/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/structure/cd_utils/ |
H A D | cuSequence.hpp | 69 int GetMMDBId (const CBioseq& bioseq); 74 TTaxId GetTaxIdInBioseq(const CBioseq& bioseq); 77 bool IsEnvironmentalSeq(const CBioseq& bioseq); 82 string GetSpeciesFromBioseq(const CBioseq& bioseq); 87 int GetSeqLength(const CBioseq& bioseq); 98 bool GetNcbieaaString(const CBioseq& bioseq, string& str); 100 bool GetNcbistdSeq(const CBioseq& bioseq, vector<char>& seqData); 104 string GetRawSequenceString(const CBioseq& bioseq); 120 bool checkAndFixPdbBioseq(CRef< CBioseq > bioseq); 161 bool AddCommentToBioseq(CBioseq& bioseq, const string& comment); [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/structure/struct_util/ |
H A D | su_sequence_set.cpp | 183 Sequence::Sequence(ncbi::objects::CBioseq& bioseq) : in Sequence() argument 184 m_bioseqASN(&bioseq), m_isProtein(false) in Sequence() 187 if (bioseq.IsSetDescr()) { in Sequence() 190 for (d=bioseq.GetDescr().Get().begin(); d!=de; ++d) { in Sequence() 217 if (bioseq.GetInst().GetRepr() == CSeq_inst::eRepr_raw && bioseq.GetInst().IsSetSeq_data()) { in Sequence() 220 if (bioseq.GetInst().GetSeq_data().IsNcbieaa()) { in Sequence() 223 } else if (bioseq.GetInst().GetSeq_data().IsIupacaa()) { in Sequence() 232 else if (bioseq.GetInst().GetSeq_data().IsIupacna()) { in Sequence() 241 } else if (bioseq.GetInst().GetSeq_data().IsNcbi4na()) { in Sequence() 250 … if (bioseq.GetInst().IsSetLength() && bioseq.GetInst().GetLength() < m_sequenceString.length()) in Sequence() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/structure/cd_utils/ |
H A D | cuSequence.cpp | 112 int GetMMDBId(const CBioseq& bioseq) { in GetMMDBId() argument 118 if (bioseq.IsSetAnnot()) { in GetMMDBId() 119 for (j = bioseq.GetAnnot().begin(); j!= bioseq.GetAnnot().end(); j++) { in GetMMDBId() 145 if (bioseq.IsSetDescr()) in GetTaxIdInBioseq() 196 if (bioseq.IsSetDescr()) { in GetSpeciesFromBioseq() 536 idEnd = bioseq->GetId().end(); in CopyGiSeqId() 571 idEnd = bioseq->GetId().end(); in CopyPdbSeqId() 611 CBioseq::TId::const_iterator idCit = bioseq.GetId().begin(), idEnd = bioseq.GetId().end(); in HasSeqIdOfType() 646 CBioseq::TId::const_iterator idCit = bioseq.GetId().begin(), idEnd = bioseq.GetId().end(); in CopySeqIdsOfType() 820 bioseq.ResetAnnot(); in SimplifyBioseqForCD() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/cddalignview/ |
H A D | cav_seqset.cpp | 206 Sequence::Sequence(const CBioseq& bioseq) : in Sequence() argument 207 status(CAV_ERROR_SEQUENCES), bioseqASN(&bioseq), seqIDs(bioseq.GetId()), mmdbLink(NOT_SET) in Sequence() 210 if (bioseq.IsSetDescr()) { in Sequence() 212 for (d=bioseq.GetDescr().Get().begin(); d!=de; ++d) { in Sequence() 224 if (bioseq.IsSetAnnot()) { in Sequence() 226 for (a=bioseq.GetAnnot().begin(); a!=ae; ++a) { in Sequence() 245 if (bioseq.GetInst().GetRepr() == CSeq_inst::eRepr_raw && bioseq.GetInst().IsSetSeq_data()) { in Sequence() 248 if (bioseq.GetInst().GetSeq_data().IsNcbieaa()) { in Sequence() 257 else if (bioseq.GetInst().GetSeq_data().IsIupacna()) { in Sequence() 268 … if (bioseq.GetInst().IsSetLength() && bioseq.GetInst().GetLength() < sequenceString.length()) in Sequence() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/streamtest/ |
