traceSegments (reference) in projects: dports

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Searched refs:traceSegments (Results 1 – 25 of 37) sorted by relevance

/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/
H A D	dp_traceback_adaptor.h	78 if (empty(traceSegments)) in _adaptTraceSegmentsTo() 136 if (empty(traceSegments)) in _adaptTraceSegmentsTo() 140 TTraceSegment traceBegin = traceSegments[length(traceSegments) - 1]; in _adaptTraceSegmentsTo() 153 … addEdge(g, addVertex(g, seqHId, traceSegments[i]._horizontalBeginPos, traceSegments[i]._length), in _adaptTraceSegmentsTo() 154 … addVertex(g, seqVId, traceSegments[i]._verticalBeginPos, traceSegments[i]._length)); in _adaptTraceSegmentsTo() 158 addVertex(g, seqVId, traceSegments[i]._verticalBeginPos, traceSegments[i]._length); in _adaptTraceSegmentsTo() 162 addVertex(g, seqHId, traceSegments[i]._horizontalBeginPos, traceSegments[i]._length); in _adaptTraceSegmentsTo() 197 …for (int i = traceSegments[k - 1]._horizontalBeginPos; i < (int) (traceSegments[k - 1]._horizontal… in _adaptTraceSegmentsTo() 207 …for (int i = traceSegments[k - 1]._verticalBeginPos; i < (int) (traceSegments[k - 1]._verticalBegi… in _adaptTraceSegmentsTo() 214 …for (int i = traceSegments[k - 1]._horizontalBeginPos; i < (int) (traceSegments[k - 1]._horizontal… in _adaptTraceSegmentsTo() [all …]
H A D	dp_setup.h	276 String<TTraceSegment, TSpec> & traceSegments, 287 …return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignC… 299 _setUpAndRunAlignment(String<TTraceSegment, TSpec> & traceSegments, 308 …return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, al… 315 _setUpAndRunAlignment(String<TTraceSegment, TSpec> & traceSegments, 323 …return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig, … 338 StringSet<String<TTraceSegment, TSpec> > & traceSegments, 349 …return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignC… 357 _setUpAndRunAlignment(StringSet<String<TTraceSegment, TSpec> > & traceSegments, 371 …return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, al… [all …]
H A D	align_interface_wrapper.h	`89 String<TraceSegment_<unsigned, unsigned> > traceSegments; // Dummy segments. in _alignWrapperSequential() 90 std::get<0>(tuple) = _setUpAndRunAlignment(traceSegments, dpScoutState, in _alignWrapperSequential() 129 String<TraceSegment_<unsigned, unsigned> > traceSegments; // Dummy segments. in _alignWrapperSequential() 130 …std::get<0>(tuple) = _setUpAndRunAlignment(traceSegments, dpScoutState, stringH, std::get<1>(tuple… in _alignWrapperSequential()`
H A D	global_alignment_unbanded.h	256 String<TTraceSegment> traceSegments; in globalAlignment() local 258 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, source(gapsH), source(gapsV),… in globalAlignment() 260 _adaptTraceSegmentsTo(gapsH, gapsV, traceSegments); in globalAlignment() 329 String<TTraceSegment> traceSegments; in globalAlignment() local 331 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, value(stringSet(alignmentGrap… in globalAlignment() 336 positionToId(stringSet(alignmentGraph), 1), traceSegments); in globalAlignment() 400 String<TTraceSegment> traceSegments; in globalAlignment() local 402 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, value(strings, 0), value(stri… in globalAlignment() 405 …TraceSegmentsTo(fragmentString, positionToId(strings, 0), positionToId(strings, 1), traceSegments); in globalAlignment() 535 String<TraceSegment_<unsigned, unsigned> > traceSegments; // Dummy segments. in SEQAN_FUNC_DISABLE_IF() local [all …]
H A D	dp_trace_segment.h	`319 inline void _recordSegment(TTraceSegments & traceSegments, 331 …appendValue(traceSegments, TTraceSegment(horizontalBeginPos, verticalBeginPos, segmentLength, Trac… 333 …appendValue(traceSegments, TTraceSegment(horizontalBeginPos, verticalBeginPos, segmentLength, Trac… 335 …appendValue(traceSegments, TTraceSegment(horizontalBeginPos, verticalBeginPos, segmentLength, Trac…`
