| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/alnmgr/ |
| H A D | sparse_ci.hpp | 51 void Init(TSignedSeqPos aln_from, in Init() argument
57 m_AlnRange.Set(aln_from, aln_to); in Init()
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| H A D | alnmap.hpp | 129 TSignedSeqPos aln_from,
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/alnmgr/ |
| H A D | sparse_ci.hpp | 51 void Init(TSignedSeqPos aln_from, in Init() argument
57 m_AlnRange.Set(aln_from, aln_to); in Init()
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| H A D | alnmap.hpp | 129 TSignedSeqPos aln_from,
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/alnmgr/ |
| H A D | alnmap.cpp | 1226 aln_from = -1, in operator []() local
1262 if (aln_from != -1) { in operator []()
1267 aln_from == -1) { in operator []()
1268 aln_from = m_AlnMap.GetAlnStart in operator []()
1281 chunk->SetAlnRange().Set(aln_from, aln_to); in operator []()
1403 TSignedSeqPos aln_from, in CreateAlignFromRange() argument
1430 TNumseg from_seg = GetSeg(aln_from); in CreateAlignFromRange()
1434 aln_from = 0; in CreateAlignFromRange()
1449 if (seg == from_seg && TSeqPos(aln_from) > aln_seg_from) { in CreateAlignFromRange()
1454 from_trim = aln_from - aln_seg_from; in CreateAlignFromRange()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/alnmgr/ |
| H A D | alnmap.cpp | 1226 aln_from = -1, in operator []() local
1262 if (aln_from != -1) { in operator []()
1267 aln_from == -1) { in operator []()
1268 aln_from = m_AlnMap.GetAlnStart in operator []()
1281 chunk->SetAlnRange().Set(aln_from, aln_to); in operator []()
1403 TSignedSeqPos aln_from, in CreateAlignFromRange() argument
1430 TNumseg from_seg = GetSeg(aln_from); in CreateAlignFromRange()
1434 aln_from = 0; in CreateAlignFromRange()
1449 if (seg == from_seg && TSeqPos(aln_from) > aln_seg_from) { in CreateAlignFromRange()
1454 from_trim = aln_from - aln_seg_from; in CreateAlignFromRange()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/ |
| H A D | phrap.cpp | 1105 TSeqPos aln_from = seq.GetAlignedFrom(); in x_AddAlignRanges() local
1106 TSeqPos aln_len = seq.GetAlignedTo() - aln_from; in x_AddAlignRanges()
1107 if (global_start >= seq.GetPaddedLength() + offset + aln_from) { in x_AddAlignRanges()
1111 TSeqPos pstart = max(offset + TSignedSeqPos(aln_from), in x_AddAlignRanges()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/readers/ |
| H A D | phrap.cpp | 1105 TSeqPos aln_from = seq.GetAlignedFrom(); in x_AddAlignRanges() local
1106 TSeqPos aln_len = seq.GetAlignedTo() - aln_from; in x_AddAlignRanges()
1107 if (global_start >= seq.GetPaddedLength() + offset + aln_from) { in x_AddAlignRanges()
1111 TSeqPos pstart = max(offset + TSignedSeqPos(aln_from), in x_AddAlignRanges()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/align_format/ |
| H A D | showalign.hpp | 815 int aln_from, int aln_to, int aln_stop,
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/align_format/ |
| H A D | showalign.hpp | 815 int aln_from, int aln_to, int aln_stop,
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| /dports/biology/ncbi-toolkit/ncbi/desktop/ |
| H A D | dlgutil1.c | 5216 Int4 aln_from, aln_offset = 0; in AdjustFromForGap() local
5224 aln_from = AlnMgr2MapSeqAlignToBioseq(salp, (*p_from) - 1, aln_row); in AdjustFromForGap()
5226 while (aln_from == -2 && (*p_from) + aln_offset < aln_len) in AdjustFromForGap()
5231 if (aln_from < 0) in AdjustFromForGap()
5237 *p_from = aln_from + 1; in AdjustFromForGap()
5757 Int4 from, to, aln_from, aln_to, aln_row, aln_len = 0; in ReadAlignedSeqLocList() local
5852 aln_from = from; in ReadAlignedSeqLocList()
5863 if (! AdjustFromForGap (&aln_from, salp, aln_len, aln_row) in ReadAlignedSeqLocList()
5865 || ! AddLocToList (seqid, aln_strand, aln_from, aln_to, in ReadAlignedSeqLocList()
5881 okay = AdjustFromForGap (&aln_from, salp, aln_len, aln_row) in ReadAlignedSeqLocList()
[all …]
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/align_format/ |
| H A D | showalign.cpp | 2915 const CSeq_loc& seqloc, int aln_from, in x_SetFeatureInfo() argument
2930 for (int j = aln_from; j <= aln_to; j++){ in x_SetFeatureInfo()
2936 feat_info->aln_range.Set(aln_from, aln_to); in x_SetFeatureInfo()
4433 static void s_MakeDomainString(int aln_from, int aln_to, const string& domain_name, in s_MakeDomainString() argument
4436 string domain_string(aln_to - aln_from + 1, ' '); in s_MakeDomainString()
4456 final_domain[i + aln_from] = domain_string[i]; in s_MakeDomainString()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/align_format/ |
| H A D | showalign.cpp | 2915 const CSeq_loc& seqloc, int aln_from, in x_SetFeatureInfo() argument
2930 for (int j = aln_from; j <= aln_to; j++){ in x_SetFeatureInfo()
2936 feat_info->aln_range.Set(aln_from, aln_to); in x_SetFeatureInfo()
4433 static void s_MakeDomainString(int aln_from, int aln_to, const string& domain_name, in s_MakeDomainString() argument
4436 string domain_string(aln_to - aln_from + 1, ' '); in s_MakeDomainString()
4456 final_domain[i + aln_from] = domain_string[i]; in s_MakeDomainString()
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