H A D | process_defline.hpp | 160 void x_FastaSeqIdWrite(const CBioseq& bioseq) in x_FastaSeqIdWrite() argument 231 const CBioseq& bioseq = *bit; in IndexedProcess() local 235 if (bioseq.IsSetInst()) { in IndexedProcess() 249 if (bioseq.IsSetInst()) { in IndexedProcess() 277 if (bioseq.IsSetInst()) { in IndexedProcess() 290 if (bioseq.IsSetInst()) { in IndexedProcess() 305 x_FastaSeqIdWrite (bioseq); in IndexedProcess() 325 const CBioseq& bioseq = *bit; in UnindexedProcess() local 329 if (bioseq.IsSetInst()) { in UnindexedProcess() 341 se = bioseq.GetParentEntry(); in UnindexedProcess() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/misc/discrepancy/ |
H A D | sequence_tests.cpp | 79 if (bioseq.CanGetInst() && !bioseq.GetInst().IsAa() && bioseq.IsSetDescr()) { 119 if (bioseq.CanGetInst() && bioseq.GetInst().IsNa()) { 139 …if (bioseq.CanGetInst() && bioseq.GetInst().IsAa() && bioseq.GetInst().IsSetLength() && bioseq.Get… 257 if (bioseq.CanGetInst() && bioseq.GetInst().IsNa()) { 306 if (bioseq.CanGetInst() && bioseq.GetInst().IsNa()) { 326 if (bioseq.CanGetInst() && bioseq.GetInst().IsNa()) { 348 if (bioseq.CanGetInst() && bioseq.GetInst().IsNa()) { 476 if (bioseq.CanGetInst() && !bioseq.GetInst().IsAa()) { 754 if (bioseq.CanGetInst() && bioseq.GetInst().IsNa()) { 1479 …if (bioseq.CanGetInst() && bioseq.GetInst().IsNa() && bioseq.IsSetLength() && bioseq.GetLength() <… [all …]
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H A D | discrepancy_case.cpp | 64 if (bioseq.CanGetInst() && bioseq.GetInst().IsNa()) { 85 if (bioseq.CanGetInst() && bioseq.GetInst().IsAa()) { 116 if (bioseq.CanGetInst() && bioseq.GetInst().IsAa() && !GetProteinId(bioseq)) { 132 if (bioseq.CanGetInst() && bioseq.GetInst().IsAa()) { 184 if (bioseq.CanGetInst() && bioseq.GetInst().IsNa()) { 208 if (bioseq.CanGetInst() && bioseq.GetInst().IsNa()) { 346 if (bioseq.IsSetInst() && bioseq.GetInst().IsNa()) { 522 if (bioseq.IsSetInst() && bioseq.GetInst().IsNa()) { 665 if (bioseq.IsNa() && bioseq.IsSetLength() && bioseq.GetLength() > kSeqLength) { 685 if (bioseq.CanGetInst() && !bioseq.GetInst().IsAa() && bioseq.GetInst().GetLength() >= 30) { [all …]
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H A D | seqdesc_per_bioseq.cpp | 54 const CBioseq& bioseq = context.CurrentBioseq(); variable 56 …if (biosrc && bioseq.IsNa() && bioseq.IsSetInst() && bioseq.GetInst().IsSetMol() && bioseq.GetInst… 87 const CBioseq& bioseq = context.CurrentBioseq(); variable 89 …if (biosrc && bioseq.IsNa() && bioseq.IsSetInst() && bioseq.GetInst().IsSetMol() && bioseq.GetInst… 133 const CBioseq& bioseq = context.CurrentBioseq(); variable 136 if (biosrc && molinfo && !bioseq.IsAa()) { 137 …() || molinfo->GetMolinfo().GetBiomol() == CMolInfo::eBiomol_genomic) && bioseq.GetInst().GetMol()… 286 const CBioseq& bioseq = context.CurrentBioseq(); variable 287 if (bioseq.IsNa()) { 359 const CBioseq& bioseq = context.CurrentBioseq(); variable [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/cn3d/ |
