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Searched refs:seq_vec (Results 1 – 25 of 30) sorted by relevance

12

/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
266 seq_vec.GetSeqData(pos, pos + 3, na_buff); in GetResidue()
268 TSeqPos size = seq_vec.size(); in GetResidue()
269 seq_vec.GetSeqData(size - pos - 3, size - pos, na_buff); in GetResidue()
274 return seq_vec[IsPositiveStrand(row) ? in GetResidue()
275 pos : seq_vec.size() - pos - 1]; in GetResidue()
298 CSeqVector& seq_vec = x_GetSeqVector(row); in GetSeqString() local
299 TSeqPos size = seq_vec.size(); in GetSeqString()
300 seq_vec.GetSeqData(size - seq_to - 1, size - seq_from, buff); in GetSeqString()
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 Dalnvec.hpp261 CSeqVector& seq_vec = x_GetSeqVector(row); in GetResidue() local
266 seq_vec.GetSeqData(pos, pos + 3, na_buff); in GetResidue()
268 TSeqPos size = seq_vec.size(); in GetResidue()
269 seq_vec.GetSeqData(size - pos - 3, size - pos, na_buff); in GetResidue()
274 return seq_vec[IsPositiveStrand(row) ? in GetResidue()
275 pos : seq_vec.size() - pos - 1]; in GetResidue()
298 CSeqVector& seq_vec = x_GetSeqVector(row); in GetSeqString() local
299 TSeqPos size = seq_vec.size(); in GetSeqString()
300 seq_vec.GetSeqData(size - seq_to - 1, size - seq_from, buff); in GetSeqString()
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 Dalnvec.cpp111 CRef<CSeqVector> seq_vec; in x_GetSeqVector() local
113 seq_vec = iter->second; in x_GetSeqVector()
122 seq_vec.Reset(new CSeqVector(vec)); in x_GetSeqVector()
123 m_SeqVectorCache[row] = seq_vec; in x_GetSeqVector()
125 if ( seq_vec->IsNucleotide() ) { in x_GetSeqVector()
127 seq_vec->SetCoding(m_NaCoding); in x_GetSeqVector()
130 seq_vec->SetIupacCoding(); in x_GetSeqVector()
133 else if ( seq_vec->IsProtein() ) { in x_GetSeqVector()
138 seq_vec->SetIupacCoding(); in x_GetSeqVector()
141 return *seq_vec; in x_GetSeqVector()
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H A Dsparse_aln.cpp424 CSeqVector& seq_vec = *m_SeqVectors[row]; in x_GetSeqVector() local
425 if ( seq_vec.IsNucleotide() ) { in x_GetSeqVector()
427 seq_vec.SetCoding(m_NaCoding); in x_GetSeqVector()
430 seq_vec.SetIupacCoding(); in x_GetSeqVector()
433 else if ( seq_vec.IsProtein() ) { in x_GetSeqVector()
435 seq_vec.SetCoding(m_AaCoding); in x_GetSeqVector()
438 seq_vec.SetIupacCoding(); in x_GetSeqVector()
442 return seq_vec; in x_GetSeqVector()
/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
113 seq_vec = iter->second; in x_GetSeqVector()
122 seq_vec.Reset(new CSeqVector(vec)); in x_GetSeqVector()
123 m_SeqVectorCache[row] = seq_vec; in x_GetSeqVector()
125 if ( seq_vec->IsNucleotide() ) { in x_GetSeqVector()
127 seq_vec->SetCoding(m_NaCoding); in x_GetSeqVector()
130 seq_vec->SetIupacCoding(); in x_GetSeqVector()
133 else if ( seq_vec->IsProtein() ) { in x_GetSeqVector()
138 seq_vec->SetIupacCoding(); in x_GetSeqVector()
141 return *seq_vec; in x_GetSeqVector()
[all …]
H A Dsparse_aln.cpp424 CSeqVector& seq_vec = *m_SeqVectors[row]; in x_GetSeqVector() local
425 if ( seq_vec.IsNucleotide() ) { in x_GetSeqVector()
427 seq_vec.SetCoding(m_NaCoding); in x_GetSeqVector()