H A D	dp_algorithm_impl.h	1284 _finishAlignment(TTraceTarget & traceSegments, in SEQAN_FUNC_ENABLE_IF() 1294 for(TSize i = 0; i < length(traceSegments); ++i) in SEQAN_FUNC_ENABLE_IF() 1303 _computeTraceback(traceSegments[i], dpTraceMatrixNavigator, in SEQAN_FUNC_ENABLE_IF() 1321 _finishAlignment(TTraceTarget & traceSegments, in SEQAN_FUNC_ENABLE_IF() 1332 _computeTraceback(traceSegments, dpTraceMatrixNavigator, dpScout, seqH, seqV, band, dpProfile); in SEQAN_FUNC_ENABLE_IF() 1350 TTraceTarget & traceSegments, in _computeAlignment() argument 1424 …return _finishAlignment(traceSegments, dpTraceMatrixNavigator, dpScout, seqH, seqV, band, dpProfil… in _computeAlignment()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/
H A D	dp_traceback_adaptor.h	78 if (empty(traceSegments)) in _adaptTraceSegmentsTo() 136 if (empty(traceSegments)) in _adaptTraceSegmentsTo() 140 TTraceSegment traceBegin = traceSegments[length(traceSegments) - 1]; in _adaptTraceSegmentsTo() 153 … addEdge(g, addVertex(g, seqHId, traceSegments[i]._horizontalBeginPos, traceSegments[i]._length), in _adaptTraceSegmentsTo() 154 … addVertex(g, seqVId, traceSegments[i]._verticalBeginPos, traceSegments[i]._length)); in _adaptTraceSegmentsTo() 158 addVertex(g, seqVId, traceSegments[i]._verticalBeginPos, traceSegments[i]._length); in _adaptTraceSegmentsTo() 162 addVertex(g, seqHId, traceSegments[i]._horizontalBeginPos, traceSegments[i]._length); in _adaptTraceSegmentsTo() 197 …for (int i = traceSegments[k - 1]._horizontalBeginPos; i < (int) (traceSegments[k - 1]._horizontal… in _adaptTraceSegmentsTo() 207 …for (int i = traceSegments[k - 1]._verticalBeginPos; i < (int) (traceSegments[k - 1]._verticalBegi… in _adaptTraceSegmentsTo() 214 …for (int i = traceSegments[k - 1]._horizontalBeginPos; i < (int) (traceSegments[k - 1]._horizontal… in _adaptTraceSegmentsTo() [all …]
H A D	dp_setup.h	276 String<TTraceSegment, TSpec> & traceSegments, 287 …return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignC… 299 _setUpAndRunAlignment(String<TTraceSegment, TSpec> & traceSegments, 308 …return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, al… 315 _setUpAndRunAlignment(String<TTraceSegment, TSpec> & traceSegments, 323 …return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig, … 338 StringSet<String<TTraceSegment, TSpec> > & traceSegments, 349 …return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignC… 357 _setUpAndRunAlignment(StringSet<String<TTraceSegment, TSpec> > & traceSegments, 371 …return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, al… [all …]
H A D	align_interface_wrapper.h	`89 String<TraceSegment_<unsigned, unsigned> > traceSegments; // Dummy segments. in _alignWrapperSequential() 90 std::get<0>(tuple) = _setUpAndRunAlignment(traceSegments, dpScoutState, in _alignWrapperSequential() 129 String<TraceSegment_<unsigned, unsigned> > traceSegments; // Dummy segments. in _alignWrapperSequential() 130 …std::get<0>(tuple) = _setUpAndRunAlignment(traceSegments, dpScoutState, stringH, std::get<1>(tuple… in _alignWrapperSequential()`
H A D	global_alignment_unbanded.h	256 String<TTraceSegment> traceSegments; in globalAlignment() local 258 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, source(gapsH), source(gapsV),… in globalAlignment() 260 _adaptTraceSegmentsTo(gapsH, gapsV, traceSegments); in globalAlignment() 329 String<TTraceSegment> traceSegments; in globalAlignment() local 331 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, value(stringSet(alignmentGrap… in globalAlignment() 336 positionToId(stringSet(alignmentGraph), 1), traceSegments); in globalAlignment() 400 String<TTraceSegment> traceSegments; in globalAlignment() local 402 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, value(strings, 0), value(stri… in globalAlignment() 405 …TraceSegmentsTo(fragmentString, positionToId(strings, 0), positionToId(strings, 1), traceSegments); in globalAlignment() 535 String<TraceSegment_<unsigned, unsigned> > traceSegments; // Dummy segments. in SEQAN_FUNC_DISABLE_IF() local [all …]
H A D	dp_trace_segment.h	`319 inline void _recordSegment(TTraceSegments & traceSegments, 331 …appendValue(traceSegments, TTraceSegment(horizontalBeginPos, verticalBeginPos, segmentLength, Trac… 333 …appendValue(traceSegments, TTraceSegment(horizontalBeginPos, verticalBeginPos, segmentLength, Trac… 335 …appendValue(traceSegments, TTraceSegment(horizontalBeginPos, verticalBeginPos, segmentLength, Trac…`