H A D | sequence_set.cpp | 205 if (bioseq.IsSetDescr()) { in Sequence() 208 for (d=bioseq.GetDescr().Get().begin(); d!=de; ++d) { in Sequence() 239 if (bioseq.IsSetAnnot()) { in Sequence() 241 for (a=bioseq.GetAnnot().begin(); a!=ae; ++a) { in Sequence() 258 if (bioseq.GetInst().GetRepr() == CSeq_inst::eRepr_raw && bioseq.GetInst().IsSetSeq_data()) { in Sequence() 261 if (bioseq.GetInst().GetSeq_data().IsNcbieaa()) { in Sequence() 264 } else if (bioseq.GetInst().GetSeq_data().IsIupacaa()) { in Sequence() 273 else if (bioseq.GetInst().GetSeq_data().IsIupacna()) { in Sequence() 282 } else if (bioseq.GetInst().GetSeq_data().IsNcbi4na()) { in Sequence() 291 … if (bioseq.GetInst().IsSetLength() && bioseq.GetInst().GetLength() < sequenceString.length()) in Sequence() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/flatfile/ |
H A D | citation.cpp | 88 void CPubInfo::SetBioseq(const objects::CBioseq* bioseq) in SetBioseq() argument 90 bioseq_ = bioseq; in SetBioseq() 143 pub_info.SetBioseq(bioseq); in FindCitInDescr() 318 if (bioseq && pub->GetBioseq() && bioseq != pub->GetBioseq()) in ProcessCit() 359 for (CTypeConstIterator<objects::CBioseq> bioseq(Begin(*(*entry))); bioseq; ++bioseq) in ProcessCitations() local 361 if (bioseq->IsSetDescr()) in ProcessCitations() 362 FindCitInDescr(pubs, bioseq->GetDescr(), &(*bioseq)); in ProcessCitations() 364 if (bioseq->IsSetAnnot()) in ProcessCitations() 377 for (CTypeIterator<objects::CBioseq> bioseq(Begin(*(*entry))); bioseq; ++bioseq) in ProcessCitations() local 379 if (bioseq->IsSetAnnot()) in ProcessCitations() [all …]
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H A D | add.h | 48 bool no_reference(const objects::CBioseq& bioseq); 52 void SeqToDelta(objects::CBioseq& bioseq, Int2 tech); 53 void GapsToDelta(objects::CBioseq& bioseq, GapFeatsPtr gfp, unsigned char* drop); 54 void AssemblyGapsToDelta(objects::CBioseq& bioseq, GapFeatsPtr gfp, unsigned char* drop); 59 bool fta_parse_tpa_tsa_block(objects::CBioseq& bioseq, char* offset, char* acnum, 69 Uint1 fta_check_con_for_wgs(objects::CBioseq& bioseq); 76 void fta_tsa_tls_comment_dblink_check(const objects::CBioseq& bioseq, bool is_tsa); 77 void fta_set_molinfo_completeness(objects::CBioseq& bioseq, IndexblkPtr ibp); 84 void fta_add_hist(ParserPtr pp, objects::CBioseq& bioseq, objects::CGB_block::TExtra_acces…
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/ |
