos; in updateResultByRescoringBacktrace() 416 maxQueryEndPos = queryPos; in updateResultByRescoringBacktrace() 424 queryPos += (letter == 'M' || letter == 'I') ? 1 : 0; in updateResultByRescoringBacktrace()
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/dports/biology/ncbi-toolkit/ncbi/api/ |
H A D | needleman.c | 335 for (queryPos = 0; queryPos < queryLength; queryPos++) { in NeedlemanWunschQuadraticByLoc() 336 … edit_array[queryPos] = ((Uint1Ptr) edit_array)+queryLength*sizeof(Uint1Ptr)+dbBytes*queryPos; in NeedlemanWunschQuadraticByLoc() 337 scoreVector[queryPos].noGap = 0; in NeedlemanWunschQuadraticByLoc() 347 for(queryPos = QueryMin; queryPos <=QueryMax; queryPos++) { in NeedlemanWunschQuadraticByLoc() 379 scoreVector[queryPos].noGap = newScore; in NeedlemanWunschQuadraticByLoc() 382 edit_array[queryPos][dbPos>>2]=edit_c; in NeedlemanWunschQuadraticByLoc() 386 bestQueryPos = queryPos; in NeedlemanWunschQuadraticByLoc() 397 queryPos = queryLength-1; in NeedlemanWunschQuadraticByLoc() 403 while(dbPos>=0 && queryPos>=0) { in NeedlemanWunschQuadraticByLoc() 431 queryPos--; in NeedlemanWunschQuadraticByLoc() [all …]
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/dports/biology/ncbi-toolkit/ncbi/demo/ |
H A D | profiles.c | 535 for (queryPos = 0; queryPos < queryLength; queryPos++) { in basicSmithWatermanScoreOnly() 544 for(queryPos = 0; queryPos < queryLength; queryPos++) { in basicSmithWatermanScoreOnly() 629 for (queryPos = 0; queryPos < queryLength; queryPos++) { in SmithWatermanFindStartGivenEnd() 638 for(queryPos = queryEnd; queryPos >= 0; queryPos--) { in SmithWatermanFindStartGivenEnd() 733 for (queryPos = 0; queryPos < queryLength; queryPos++) { in specialSmithWatermanScoreOnly() 742 for(queryPos = 0; queryPos < queryLength; queryPos++) { in specialSmithWatermanScoreOnly() 779 bestQueryPos = queryPos; in specialSmithWatermanScoreOnly() 842 for (queryPos = 0; queryPos < queryLength; queryPos++) { in specialSmithWatermanFindStartGivenEnd() 851 for(queryPos = queryEnd; queryPos >= 0; queryPos--) { in specialSmithWatermanFindStartGivenEnd() 1571 for (queryPos= 0; queryPos < queryLength; queryPos++) in Main() [all …]
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H A D | seedtop.c | 163 Int4 queryPos; /*index over query sequence*/ in Main() local 321 for (queryPos = 0; queryPos < queryLength; queryPos++) in Main() 322 query[queryPos] = seedSearch->order[query[queryPos]]; in Main() 324 for (queryPos = 0; queryPos < queryLength; queryPos++) in Main() 325 unfilter_query[queryPos] = seedSearch->order[unfilter_query[queryPos]]; in Main()
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/dports/www/bolt/bolt-2.2.24/vendor/guzzle/guzzle/src/Guzzle/Parser/Url/ |
H A D | UrlParser.php | 38 $queryPos = strpos($url, '?'); 40 $parts['query'] = substr($url, $queryPos + 1, strpos($url, '#') - $queryPos - 1); 42 $parts['query'] = substr($url, $queryPos + 1);
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/dports/java/openjdk11/jdk11u-jdk-11.0.13-8-1/src/java.desktop/share/classes/sun/awt/ |
H A D | GlobalCursorManager.java | 174 Point queryPos = null, p = null; in _updateCursor() local 190 queryPos = new Point(); in _updateCursor() 191 getCursorPos(queryPos); in _updateCursor() 194 queryPos.x - p.x, queryPos.y - p.y, false); in _updateCursor()
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/dports/java/openjdk13/jdk13u-jdk-13.0.10-1-1/src/java.desktop/share/classes/sun/awt/ |
H A D | GlobalCursorManager.java | 174 Point queryPos = null, p = null; in _updateCursor() local 190 queryPos = new Point(); in _updateCursor() 191 getCursorPos(queryPos); in _updateCursor() 194 queryPos.x - p.x, queryPos.y - p.y, false); in _updateCursor()
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/dports/java/openjdk11-jre/jdk11u-jdk-11.0.13-8-1/src/java.desktop/share/classes/sun/awt/ |
H A D | GlobalCursorManager.java | 174 Point queryPos = null, p = null; in _updateCursor() local 190 queryPos = new Point(); in _updateCursor() 191 getCursorPos(queryPos); in _updateCursor() 194 queryPos.x - p.x, queryPos.y - p.y, false); in _updateCursor()
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/dports/java/openjdk8/jdk8u-jdk8u312-b07.1/jdk/src/share/classes/sun/awt/ |
H A D | GlobalCursorManager.java | 174 Point queryPos = null, p = null; in _updateCursor() local 190 queryPos = new Point(); in _updateCursor() 191 getCursorPos(queryPos); in _updateCursor() 194 queryPos.x - p.x, queryPos.y - p.y, false); in _updateCursor()
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/dports/java/openjdk16/jdk16u-jdk-16.0.2-7-1/src/java.desktop/share/classes/sun/awt/ |
H A D | GlobalCursorManager.java | 174 Point queryPos = null, p = null; in _updateCursor() local 190 queryPos = new Point(); in _updateCursor() 191 getCursorPos(queryPos); in _updateCursor() 194 queryPos.x - p.x, queryPos.y - p.y, false); in _updateCursor()
