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Searched refs:bioseq (Results 1 – 25 of 496) sorted by relevance

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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/structure/cd_utils/
H A DcuSequence.hpp69 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);
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/structure/struct_util/
H A Dsu_sequence_set.cpp183 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/structure/cd_utils/
H A DcuSequence.cpp112 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/cddalignview/
H A Dcav_seqset.cpp206 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/streamtest/
H A Dprocess_defline.hpp160 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/misc/discrepancy/
H A Dsequence_tests.cpp79 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() <…
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H A Ddiscrepancy_case.cpp64 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) {
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H A Dseqdesc_per_bioseq.cpp54 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
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/cn3d/
H A Dsequence_set.cpp205 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/flatfile/
H A Dcitation.cpp88 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()
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H A Dadd.h48 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…
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/
H A Dgaps_edit.cpp251 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/edit/
H A Dgaps_edit.cpp251 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/blastinput/
H A Dblast_fasta_input.cpp143 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/blastinput/
H A Dblast_fasta_input.cpp143 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/seqedit/
H A Dseqedit.asn30 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
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/seqedit/
H A Dseqedit.asn30 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
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/macro/
H A DMolinfo_field.cpp56 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/macro/
H A DMolinfo_field.cpp56 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/
H A Dseq_table_ci.cpp57 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()
H A Dalign_ci.cpp47 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/
H A Dseq_table_ci.cpp57 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()
H A Dalign_ci.cpp47 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/blastdb_format/
H A Dseq_writer.cpp234 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/blastdb_format/
H A Dseq_writer.cpp234 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()
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