H A D | gaps_edit.cpp | 251 if (!bioseq.IsSetInst()) in CreateGap() 315 void CGapsEditor::ConvertNs2Gaps(CBioseq& bioseq) in ConvertNs2Gaps() argument 317 …if (bioseq.IsSetInst() && bioseq.GetInst().IsSetSeq_data() && !bioseq.GetInst().GetSeq_data().IsGa… in ConvertNs2Gaps() 319 ConvertNs2Gaps(bioseq.SetInst()); in ConvertNs2Gaps() 323 if (!bioseq.IsSetInst() || !bioseq.GetInst().IsSetExt() || !bioseq.GetInst().GetExt().IsDelta()) in ConvertNs2Gaps() 328 CSeq_inst& inst = bioseq.SetInst(); in ConvertNs2Gaps() 428 TSeqPos len = bioseq.GetInst().GetLength(); in ConvertBioseqToDelta() 434 bioseq.SetInst().ResetSeq_data(); in ConvertBioseqToDelta() 438 void CGapsEditor::AppendGap(CBioseq& bioseq) in AppendGap() argument 447 bioseq.SetInst().SetLength() += len; in AppendGap() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/edit/ |
H A D | gaps_edit.cpp | 251 if (!bioseq.IsSetInst()) in CreateGap() 315 void CGapsEditor::ConvertNs2Gaps(CBioseq& bioseq) in ConvertNs2Gaps() argument 317 …if (bioseq.IsSetInst() && bioseq.GetInst().IsSetSeq_data() && !bioseq.GetInst().GetSeq_data().IsGa… in ConvertNs2Gaps() 319 ConvertNs2Gaps(bioseq.SetInst()); in ConvertNs2Gaps() 323 if (!bioseq.IsSetInst() || !bioseq.GetInst().IsSetExt() || !bioseq.GetInst().GetExt().IsDelta()) in ConvertNs2Gaps() 328 CSeq_inst& inst = bioseq.SetInst(); in ConvertNs2Gaps() 428 TSeqPos len = bioseq.GetInst().GetLength(); in ConvertBioseqToDelta() 434 bioseq.SetInst().ResetSeq_data(); in ConvertBioseqToDelta() 438 void CGapsEditor::AppendGap(CBioseq& bioseq) in AppendGap() argument 447 bioseq.SetInst().SetLength() += len; in AppendGap() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/blastinput/ |
H A D | blast_fasta_input.cpp | 143 retval->SetSeq(*bioseq); in ReadOneSeq() 738 bioseq.SetId().clear(); in x_ReadFastc() 764 bioseq.SetId().clear(); in x_ReadFastc() 834 bioseq.SetId().clear(); in x_ReadFastaOneSeq() 838 bioseq.SetId().push_back(seqid); in x_ReadFastaOneSeq() 839 bioseq.SetDescr(); in x_ReadFastaOneSeq() 849 bioseq.SetInst().SetLength(start); in x_ReadFastaOneSeq() 900 bioseq.SetId().clear(); in x_ReadFastqOneSeq() 904 bioseq.SetId().push_back(seqid); in x_ReadFastqOneSeq() 905 bioseq.SetDescr(); in x_ReadFastqOneSeq() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/blastinput/ |
H A D | blast_fasta_input.cpp | 143 retval->SetSeq(*bioseq); in ReadOneSeq() 738 bioseq.SetId().clear(); in x_ReadFastc() 764 bioseq.SetId().clear(); in x_ReadFastc() 834 bioseq.SetId().clear(); in x_ReadFastaOneSeq() 838 bioseq.SetId().push_back(seqid); in x_ReadFastaOneSeq() 839 bioseq.SetDescr(); in x_ReadFastaOneSeq() 849 bioseq.SetInst().SetLength(start); in x_ReadFastaOneSeq() 900 bioseq.SetId().clear(); in x_ReadFastqOneSeq() 904 bioseq.SetId().push_back(seqid); in x_ReadFastqOneSeq() 905 bioseq.SetDescr(); in x_ReadFastqOneSeq() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/seqedit/ |
H A D | seqedit.asn | 30 bioseq-id Seq-id, 35 -- Add a new seq-id to bioseq 41 -- Remove a seq-id from bioseq 47 -- Reset ids field of bioseq 53 -- Change bioseq's attribure 70 -- Reset bioseq's attribute 101 -- Reset bioseq-set's attibute 176 -- Add an annotation to a bioseq or a bioseq-set 182 -- Remove an annotation object from a bioseq or a bioseq-set 194 -- Add an annotaion object to a bioseq or a bioseq-set [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/seqedit/ |