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/dports/java/openjdk17/jdk17u-jdk-17.0.1-12-1/src/java.desktop/share/classes/sun/awt/ |
H A D | GlobalCursorManager.java | 174 Point queryPos = null, p = null; in _updateCursor() local 190 queryPos = new Point(); in _updateCursor() 191 getCursorPos(queryPos); in _updateCursor() 194 queryPos.x - p.x, queryPos.y - p.y, false); in _updateCursor()
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/dports/java/openjdk12/openjdk-jdk12u-jdk-12.0.2-10-4/src/java.desktop/share/classes/sun/awt/ |
H A D | GlobalCursorManager.java | 174 Point queryPos = null, p = null; in _updateCursor() local 190 queryPos = new Point(); in _updateCursor() 191 getCursorPos(queryPos); in _updateCursor() 194 queryPos.x - p.x, queryPos.y - p.y, false); in _updateCursor()
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/dports/java/openjdk15/jdk15u-jdk-15.0.6-1-1/src/java.desktop/share/classes/sun/awt/ |
H A D | GlobalCursorManager.java | 174 Point queryPos = null, p = null; in _updateCursor() local 190 queryPos = new Point(); in _updateCursor() 191 getCursorPos(queryPos); in _updateCursor() 194 queryPos.x - p.x, queryPos.y - p.y, false); in _updateCursor()
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/dports/java/openjdk14/jdk14u-jdk-14.0.2-12-1/src/java.desktop/share/classes/sun/awt/ |
H A D | GlobalCursorManager.java | 174 Point queryPos = null, p = null; in _updateCursor() local 190 queryPos = new Point(); in _updateCursor() 191 getCursorPos(queryPos); in _updateCursor() 194 queryPos.x - p.x, queryPos.y - p.y, false); in _updateCursor()
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/dports/java/openjdk8-jre/jdk8u-jdk8u312-b07.1/jdk/src/share/classes/sun/awt/ |
H A D | GlobalCursorManager.java | 174 Point queryPos = null, p = null; in _updateCursor() local 190 queryPos = new Point(); in _updateCursor() 191 getCursorPos(queryPos); in _updateCursor() 194 queryPos.x - p.x, queryPos.y - p.y, false); in _updateCursor()
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/dports/biology/mmseqs2/MMseqs2-13-45111/src/test/ |
H A D | TestProfileAlignment.cpp | 802 int32_t targetPos = alignment.dbStartPos1, queryPos = alignment.qStartPos1; in main() local 809 if (dbSeq->numSequence[targetPos] == s->numSequence[queryPos]){ in main() 813 fprintf(stdout,"%c",subMat.num2aa[s->numSequence[queryPos]]); in main() 814 ++queryPos; in main() 818 fprintf(stdout,"%c |",subMat.num2aa[s->numSequence[queryPos]]); in main() 819 ++queryPos; in main()
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H A D | TestAlignment.cpp | 94 int32_t targetPos = alignment.dbStartPos1, queryPos = alignment.qStartPos1; in main() local 100 fprintf(stdout,"%c",subMat.num2aa[s->numSequence[queryPos]]); in main() 102 if (dbSeq->numSequence[targetPos] == s->numSequence[queryPos]){ in main() 109 ++queryPos; in main() 113 fprintf(stdout,"%c",subMat.num2aa[s->numSequence[queryPos]]); in main() 116 ++queryPos; in main()
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/dports/devel/liteide/gotools-eff8693b15f0/oracle/oracle/ |
H A D | oracle.go | 54 type queryPos struct { struct 63 func (qpos *queryPos) typeString(T types.Type) string { argument 68 func (qpos *queryPos) objectString(obj types.Object) string { argument 73 func (qpos *queryPos) selectionString(sel *types.Selection) string { argument 275 func parseQueryPos(lprog *loader.Program, posFlag string, needExact bool) (*queryPos, error) { 291 return &queryPos{lprog.Fset, start, end, path, exact, info}, nil 357 case *queryPos:
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/dports/audio/faust/faust-2.37.3/tools/physicalModeling/mesh2faust/vega/libraries/sceneObjectReduced/ |
H A D | sceneObjectReducedCPU6DOF.cpp | 127 int SceneObjectReducedCPU6DOF::GetClosestVertex(Vec3d & queryPos, double * distance, double * auxVe… in GetClosestVertex() argument 130 double queryPosv[3] = { queryPos[0], queryPos[1], queryPos[2] }; in GetClosestVertex()
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/dports/security/vault/vault-1.8.2/vendor/golang.org/x/tools/cmd/guru/ |
H A D | peers.go | 130 queryPos: opPos, 145 func findOp(qpos *queryPos) token.Pos { argument 199 queryPos token.Pos // of queried channel op member 206 printf(r.queryPos, "This channel can't point to anything.") 209 printf(r.queryPos, "This channel of type %s may be:", r.queryType) 226 Pos: fset.Position(r.queryPos).String(),
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/dports/net/evans/evans-0.9.1/vendor/golang.org/x/tools/cmd/guru/ |
H A D | peers.go | 130 queryPos: opPos, 145 func findOp(qpos *queryPos) token.Pos { argument 199 queryPos token.Pos // of queried channel op member 206 printf(r.queryPos, "This channel can't point to anything.") 209 printf(r.queryPos, "This channel of type %s may be:", r.queryType) 226 Pos: fset.Position(r.queryPos).String(),
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