| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/align/ |
| H A D | test_align_alignment_operations.h | 60 insertGaps(row(align, 1), 4, 4); in SEQAN_DEFINE_TEST()
71 insertGaps(row(alignInf, 1), 0, 4); in SEQAN_DEFINE_TEST()
98 insertGaps(row(align, 1), 5, 4); in SEQAN_DEFINE_TEST()
109 insertGaps(row(alignInf, 1), 5, 2); in SEQAN_DEFINE_TEST()
110 insertGaps(row(alignInf, 1), 4, 1); in SEQAN_DEFINE_TEST()
137 insertGaps(row(align, 1), 0, 4); in SEQAN_DEFINE_TEST()
148 insertGaps(row(alignInf, 1), 0, 4); in SEQAN_DEFINE_TEST()
175 insertGaps(row(align, 1), 0, 4); in SEQAN_DEFINE_TEST()
186 insertGaps(row(alignInf, 1), 5, 2); in SEQAN_DEFINE_TEST()
187 insertGaps(row(alignInf, 1), 4, 1); in SEQAN_DEFINE_TEST()
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| H A D | test_align_stream.h | 48 insertGaps(gaps, 8, 2); in SEQAN_DEFINE_TEST()
49 insertGaps(gaps, 5, 1); in SEQAN_DEFINE_TEST()
50 insertGaps(gaps, 0, 2); in SEQAN_DEFINE_TEST()
66 insertGaps(gaps, 8, 2); in SEQAN_DEFINE_TEST()
67 insertGaps(gaps, 5, 1); in SEQAN_DEFINE_TEST()
68 insertGaps(gaps, 0, 2); in SEQAN_DEFINE_TEST()
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| H A D | test_align_gaps_iterator.h | 99 insertGaps(gaps, 2, 2); in testAlignGapsIteratorRootedRandomAccessIteratorFunctions()
162 insertGaps(gaps, 2, 2); in testAlignGapsIteratorMovement()
297 insertGaps(gaps, 2, 2); in testAlignGapsIteratorRelations()
334 insertGaps(gaps, 2, 2); in testAlignGapsIteratorPointerArithmetic()
361 insertGaps(gaps, 4, 2); in testAlignGapsIteratorForwardIteration()
362 insertGaps(gaps, 2, 2); in testAlignGapsIteratorForwardIteration()
363 insertGaps(gaps, 0, 2); in testAlignGapsIteratorForwardIteration()
391 insertGaps(gaps, 4, 2); in testAlignGapsIteratorReverseIteration()
693 insertGaps(it, 2); in testAlignGapsIteratorGapOperationsCenter()
717 insertGaps(it, 3); in testAlignGapsIteratorGapOperationsCenter()
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| H A D | test_align_gaps.h | 234 insertGaps(gaps, 4, 2); in testAlignGapsGapOperationsGapCenter()
269 insertGaps(gaps, 4, 3); in testAlignGapsGapOperationsGapCenter()
311 insertGaps(gaps, 4, 4); in testAlignGapsGapOperationsGapCenter()
353 insertGaps(gaps, 4, 4); in testAlignGapsGapOperationsGapCenter()
429 insertGaps(gaps, 0, 2); in testAlignGapsGapOperationsGapsLeading()
461 insertGaps(gaps, 0, 3); in testAlignGapsGapOperationsGapsLeading()
494 insertGaps(gaps, 0, 4); in testAlignGapsGapOperationsGapsLeading()
1132 insertGaps(gaps, 1, 2); in testAlignGapsClippingGapsLeading()
1178 insertGaps(gaps, 3, 2); in testAlignGapsClippingGapsTrailing()
1580 insertGaps(gaps, 1, 2); in SEQAN_DEFINE_TEST()
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| H A D | test_align_align.h | 59 insertGaps(row(ali1, 0), 2, 3); in testAlignBasics()
129 insertGaps(row(ali1, 0), 2, 3); in testAlignColsBase()
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| /dports/biology/seqan1/seqan-1.3.1/seqan/align/ |
| H A D | align_algorithms.h | 88 insertGaps(it1, siz); in _pumpTraceToAlign()
92 insertGaps(it0, siz); in _pumpTraceToAlign()
144 insertGaps(it, beginPosition(infixRow)); in integrateAlign()
152 insertGaps(it, gapSize); in integrateAlign()
169 insertGaps(iter(row(align, i), value(viewPos, i) + endPosition(infixRow)), diffLen); in integrateAlign()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/alignment/ |
| H A D | align_assignment1.cpp | 29 insertGaps(row1, 2, 2); in main()
31 insertGaps(row2, 9, 2); in main()
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| /dports/biology/ugene/ugene-40.1/src/plugins/api_tests/src/core/datatype/msa/ |
| H A D | MsaRowUnitTests.cpp | 524 almnt->insertGaps(0, 0, 2, os); in IMPLEMENT_TEST()
534 almnt->insertGaps(0, 3, 1, os); in IMPLEMENT_TEST()
540 almnt->insertGaps(0, 7, 2, os); in IMPLEMENT_TEST()
551 almnt->insertGaps(0, 2, 1, os); in IMPLEMENT_TEST()
557 almnt->insertGaps(0, 5, 2, os); in IMPLEMENT_TEST()
568 almnt->insertGaps(0, 1, 2, os); in IMPLEMENT_TEST()
579 almnt->insertGaps(0, 4, 2, os); in IMPLEMENT_TEST()
590 almnt->insertGaps(0, 0, 3, os); in IMPLEMENT_TEST()
601 almnt->insertGaps(0, 0, 3, os); in IMPLEMENT_TEST()