H A D | seqedit.asn | 30 bioseq-id Seq-id, 35 -- Add a new seq-id to bioseq 41 -- Remove a seq-id from bioseq 47 -- Reset ids field of bioseq 53 -- Change bioseq's attribure 70 -- Reset bioseq's attribute 101 -- Reset bioseq-set's attibute 176 -- Add an annotation to a bioseq or a bioseq-set 182 -- Remove an annotation object from a bioseq or a bioseq-set 194 -- Add an annotaion object to a bioseq or a bioseq-set [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/macro/ |
H A D | Molinfo_field.cpp | 56 string CMolinfo_field :: GetSequenceQualFromBioseq (CConstRef <CBioseq> bioseq) const in GetSequenceQualFromBioseq() 58 if (bioseq.Empty()) return kEmptyStr; in GetSequenceQualFromBioseq() 60 if (bioseq->CanGetDescr()) { in GetSequenceQualFromBioseq() 61 ITERATE (list <CRef <CSeqdesc> >, it, bioseq->GetDescr().Get()) { in GetSequenceQualFromBioseq() 90 ->FindName(bioseq->GetInst().GetMol(), true); in GetSequenceQualFromBioseq() 102 if (bioseq->GetInst().CanGetTopology()) { in GetSequenceQualFromBioseq() 104 ->FindName(bioseq->GetInst().GetTopology(), true); in GetSequenceQualFromBioseq() 108 if (bioseq->GetInst().CanGetStrand()) { in GetSequenceQualFromBioseq() 110 ->FindName(bioseq->GetInst().GetStrand(), true); in GetSequenceQualFromBioseq()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/macro/ |
H A D | Molinfo_field.cpp | 56 string CMolinfo_field :: GetSequenceQualFromBioseq (CConstRef <CBioseq> bioseq) const in GetSequenceQualFromBioseq() 58 if (bioseq.Empty()) return kEmptyStr; in GetSequenceQualFromBioseq() 60 if (bioseq->CanGetDescr()) { in GetSequenceQualFromBioseq() 61 ITERATE (list <CRef <CSeqdesc> >, it, bioseq->GetDescr().Get()) { in GetSequenceQualFromBioseq() 90 ->FindName(bioseq->GetInst().GetMol(), true); in GetSequenceQualFromBioseq() 102 if (bioseq->GetInst().CanGetTopology()) { in GetSequenceQualFromBioseq() 104 ->FindName(bioseq->GetInst().GetTopology(), true); in GetSequenceQualFromBioseq() 108 if (bioseq->GetInst().CanGetStrand()) { in GetSequenceQualFromBioseq() 110 ->FindName(bioseq->GetInst().GetStrand(), true); in GetSequenceQualFromBioseq()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/ |
H A D | seq_table_ci.cpp | 57 CSeq_table_CI::CSeq_table_CI(const CBioseq_Handle& bioseq) in CSeq_table_CI() argument 59 bioseq, in CSeq_table_CI() 66 CSeq_table_CI::CSeq_table_CI(const CBioseq_Handle& bioseq, in CSeq_table_CI() argument 70 bioseq, in CSeq_table_CI() 77 CSeq_table_CI::CSeq_table_CI(const CBioseq_Handle& bioseq, in CSeq_table_CI() argument 80 bioseq, in CSeq_table_CI() 88 CSeq_table_CI::CSeq_table_CI(const CBioseq_Handle& bioseq, in CSeq_table_CI() argument 92 bioseq, in CSeq_table_CI() 100 CSeq_table_CI::CSeq_table_CI(const CBioseq_Handle& bioseq, in CSeq_table_CI() argument 105 bioseq, in CSeq_table_CI()