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/
H A D	dp_traceback_adaptor.h	78 if (empty(traceSegments)) in _adaptTraceSegmentsTo() 136 if (empty(traceSegments)) in _adaptTraceSegmentsTo() 140 TTraceSegment traceBegin = traceSegments[length(traceSegments) - 1]; in _adaptTraceSegmentsTo() 153 … addEdge(g, addVertex(g, seqHId, traceSegments[i]._horizontalBeginPos, traceSegments[i]._length), in _adaptTraceSegmentsTo() 154 … addVertex(g, seqVId, traceSegments[i]._verticalBeginPos, traceSegments[i]._length)); in _adaptTraceSegmentsTo() 158 addVertex(g, seqVId, traceSegments[i]._verticalBeginPos, traceSegments[i]._length); in _adaptTraceSegmentsTo() 162 addVertex(g, seqHId, traceSegments[i]._horizontalBeginPos, traceSegments[i]._length); in _adaptTraceSegmentsTo() 197 …for (int i = traceSegments[k - 1]._horizontalBeginPos; i < (int) (traceSegments[k - 1]._horizontal… in _adaptTraceSegmentsTo() 207 …for (int i = traceSegments[k - 1]._verticalBeginPos; i < (int) (traceSegments[k - 1]._verticalBegi… in _adaptTraceSegmentsTo() 214 …for (int i = traceSegments[k - 1]._horizontalBeginPos; i < (int) (traceSegments[k - 1]._horizontal… in _adaptTraceSegmentsTo() [all …]
H A D	dp_setup.h	271 String<TTraceSegment, TSpec> & traceSegments, 282 …return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignC… 291 String<TTraceSegment, TSpec> & traceSegments, 302 …return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignC… 311 String<TTraceSegment, TSpec> & traceSegments, 322 …return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignC… 330 _setUpAndRunAlignment(String<TTraceSegment, TSpec> & traceSegments, 341 …return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, al… 346 …return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, al… 351 …return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, al… [all …]
H A D	global_alignment_unbanded.h	256 String<TTraceSegment> traceSegments; in globalAlignment() local 258 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, source(gapsH), source(gapsV),… in globalAlignment() 260 _adaptTraceSegmentsTo(gapsH, gapsV, traceSegments); in globalAlignment() 329 String<TTraceSegment> traceSegments; in globalAlignment() local 331 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, value(stringSet(alignmentGrap… in globalAlignment() 336 positionToId(stringSet(alignmentGraph), 1), traceSegments); in globalAlignment() 400 String<TTraceSegment> traceSegments; in globalAlignment() local 402 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, value(strings, 0), value(stri… in globalAlignment() 405 …TraceSegmentsTo(fragmentString, positionToId(strings, 0), positionToId(strings, 1), traceSegments); in globalAlignment() 511 String<TraceSegment_<unsigned, unsigned> > traceSegments; // Dummy segments. in globalAlignmentScore() local [all …]
H A D	dp_trace_segment.h	`319 inline void _recordSegment(TTraceSegments & traceSegments, 331 …appendValue(traceSegments, TTraceSegment(horizontalBeginPos, verticalBeginPos, segmentLength, +Tra… 333 …appendValue(traceSegments, TTraceSegment(horizontalBeginPos, verticalBeginPos, segmentLength, +Tra… 335 …appendValue(traceSegments, TTraceSegment(horizontalBeginPos, verticalBeginPos, segmentLength, +Tra…`
H A D	global_alignment_banded.h	`416 String<TraceSegment_<unsigned, unsigned> > traceSegments; // Dummy segments. in globalAlignmentScore() local 417 return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, in globalAlignmentScore() 492 String<TraceSegment_<unsigned, unsigned> > traceSegments; // Dummy segments. in globalAlignmentScore() local 493 return _setUpAndRunAlignment(traceSegments, dpScoutState, strings[0], strings[1], scoringScheme, in globalAlignmentScore()`
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/align/
