/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/ |
H A D | seq_edit.cpp | 52 CSeqVector seq_vec(bioseq, pScope, CBioseq_Handle::eCoding_Iupac); in BEGIN_SCOPE() local
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H A D | seq_entry_edit.cpp | 248 CSeqVector seq_vec(seq_hl, CBioseq_Handle::eCoding_Iupac, eNa_strand_plus); in Does5primerAbutGap() local 263 CSeqVector seq_vec(seq_hl, CBioseq_Handle::eCoding_Iupac, eNa_strand_plus); in Does3primerAbutGap() local
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/edit/ |
H A D | seq_edit.cpp | 52 CSeqVector seq_vec(bioseq, pScope, CBioseq_Handle::eCoding_Iupac); in BEGIN_SCOPE() local
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H A D | seq_entry_edit.cpp | 248 CSeqVector seq_vec(seq_hl, CBioseq_Handle::eCoding_Iupac, eNa_strand_plus); in Does5primerAbutGap() local 263 CSeqVector seq_vec(seq_hl, CBioseq_Handle::eCoding_Iupac, eNa_strand_plus); in Does3primerAbutGap() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/prosplign/ |
H A D | PSeq.cpp | 48 CSeqVector seq_vec(seqloc,scope,CBioseq_Handle::eCoding_Iupac); in BEGIN_SCOPE() local
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H A D | NSeq.cpp | 124 CSeqVector seq_vec(*extended_seqloc,scope,CBioseq_Handle::eCoding_Ncbi); in Init() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/alnmgr/ |
H A D | alnvec.hpp | 261 CSeqVector& seq_vec = x_GetSeqVector(row); in GetResidue() local 298 CSeqVector& seq_vec = x_GetSeqVector(row); in GetSeqString() local 307 CSeqVector& seq_vec = x_GetSeqVector(row); in GetSeqString() local
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/alnmgr/ |
H A D | alnvec.hpp | 261 CSeqVector& seq_vec = x_GetSeqVector(row); in GetResidue() local 298 CSeqVector& seq_vec = x_GetSeqVector(row); in GetSeqString() local 307 CSeqVector& seq_vec = x_GetSeqVector(row); in GetSeqString() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/alnmgr/ |
H A D | alnvec.cpp | 111 CRef<CSeqVector> seq_vec; in x_GetSeqVector() local 152 CSeqVector& seq_vec = x_GetSeqVector(row); in GetAlnSeqString() local 790 CSeqVector & seq_vec = x_GetSeqVector(i); in RetrieveSegmentSequences() local 1010 CSeqVector& seq_vec = x_GetSeqVector(row); in GetColumnVector() local
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H A D | sparse_aln.cpp | 424 CSeqVector& seq_vec = *m_SeqVectors[row]; in x_GetSeqVector() local
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/alnmgr/ |
H A D | alnvec.cpp | 111 CRef<CSeqVector> seq_vec; in x_GetSeqVector() local 152 CSeqVector& seq_vec = x_GetSeqVector(row); in GetAlnSeqString() local 790 CSeqVector & seq_vec = x_GetSeqVector(i); in RetrieveSegmentSequences() local 1010 CSeqVector& seq_vec = x_GetSeqVector(row); in GetColumnVector() local
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H A D | sparse_aln.cpp | 424 CSeqVector& seq_vec = *m_SeqVectors[row]; in x_GetSeqVector() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/ |
H A D | gap_analysis.cpp | 350 CSeqVector seq_vec( in x_AddGapsFromBases() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/misc/hgvs/ |
H A D | objcoords.cpp | 833 CSeqVector seq_vec = in GetCoordinates() local 1067 static string x_GetSequence(CSeqVector& seq_vec, TSignedSeqPos pos, TSignedSeqPos adjustment) in x_GetSequence()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/ |
H A D | aln_writer.cpp | 131 CSeqVector seq_vec = bsh.GetSeqVector(CBioseq_Handle::eCoding_Iupac, strand); in GetSeqString() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/ |
H A D | cdregion_validator.cpp | 1812 CSeqVector seq_vec(m_LocationBioseq, CBioseq_Handle::eCoding_Iupac); in x_ValidateParentPartialness() local 1837 CSeqVector seq_vec(m_LocationBioseq, CBioseq_Handle::eCoding_Iupac); in x_ValidateParentPartialness() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/contig_assembly/ |
H A D | contig_assembly.cpp | 838 CSeqVector seq_vec = vec.GetBioseqHandle(row).GetSeqVector(); in GatherAlignStats() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/unit_test/ |
H A D | unit_test_fasta_reader_old.cpp | 1354 CSeqVector seq_vec(*pBioseq, NULL, CBioseq_Handle::eCoding_Iupac); in BOOST_AUTO_TEST_CASE() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/misc/discrepancy/ |
H A D | discrepancy_case.cpp | 688 … CSeqVector seq_vec(bioseq, &context.GetScope(), CBioseq_Handle::eCoding_Iupac, eNa_strand_plus); variable
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/table2asn/ |
H A D | feature_table_reader.cpp | 324 CSeqVector seq_vec(bioseq); in FindORF() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/flatfile/ |
H A D | asci_blk.cpp | 3918 const std::vector<Char>* seq_vec = nullptr; in PackSeqData() local
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/format/ |
H A D | feature_item.cpp | 5568 CSeqVector seq_vec(loc, ctx.GetScope(), CBioseq_Handle::eCoding_Iupac); in x_AddFTableAnticodon() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/format/ |
H A D | feature_item.cpp | 5638 CSeqVector seq_vec(loc, ctx.GetScope(), CBioseq_Handle::eCoding_Iupac); in x_AddFTableAnticodon() local
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/util/ |
H A D | sequence.cpp | 4800 CSeqVector seq_vec = bsh.GetSeqVector(CBioseq_Handle::eCoding_Iupac); in Search() local
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/util/ |
H A D | sequence.cpp | 4800 CSeqVector seq_vec = bsh.GetSeqVector(CBioseq_Handle::eCoding_Iupac); in Search() local
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