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Searched defs:aln_len (Results 1 – 25 of 30) sorted by relevance

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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/alnmgr/
H A Dalnvecprint.cpp95 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
H A Daln_builders.cpp346 CPairwiseAln::TPos aln_len = 0; in s_TranslateAnchorToAlnCoords() local
H A Dalnvec.cpp224 TSeqPos aln_len = GetAlnStop() + 1; in GetWholeAlnSeqString() local
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/alnmgr/
H A Dalnvecprint.cpp95 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
H A Daln_builders.cpp346 CPairwiseAln::TPos aln_len = 0; in s_TranslateAnchorToAlnCoords() local
H A Dalnvec.cpp224 TSeqPos aln_len = GetAlnStop() + 1; in GetWholeAlnSeqString() local
/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/kalign/src/kalign2/
H A Dkalign2_output.c132 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
/dports/biology/rainbow/rainbow_2.0.4/
H A Dmergecontig.c147 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
/dports/biology/stacks/stacks-2.4/src/
H A DSuffixTree.h85 size_t aln_len; variable
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/alnmgr/demo/
H A Daln_test_app.cpp258 size_t aln_len = sequence.size(); in DumpSparseAln() local
/dports/biology/ncbi-toolkit/ncbi/api/
H A Dalignval.c2004 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
H A Daceread.c482 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
H A Dsalpstat.c1794 … 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/util/
H A Dblast_tabular.cpp56 TCoord spaces (0), gaps (0), aln_len (0); in CBlastTabular() local
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/
H A Dvaliderror_align.cpp321 TSeqPos aln_len = av->GetAlnStop() + 1; in s_CalculateMatchingColumns() local
512 TSeqPos aln_len = sparse_aln.GetAlnRange().GetLength(); in x_ValidateAlignPercentIdentity() local
/dports/biology/diamond/diamond-2.0.13/src/dp/swipe/
H A Dswipe_wrapper.cpp281 static Loc mismatch_est(const Loc query_len, const Loc target_len, const int32_t aln_len, const Hsp… in mismatch_est()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/readers/sra/test/
H A Dvdb_test.cpp811 TSeqPos aln_len = it.GetRefSeqLen(); in Run() local
/dports/biology/ncbi-toolkit/ncbi/desktop/
H A Dseqpanel.c1176 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
H A Ddlgutil1.c5214 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
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/demo/
H A Dxcompareannotsdemo.cpp131 TSeqPos aln_len, in GetBiasedSymmetricIdentity()
/dports/biology/ncbi-toolkit/ncbi/tools/
H A Dsalptool.c1707 Int4 seq_offset, aln_len; in CutAlignmentAtGaps() local
H A Dactutils.c1491 Int4 aln_len; in ResolveSpinConflict() local
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/
H A Dphrap.cpp1106 TSeqPos aln_len = seq.GetAlignedTo() - aln_from; in x_AddAlignRanges() local
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/readers/
H A Dphrap.cpp1106 TSeqPos aln_len = seq.GetAlignedTo() - aln_from; in x_AddAlignRanges() local
/dports/biology/iqtree/IQ-TREE-2.0.6/main/
H A Dphylotesting.cpp198 size_t aln_len = 0; in getUsualModel() local

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