612 almnt->insertGaps(0, 7, 2, os); in IMPLEMENT_TEST()
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| H A D | MsaUnitTests.cpp | 459 almnt->insertGaps(0, 4, 3, os); in IMPLEMENT_TEST()
474 almnt->insertGaps(1, 0, 2, os); in IMPLEMENT_TEST()
483 almnt->insertGaps(-1, 4, 3, os); in IMPLEMENT_TEST()
491 almnt->insertGaps(2, 4, 3, os); in IMPLEMENT_TEST()
499 almnt->insertGaps(0, -1, 3, os); in IMPLEMENT_TEST()
507 almnt->insertGaps(0, 10, 3, os); in IMPLEMENT_TEST()
515 almnt->insertGaps(0, 4, -1, os); in IMPLEMENT_TEST()
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| /dports/biology/seqan/seqan-library-2.4.0/share/doc/seqan/html/demos/dox/align/ |
| H A D | gaps_example.cpp | 18 insertGaps(gaps, 7, 2); in main()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/dox/align/ |
| H A D | gaps_example.cpp | 18 insertGaps(gaps, 7, 2); in main()
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/ |
| H A D | gaps_base.h | 449 insertGaps(gaps, clippedViewPos, 1u);
836 insertGaps(itV, size);
840 insertGaps(itH, size);
956 insertGaps(lhsIt, num);
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| H A D | dp_traceback_adaptor.h | 104 insertGaps(it1, segmentSize); in _adaptTraceSegmentsTo()
108 insertGaps(it0, segmentSize); in _adaptTraceSegmentsTo()
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| H A D | alignment_operations.h | 114 insertGaps(it, gapSize); in integrateAlign()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/howto/ |
| H A D | align_gaps_clipping.cpp | 17 insertGaps(gaps, 2, 2); in main()
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| /dports/biology/seqan1/seqan-1.3.1/seqan/seeds/ |
| H A D | seed_multi.h | 619 insertGaps(row(aligned,0),position1, gapLength); in getAlignment()
627 insertGaps(row(aligned,1),position2,gapLength); in getAlignment()
658 insertGaps(row(aligned,1),position2,row(alignSeg,1).data_arr[j]); in getAlignment()
677 insertGaps(row(aligned,0),position1,row(alignSeg,0).data_arr[j]); in getAlignment()
690 insertGaps(row(aligned,1),position2,tmp1-tmp2); in getAlignment()
694 insertGaps(row(aligned,0),position1,tmp2-tmp1); in getAlignment()
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| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/ |
| H A D | gaps_base.h | 513 insertGaps(gaps, clippedViewPos, 1u);
1006 insertGaps(itV, size);
1010 insertGaps(itH, size);
1126 insertGaps(lhsIt, num);
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| H A D | dp_traceback_adaptor.h | 104 insertGaps(it1, segmentSize); in _adaptTraceSegmentsTo()
108 insertGaps(it0, segmentSize); in _adaptTraceSegmentsTo()
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| H A D | alignment_operations.h | 81 insertGaps(it, gapSize); in integrateGaps()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/ |
| H A D | gaps_base.h | 513 insertGaps(gaps, clippedViewPos, 1u);
1006 insertGaps(itV, size);
1010 insertGaps(itH, size);
1126 insertGaps(lhsIt, num);
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| H A D | dp_traceback_adaptor.h | 104 insertGaps(it1, segmentSize); in _adaptTraceSegmentsTo()
108 insertGaps(it0, segmentSize); in _adaptTraceSegmentsTo()
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| H A D | alignment_operations.h | 81 insertGaps(it, gapSize); in integrateGaps()
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/util/ |
| H A D | MsaRowUtils.h | 53 …static void insertGaps(U2OpStatus &os, U2MsaRowGapModel &gaps, int rowLengthWithoutTrailing, int p…
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| /dports/biology/seqan1/seqan-1.3.1/seqan/seeds2/ |
| H A D | align_dynprog_linear.h | 335 insertGaps(alignmentIt1, origPos0 - pos0); in _alignTraceback()
337 insertGaps(alignmentIt0, origPos1 - pos1); in _alignTraceback()
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| /dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/blast_plus/align_worker_subtasks/ |
| H A D | ComposeResultSubTask.cpp | 177 result->insertGaps(rowsCounter, gap.offset, gap.gap, stateInfo); in createAlignmentAndAnnotations()
379 alignment->insertGaps(rowNum, globalOffset + gap.offset, gap.gap, stateInfo); in insertShiftedGapsIntoRead()
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