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Searched defs:seq_vec (Results 1 – 25 of 27) sorted by relevance

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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/
H A Dseq_edit.cpp52 CSeqVector seq_vec(bioseq, pScope, CBioseq_Handle::eCoding_Iupac); in BEGIN_SCOPE() local
H A Dseq_entry_edit.cpp248 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
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/edit/
H A Dseq_edit.cpp52 CSeqVector seq_vec(bioseq, pScope, CBioseq_Handle::eCoding_Iupac); in BEGIN_SCOPE() local
H A Dseq_entry_edit.cpp248 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
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/prosplign/
H A DPSeq.cpp48 CSeqVector seq_vec(seqloc,scope,CBioseq_Handle::eCoding_Iupac); in BEGIN_SCOPE() local
H A DNSeq.cpp124 CSeqVector seq_vec(*extended_seqloc,scope,CBioseq_Handle::eCoding_Ncbi); in Init() local
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/alnmgr/
H A Dalnvec.hpp261 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
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/alnmgr/
H A Dalnvec.hpp261 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
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/alnmgr/
H A Dalnvec.cpp111 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
H A Dsparse_aln.cpp424 CSeqVector& seq_vec = *m_SeqVectors[row]; in x_GetSeqVector() local
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/alnmgr/
H A Dalnvec.cpp111 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
H A Dsparse_aln.cpp424 CSeqVector& seq_vec = *m_SeqVectors[row]; in x_GetSeqVector() local
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/
H A Dgap_analysis.cpp350 CSeqVector seq_vec( in x_AddGapsFromBases() local
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/misc/hgvs/
H A Dobjcoords.cpp833 CSeqVector seq_vec = in GetCoordinates() local
1067 static string x_GetSequence(CSeqVector& seq_vec, TSignedSeqPos pos, TSignedSeqPos adjustment) in x_GetSequence()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/
H A Daln_writer.cpp131 CSeqVector seq_vec = bsh.GetSeqVector(CBioseq_Handle::eCoding_Iupac, strand); in GetSeqString() local
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/
H A Dcdregion_validator.cpp1812 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
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/contig_assembly/
H A Dcontig_assembly.cpp838 CSeqVector seq_vec = vec.GetBioseqHandle(row).GetSeqVector(); in GatherAlignStats() local
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/unit_test/
H A Dunit_test_fasta_reader_old.cpp1354 CSeqVector seq_vec(*pBioseq, NULL, CBioseq_Handle::eCoding_Iupac); in BOOST_AUTO_TEST_CASE() local
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/misc/discrepancy/
H A Ddiscrepancy_case.cpp688 … CSeqVector seq_vec(bioseq, &context.GetScope(), CBioseq_Handle::eCoding_Iupac, eNa_strand_plus); variable
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/table2asn/
H A Dfeature_table_reader.cpp324 CSeqVector seq_vec(bioseq); in FindORF() local
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/flatfile/
H A Dasci_blk.cpp3918 const std::vector<Char>* seq_vec = nullptr; in PackSeqData() local
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/format/
H A Dfeature_item.cpp5568 CSeqVector seq_vec(loc, ctx.GetScope(), CBioseq_Handle::eCoding_Iupac); in x_AddFTableAnticodon() local
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/format/
H A Dfeature_item.cpp5638 CSeqVector seq_vec(loc, ctx.GetScope(), CBioseq_Handle::eCoding_Iupac); in x_AddFTableAnticodon() local
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/util/
H A Dsequence.cpp4800 CSeqVector seq_vec = bsh.GetSeqVector(CBioseq_Handle::eCoding_Iupac); in Search() local
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/util/
H A Dsequence.cpp4800 CSeqVector seq_vec = bsh.GetSeqVector(CBioseq_Handle::eCoding_Iupac); in Search() local

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