430 seq_vec.SetIupacCoding(); in x_GetSeqVector()
433 else if ( seq_vec.IsProtein() ) { in x_GetSeqVector()
435 seq_vec.SetCoding(m_AaCoding); in x_GetSeqVector()
438 seq_vec.SetIupacCoding(); in x_GetSeqVector()
442 return seq_vec; in x_GetSeqVector()
/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
54 seq_vec.GetSeqData(0, seq_inst.GetLength(), seqdata); in BEGIN_SCOPE()
56 Ref(new CSeq_data(seqdata, seq_vec.GetCoding())); in BEGIN_SCOPE()
H A Dseq_entry_edit.cpp248 CSeqVector seq_vec(seq_hl, CBioseq_Handle::eCoding_Iupac, eNa_strand_plus); in Does5primerAbutGap() local
250 for (CSeqVector_CI it = seq_vec.begin(); it; ++ it, i++) { in Does5primerAbutGap()
263 CSeqVector seq_vec(seq_hl, CBioseq_Handle::eCoding_Iupac, eNa_strand_plus); in Does3primerAbutGap() local
264 if (stop >= seq_vec.size() - 1) return false; in Does3primerAbutGap()
266 for (CSeqVector_CI it = seq_vec.begin(); it; ++ it, i++) { in Does3primerAbutGap()
/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
54 seq_vec.GetSeqData(0, seq_inst.GetLength(), seqdata); in BEGIN_SCOPE()
56 Ref(new CSeq_data(seqdata, seq_vec.GetCoding())); in BEGIN_SCOPE()
H A Dseq_entry_edit.cpp248 CSeqVector seq_vec(seq_hl, CBioseq_Handle::eCoding_Iupac, eNa_strand_plus); in Does5primerAbutGap() local
250 for (CSeqVector_CI it = seq_vec.begin(); it; ++ it, i++) { in Does5primerAbutGap()
263 CSeqVector seq_vec(seq_hl, CBioseq_Handle::eCoding_Iupac, eNa_strand_plus); in Does3primerAbutGap() local
264 if (stop >= seq_vec.size() - 1) return false; in Does3primerAbutGap()
266 for (CSeqVector_CI it = seq_vec.begin(); it; ++ it, i++) { in Does3primerAbutGap()
/dports/science/py-DendroPy/DendroPy-4.4.0/src/dendropy/dataio/
H A Dphylipwriter.py100 seq_vec = char_matrix[taxon].symbols_as_string()
102 seq_vec = ""
103 if len(seq_vec) or (not self.suppress_missing_taxa):
104 stream.write("%s%s%s\n" % ( label.ljust(maxlen), spacer, str(seq_vec)))
/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
49 for (CSeqVector_CI i(seq_vec); i; ++i) { in BEGIN_SCOPE()
H A DNSeq.cpp124 CSeqVector seq_vec(*extended_seqloc,scope,CBioseq_Handle::eCoding_Ncbi); in Init() local
133 for (CSeqVector_CI i(seq_vec); i; ++i) { in Init()
/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
352 const char kGapChar = seq_vec.GetGapChar( in x_AddGapsFromBases()
359 CSeqVector_CI seq_vec_ci = seq_vec.begin(); in x_AddGapsFromBases()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/misc/hgvs/
H A Dobjcoords.cpp76 static string x_GetSequence(CSeqVector& seq_vec, TSignedSeqPos pos, TSignedSeqPos adjustment=0);
833 CSeqVector seq_vec = in GetCoordinates() local
863 ref->SetSequence( x_GetSequence(seq_vec, pos) ); in GetCoordinates()
1067 static string x_GetSequence(CSeqVector& seq_vec, TSignedSeqPos pos, TSignedSeqPos adjustment) in x_GetSequence() argument
1070 TSignedSeqPos seq_len = seq_vec.size(); in x_GetSequence()
1078 seq_vec.GetSeqData(before_from, max(0, pos), seq_before); in x_GetSequence()
1097 seq_vec.GetSeqData(pos, pos+1, seq_pos); in x_GetSequence()
1105 seq_vec.GetSeqData(max(0, pos+1), 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
133 seq_vec.GetSeqData(0, bsh.GetBioseqLength(), seq); in GetSeqString()