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H A D | align_ci.cpp | 47 CAlign_CI::CAlign_CI(const CBioseq_Handle& bioseq) in BEGIN_SCOPE() 49 bioseq, in BEGIN_SCOPE() 56 CAlign_CI::CAlign_CI(const CBioseq_Handle& bioseq, in CAlign_CI() argument 60 bioseq, in CAlign_CI() 67 CAlign_CI::CAlign_CI(const CBioseq_Handle& bioseq, in CAlign_CI() argument 70 bioseq, in CAlign_CI() 78 CAlign_CI::CAlign_CI(const CBioseq_Handle& bioseq, in CAlign_CI() argument 82 bioseq, in CAlign_CI() 90 CAlign_CI::CAlign_CI(const CBioseq_Handle& bioseq, in CAlign_CI() argument 95 bioseq, in CAlign_CI()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/ |
H A D | seq_table_ci.cpp | 57 CSeq_table_CI::CSeq_table_CI(const CBioseq_Handle& bioseq) in CSeq_table_CI() argument 59 bioseq, in CSeq_table_CI() 66 CSeq_table_CI::CSeq_table_CI(const CBioseq_Handle& bioseq, in CSeq_table_CI() argument 70 bioseq, in CSeq_table_CI() 77 CSeq_table_CI::CSeq_table_CI(const CBioseq_Handle& bioseq, in CSeq_table_CI() argument 80 bioseq, in CSeq_table_CI() 88 CSeq_table_CI::CSeq_table_CI(const CBioseq_Handle& bioseq, in CSeq_table_CI() argument 92 bioseq, in CSeq_table_CI() 100 CSeq_table_CI::CSeq_table_CI(const CBioseq_Handle& bioseq, in CSeq_table_CI() argument 105 bioseq, in CSeq_table_CI()
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H A D | align_ci.cpp | 47 CAlign_CI::CAlign_CI(const CBioseq_Handle& bioseq) in BEGIN_SCOPE() 49 bioseq, in BEGIN_SCOPE() 56 CAlign_CI::CAlign_CI(const CBioseq_Handle& bioseq, in CAlign_CI() argument 60 bioseq, in CAlign_CI() 67 CAlign_CI::CAlign_CI(const CBioseq_Handle& bioseq, in CAlign_CI() argument 70 bioseq, in CAlign_CI() 78 CAlign_CI::CAlign_CI(const CBioseq_Handle& bioseq, in CAlign_CI() argument 82 bioseq, in CAlign_CI() 90 CAlign_CI::CAlign_CI(const CBioseq_Handle& bioseq, in CAlign_CI() argument 95 bioseq, in CAlign_CI()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/blastdb_format/ |
H A D | seq_writer.cpp | 234 static string s_GetTitle(CConstRef<CBioseq> bioseq) in s_GetTitle() argument 244 static void s_ReplaceCtrlAsInTitle(CRef<CBioseq> bioseq) in s_ReplaceCtrlAsInTitle() argument 283 CRef<CBioseq> bioseq; in DumpAll() local 285 bioseq.Reset(blastdb.GetBioseq(i)); in DumpAll() 286 if (bioseq.Empty()) { in DumpAll() 290 CRef<CSeq_id> id(*(bioseq->GetId().begin())); in DumpAll() 293 m_Out << ">" << s_GetTitle(bioseq) << '\n'; in DumpAll() 307 s_ReplaceCtrlAsInTitle(bioseq); in DumpAll() 309 fasta.Write(*bioseq, 0, true); in DumpAll() 319 string title = s_GetTitle(bioseq); in DumpAll() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/blastdb_format/ |
H A D | seq_writer.cpp | 234 static string s_GetTitle(CConstRef<CBioseq> bioseq) in s_GetTitle() argument 244 static void s_ReplaceCtrlAsInTitle(CRef<CBioseq> bioseq) in s_ReplaceCtrlAsInTitle() argument 283 CRef<CBioseq> bioseq; in DumpAll() local 285 bioseq.Reset(blastdb.GetBioseq(i)); in DumpAll() 286 if (bioseq.Empty()) { in DumpAll() 290 CRef<CSeq_id> id(*(bioseq->GetId().begin())); in DumpAll() 293 m_Out << ">" << s_GetTitle(bioseq) << '\n'; in DumpAll() 307 s_ReplaceCtrlAsInTitle(bioseq); in DumpAll() 309 fasta.Write(*bioseq, 0, true); in DumpAll() 319 string title = s_GetTitle(bioseq); in DumpAll() [all …]
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