H A D	test_alignment_dp_adapt_tracesegments.h	201 String<TTraceSegment> traceSegments; in testAlign2TraceAdaptorAdaptFile() local 204 appendValue(traceSegments, TTraceSegment(8, 4, 4, TraceBitMap_<>::DIAGONAL)); in testAlign2TraceAdaptorAdaptFile() 213 _adaptTraceSegmentsTo(stream, seq0, seq1, traceSegments); in testAlign2TraceAdaptorAdaptFile() 273 String<TTraceSegment> traceSegments; in testAlign2TraceAdaptorAdaptAlign() local 303 _adaptTraceSegmentsTo(row(align, 0), row(align, 1), traceSegments); in testAlign2TraceAdaptorAdaptAlign() 317 String<TTraceSegment> traceSegments; in testAlign2TraceAdaptorAdaptFragments() local 326 _adaptTraceSegmentsTo(fragmentString, 0, 1, traceSegments); in testAlign2TraceAdaptorAdaptFragments() 345 String<TTraceSegment> traceSegments; in testAlign2TraceAdaptorAdaptAlignmentGraph() local 354 _adaptTraceSegmentsTo(alignGraph, 0, 1, traceSegments); in testAlign2TraceAdaptorAdaptAlignmentGraph() 384 seqan::StringSet<seqan::TraceSegment_<int, int> > traceSegments; in SEQAN_DEFINE_TEST() local [all …]
H A D	test_alignment_dp_trace_segment.h	`374 seqan::StringSet<seqan::TraceSegment_<int, int> > traceSegments; in SEQAN_DEFINE_TEST() local 375 testAlignmentTracebackRecordTrace(traceSegments); in SEQAN_DEFINE_TEST()`
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/yara/
H A D	find_verifier.h	`64 TTrace traceSegments; member 111 clear(me.traceSegments); in verify() 113 me.traceSegments, in verify() 119 _adaptTraceSegmentsTo(contigGaps, readGaps, me.traceSegments); in verify()`
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/journaled_set/
H A D	journal_alignment_traceback_adaptor.h	`69 String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments) in _adaptTraceSegmentsTo() argument 91 TTraceIterator traceSegIter = end(traceSegments, Standard()) - 1; in _adaptTraceSegmentsTo() 92 TTraceIterator traceSegIterEnd = begin(traceSegments, Standard()) - 1; in _adaptTraceSegmentsTo()`
H A D	journal_alignment_interface.h	84 String<TTraceSegment> traceSegments; in globalAlignment() local 87 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, reference, source, scoringSch… in globalAlignment() 89 _adaptTraceSegmentsTo(journaledString, reference, source, traceSegments); in globalAlignment() 177 String<TTraceSegment> traceSegments; in globalAlignment() local 180 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, reference, source, scoringSch… in globalAlignment() 183 _adaptTraceSegmentsTo(journaledString, reference, source, traceSegments); in globalAlignment()
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/journaled_set/
H A D	journal_alignment_traceback_adaptor.h	`69 String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments) in _adaptTraceSegmentsTo() argument 91 TTraceIterator traceSegIter = end(traceSegments, Standard()) - 1; in _adaptTraceSegmentsTo() 92 TTraceIterator traceSegIterEnd = begin(traceSegments, Standard()) - 1; in _adaptTraceSegmentsTo()`
H A D	journal_alignment_interface.h	84 String<TTraceSegment> traceSegments; in globalAlignment() local 87 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, reference, source, scoringSch… in globalAlignment() 89 _adaptTraceSegmentsTo(journaledString, reference, source, traceSegments); in globalAlignment() 177 String<TTraceSegment> traceSegments; in globalAlignment() local 180 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, reference, source, scoringSch… in globalAlignment() 183 _adaptTraceSegmentsTo(journaledString, reference, source, traceSegments); in globalAlignment()
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/journaled_set/
H A D	journal_alignment_traceback_adaptor.h	`69 String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments) in _adaptTraceSegmentsTo() argument 91 TTraceIterator traceSegIter = end(traceSegments, Standard()) - 1; in _adaptTraceSegmentsTo() 92 TTraceIterator traceSegIterEnd = begin(traceSegments, Standard()) - 1; in _adaptTraceSegmentsTo()`
H A D	journal_alignment_interface.h	84 String<TTraceSegment> traceSegments; in globalAlignment() local 87 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, reference, source, scoringSch… in globalAlignment() 89 _adaptTraceSegmentsTo(journaledString, reference, source, traceSegments); in globalAlignment() 177 String<TTraceSegment> traceSegments; in globalAlignment() local 180 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, reference, source, scoringSch… in globalAlignment() 183 _adaptTraceSegmentsTo(journaledString, reference, source, traceSegments); in globalAlignment()