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Searched refs:queryPos (Results 1 – 25 of 440) sorted by relevance

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/dports/biology/ncbi-toolkit/ncbi/algo/blast/composition_adjustment/
H A Dsmith_waterman.c86 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/composition_adjustment/
H A Dsmith_waterman.c86 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/composition_adjustment/
H A Dsmith_waterman.c86 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()
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/dports/biology/mmseqs2/MMseqs2-13-45111/src/alignment/
H A DMultipleAlignment.cpp53 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()
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H A DMatcher.cpp96 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()
/dports/biology/ncbi-toolkit/ncbi/api/
H A Dneedleman.c335 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()
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/dports/biology/ncbi-toolkit/ncbi/demo/
H A Dprofiles.c535 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 …]
H A Dseedtop.c163 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()
/dports/www/bolt/bolt-2.2.24/vendor/guzzle/guzzle/src/Guzzle/Parser/Url/
H A DUrlParser.php38 $queryPos = strpos($url, '?');
40 $parts['query'] = substr($url, $queryPos + 1, strpos($url, '#') - $queryPos - 1);
42 $parts['query'] = substr($url, $queryPos + 1);
/dports/java/openjdk11/jdk11u-jdk-11.0.13-8-1/src/java.desktop/share/classes/sun/awt/
H A DGlobalCursorManager.java174 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()
/dports/java/openjdk13/jdk13u-jdk-13.0.10-1-1/src/java.desktop/share/classes/sun/awt/
H A DGlobalCursorManager.java174 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()
/dports/java/openjdk11-jre/jdk11u-jdk-11.0.13-8-1/src/java.desktop/share/classes/sun/awt/
H A DGlobalCursorManager.java174 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()
/dports/java/openjdk8/jdk8u-jdk8u312-b07.1/jdk/src/share/classes/sun/awt/
H A DGlobalCursorManager.java174 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()
/dports/java/openjdk16/jdk16u-jdk-16.0.2-7-1/src/java.desktop/share/classes/sun/awt/
H A DGlobalCursorManager.java174 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()
/dports/java/openjdk17/jdk17u-jdk-17.0.1-12-1/src/java.desktop/share/classes/sun/awt/
H A DGlobalCursorManager.java174 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()
/dports/java/openjdk12/openjdk-jdk12u-jdk-12.0.2-10-4/src/java.desktop/share/classes/sun/awt/
H A DGlobalCursorManager.java174 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()
/dports/java/openjdk15/jdk15u-jdk-15.0.6-1-1/src/java.desktop/share/classes/sun/awt/
H A DGlobalCursorManager.java174 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()
/dports/java/openjdk14/jdk14u-jdk-14.0.2-12-1/src/java.desktop/share/classes/sun/awt/
H A DGlobalCursorManager.java174 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()
/dports/java/openjdk8-jre/jdk8u-jdk8u312-b07.1/jdk/src/share/classes/sun/awt/
H A DGlobalCursorManager.java174 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()
/dports/biology/mmseqs2/MMseqs2-13-45111/src/test/
H A DTestProfileAlignment.cpp802 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()
H A DTestAlignment.cpp94 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()
/dports/devel/liteide/gotools-eff8693b15f0/oracle/oracle/
H A Doracle.go54 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:
/dports/audio/faust/faust-2.37.3/tools/physicalModeling/mesh2faust/vega/libraries/sceneObjectReduced/
H A DsceneObjectReducedCPU6DOF.cpp127 int SceneObjectReducedCPU6DOF::GetClosestVertex(Vec3d & queryPos, double * distance, double * auxVe… in GetClosestVertex() argument
130 double queryPosv[3] = { queryPos[0], queryPos[1], queryPos[2] }; in GetClosestVertex()
/dports/security/vault/vault-1.8.2/vendor/golang.org/x/tools/cmd/guru/
H A Dpeers.go130 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(),
/dports/net/evans/evans-0.9.1/vendor/golang.org/x/tools/cmd/guru/
H A Dpeers.go130 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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