136 seq_vec.GetSeqData(range.GetFrom(), range.GetTo(), seq); in GetSeqString()
/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
1360 seq_vec.begin(), seq_vec.end() ); in BOOST_AUTO_TEST_CASE()
/dports/biology/mafft/mafft-7.267-without-extensions/core/
H A DFalign_localhom.c69 static void seq_vec( Fukusosuu *result, char query, double incr, char *seq )
392 seq_vec( seqVector1[j], amino[j], eff1[i], tmpseq1[i] ); in Falign_localhom()
431 seq_vec( seqVector2[j], amino[j], eff2[i], tmpseq2[i] ); in Falign_localhom()
H A DFalign.c100 static void seq_vec( Fukusosuu *result, char query, double incr, char *seq )
353 seq_vec( seqVector1[j], amino[j], eff1[i], tmpseq1[i] ); in Fgetlag()
392 seq_vec( seqVector2[j], amino[j], eff2[i], tmpseq2[i] ); in Fgetlag()
1010 seq_vec( seqVector1[j], amino[j], eff1[i], tmpseq1[i] ); in Falign()
1053 seq_vec( seqVector2[j], amino[j], eff2[i], tmpseq2[i] ); in Falign()
/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
839 seq_vec.SetIupacCoding(); in GatherAlignStats()
841 CRef<CPacked_seqint> res = masker.GetMaskedInts(id, seq_vec); in GatherAlignStats()
/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
1817 has_abutting_gap = x_CheckPosNOrGap(pos, seq_vec); in x_ValidateParentPartialness()
1837 CSeqVector seq_vec(m_LocationBioseq, CBioseq_Handle::eCoding_Iupac); in x_ValidateParentPartialness() local
1842 has_abutting_gap = x_CheckPosNOrGap(pos, seq_vec); in x_ValidateParentPartialness()
/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
3932 seq_vec = &seq_data.GetNcbi8aa().Get(); in PackSeqData()
3934 old_size = seq_vec->size(); in PackSeqData()
3938 seq_vec = &seq_data.GetNcbistdaa().Get(); in PackSeqData()
3940 old_size = seq_vec->size(); in PackSeqData()
3950 else if (seq_vec != nullptr) in PackSeqData()
3951 …new_size = CSeqConvert::Convert(&(*seq_vec)[0], old_coding, 0, static_cast<TSeqPos>(old_size), &ne… in PackSeqData()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/
H A Dbl2seq_unit_test.cpp3342 TSeqLocVector seq_vec; in BOOST_AUTO_TEST_CASE() local
3348 seq_vec.push_back(*sl); in BOOST_AUTO_TEST_CASE()
3354 CBl2Seq blaster(seq_vec, seq_vec, *prot_opts); in BOOST_AUTO_TEST_CASE()
3407 int seqlen = (int)sequence::GetLength(*seq_vec[q].seqloc, in BOOST_AUTO_TEST_CASE()
3408 &*seq_vec[q].scope); in BOOST_AUTO_TEST_CASE()
3471 int seqlen = (int)sequence::GetLength(*seq_vec[q].seqloc, in BOOST_AUTO_TEST_CASE()
3472 &*seq_vec[q].scope); in BOOST_AUTO_TEST_CASE()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/
H A Dbl2seq_unit_test.cpp3342 TSeqLocVector seq_vec; in BOOST_AUTO_TEST_CASE() local
3348 seq_vec.push_back(*sl); in BOOST_AUTO_TEST_CASE()
3354 CBl2Seq blaster(seq_vec, seq_vec, *prot_opts); in BOOST_AUTO_TEST_CASE()
3407 int seqlen = (int)sequence::GetLength(*seq_vec[q].seqloc, in BOOST_AUTO_TEST_CASE()
3408 &*seq_vec[q].scope); in BOOST_AUTO_TEST_CASE()
3471 int seqlen = (int)sequence::GetLength(*seq_vec[q].seqloc, in BOOST_AUTO_TEST_CASE()
3472 &*seq_vec[q].scope); in BOOST_AUTO_TEST_CASE()
/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
691 … seq_vec.GetSeqData(bioseq.GetInst().GetLength() - TAIL, bioseq.GetInst().GetLength(), seq_data);

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