/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/alnmgr/ |
H A D | alnvecprint.cpp | 95 TSeqPos aln_len = m_AlnVec.GetAlnStop() + 1; in PopsetStyle() local 222 TSeqPos pos = 0, aln_len = m_AlnVec.GetAlnStop() + 1; in PopsetStyle() local 259 TSeqPos aln_len = m_AlnVec.GetAlnStop() + 1; in ClustalStyle() local 403 const TSeqPos aln_len = m_AlnVec.GetAlnStop() + 1; in ClustalStyle() local
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H A D | aln_builders.cpp | 346 CPairwiseAln::TPos aln_len = 0; in s_TranslateAnchorToAlnCoords() local
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H A D | alnvec.cpp | 224 TSeqPos aln_len = GetAlnStop() + 1; in GetWholeAlnSeqString() local
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/alnmgr/ |
H A D | alnvecprint.cpp | 95 TSeqPos aln_len = m_AlnVec.GetAlnStop() + 1; in PopsetStyle() local 222 TSeqPos pos = 0, aln_len = m_AlnVec.GetAlnStop() + 1; in PopsetStyle() local 259 TSeqPos aln_len = m_AlnVec.GetAlnStop() + 1; in ClustalStyle() local 403 const TSeqPos aln_len = m_AlnVec.GetAlnStop() + 1; in ClustalStyle() local
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H A D | aln_builders.cpp | 346 CPairwiseAln::TPos aln_len = 0; in s_TranslateAnchorToAlnCoords() local
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H A D | alnvec.cpp | 224 TSeqPos aln_len = GetAlnStop() + 1; in GetWholeAlnSeqString() local
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/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/kalign/src/kalign2/ |
H A D | kalign2_output.c | 132 int aln_len = 0; in msf_output() local 275 int aln_len = 0; in clustal_output() local 381 int aln_len = 0; in aln_output() local
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/dports/biology/rainbow/rainbow_2.0.4/ |
H A D | mergecontig.c | 147 int k, mn, mm, off0, off1, aln_len; in pw_aln_contigs_brute() local 196 int k, mn, mm, score, seqlen, aln_len, count, pre, idx, lastid; in pw_aln_contigs() local
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/dports/biology/stacks/stacks-2.4/src/ |
H A D | SuffixTree.h | 85 size_t aln_len; variable
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/alnmgr/demo/ |
H A D | aln_test_app.cpp | 258 size_t aln_len = sequence.size(); in DumpSparseAln() local
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/dports/biology/ncbi-toolkit/ncbi/api/ |
H A D | alignval.c | 2004 Int4 aln_len, start, stop; in CheckAlnSeqLens() local 2510 Int4 aln_len, num_rows, row, col_count = 0; in GetAlignmentColumnPercentIdentities() local 2670 Int4 aln_len, num_rows, row, col_count = 0; in AlignmentPercentIdentityEx() local
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H A D | aceread.c | 482 int numseg = 0, aln_len, pos, seg, con_offset = 0, read_offset = 0; in GetConsensusReadAln() local 1757 int aln_len, in s_AlignmentSeqFromContigSeq() 1816 int consensus_pad = 0, pad, end_pad = 0, aln_len; in AlignmentFileFromContig() local
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H A D | salpstat.c | 1794 … sap,BioseqPtr query_bsp, BioseqPtr subject_bsp, Int4Ptr Overlap_len,Int4Ptr aln_len,Int4Ptr virtu… in SeqAlignAlignability() 1836 … sap,SeqLocPtr query_slp, SeqLocPtr subject_slp, Int4Ptr Overlap_len,Int4Ptr aln_len,Int4Ptr virtu… in AlignabilityByLoc()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/util/ |
H A D | blast_tabular.cpp | 56 TCoord spaces (0), gaps (0), aln_len (0); in CBlastTabular() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/ |
H A D | validerror_align.cpp | 321 TSeqPos aln_len = av->GetAlnStop() + 1; in s_CalculateMatchingColumns() local 512 TSeqPos aln_len = sparse_aln.GetAlnRange().GetLength(); in x_ValidateAlignPercentIdentity() local
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/dports/biology/diamond/diamond-2.0.13/src/dp/swipe/ |
H A D | swipe_wrapper.cpp | 281 static Loc mismatch_est(const Loc query_len, const Loc target_len, const int32_t aln_len, const Hsp… in mismatch_est()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/readers/sra/test/ |
H A D | vdb_test.cpp | 811 TSeqPos aln_len = it.GetRefSeqLen(); in Run() local
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/dports/biology/ncbi-toolkit/ncbi/desktop/ |
H A D | seqpanel.c | 1176 Int4 aln_len; in GetAlignmentColumnPercentIDsForAlignmentSection() local 4438 Int4 aln_pos, aln_end_pos, aln_len; in SeqEdUpdateStatus() local 7720 Int4 aln_len; in ObjMgrSelectSeqEdSelection() local 8346 Int4 aln_len; in SeqAlnScrollToAlnPosEx() local 8624 Int4 aln_len = AlnMgr2GetAlnLength(salp, FALSE); in WriteAlignmentInterleaveToFileEx() local 8702 Int4Ptr aln_len = NULL; in WriteAlignmentContiguousToFile() local 9165 Int4 real_start, real_stop, aln_len; in GetSeqLocForAlignmentEdit() local 9985 Int4 start, stop, aln_start, aln_stop, orig_aln_len, aln_len, aln_pos, s,e; in FeatureLocationAlignment() local
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H A D | dlgutil1.c | 5214 extern Boolean AdjustFromForGap (Int4Ptr p_from, SeqAlignPtr salp, Int4 aln_len, Int4 aln_row) in AdjustFromForGap() 5321 Int4 aln_len; in TestIntervalEditor() local 5642 Int4 from, to, aln_row, aln_len; in ReadSingleSeqLoc() local 5757 Int4 from, to, aln_from, aln_to, aln_row, aln_len = 0; in ReadAlignedSeqLocList() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/demo/ |
H A D | xcompareannotsdemo.cpp | 131 TSeqPos aln_len, in GetBiasedSymmetricIdentity()
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/dports/biology/ncbi-toolkit/ncbi/tools/ |
H A D | salptool.c | 1707 Int4 seq_offset, aln_len; in CutAlignmentAtGaps() local
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H A D | actutils.c | 1491 Int4 aln_len; in ResolveSpinConflict() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/ |
H A D | phrap.cpp | 1106 TSeqPos aln_len = seq.GetAlignedTo() - aln_from; in x_AddAlignRanges() local
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/readers/ |
H A D | phrap.cpp | 1106 TSeqPos aln_len = seq.GetAlignedTo() - aln_from; in x_AddAlignRanges() local
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/dports/biology/iqtree/IQ-TREE-2.0.6/main/ |
H A D | phylotesting.cpp | 198 size_t aln_len = 0; in getUsualModel() local
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