| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/readers/hgvs/ |
| H A D | semantic_actions.hpp | 26 void AssignNonsense(CRef<CAaSite> initial, CRef<CSimpleVariant>& result);
30 void AssignAaDup(CRef<CAaLocation> aa_loc, CRef<CSimpleVariant>& result);
34 void AssignNtermExtension(CRef<CAaSite> initial_start_site, CRef<CCount> new_start_site, CRef<CSimp…
44 void AssignAaInterval(CRef<CAaSite> start, CRef<CAaSite>& stop, CRef<CAaInterval>& result);
58 void AssignAaSSR(CRef<CAaLocation> aa_loc, CRef<CCount> count, CRef<CSimpleVariant>& result);
64 void AssignAaInsertionSize(CRef<CAaInterval> aa_interval, CRef<CCount> seq_size, CRef<CSimpleVarian…
70 void AssignAaDelinsSize(CRef<CAaLocation> aa_loc, CRef<CCount> seq_size, CRef<CSimpleVariant>& resu…
94 void AssignNtSiteRange(CRef<CNtSite> start, CRef<CNtSite> stop, CRef<CNtLocation>& result);
98 void AssignNtInterval(CRef<CNtLocation> start, CRef<CNtLocation> stop, CRef<CNtLocation>& result);
104 void AssignNtSSR(CRef<CNtLocation> nt_loc, CRef<CCount> count, CRef<CSimpleVariant>& result);
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| H A D | variation_ref_utils.hpp | 10 CRef<CVariation_ref> g_CreateSNV(const CSeq_data& nucleotide,
12 CRef<CDelta_item> offset=null);
14 CRef<CVariation_ref> g_CreateMNP(const CSeq_data& nucleotide,
17 CRef<CDelta_item> offset=null);
19 CRef<CVariation_ref> g_CreateMissense(const CSeq_data& amino_acid,
33 CRef<CVariation_ref> g_CreateIdentity(CRef<CSeq_literal> seq_literal,
39 CRef<CVariation_ref> g_CreateVarref(CRef<CSeq_literal> seq_literal,
46 CRef<CVariation_ref> g_CreateDelins(CSeq_literal& insertion,
52 CRef<CVariation_ref> g_CreateInsertion(CSeq_literal& insertion,
63 CRef<CVariation_ref> g_CreateMicrosatellite(CRef<CDelta_item> repeat_info,
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/unit_test_util/ |
| H A D | unit_test_util.hpp | 123 NCBI_UNIT_TEST_UTIL_EXPORT CRef<objects::CSeq_feat> AddProtFeat(CRef<objects::CSeq_entry> entry) ;
126 NCBI_UNIT_TEST_UTIL_EXPORT CRef<objects::CSeq_id> IdFromEntry(CRef<objects::CSeq_entry> entry);
170 NCBI_UNIT_TEST_UTIL_EXPORT void ChangeId(CRef<objects::CSeq_annot> annot, CRef<objects::CSeq_id> id…
178 NCBI_UNIT_TEST_UTIL_EXPORT CRef<objects::CSeq_entry> BuildGenProdSetNucProtSet (CRef<objects::CSeq_…
179 NCBI_UNIT_TEST_UTIL_EXPORT CRef<objects::CSeq_feat> MakemRNAForCDS (CRef<objects::CSeq_feat> feat);
198 NCBI_UNIT_TEST_UTIL_EXPORT CRef<objects::CSeq_feat> BuildtRNA(CRef<objects::CSeq_id> id);
199 NCBI_UNIT_TEST_UTIL_EXPORT CRef<objects::CSeq_feat> BuildGoodtRNA(CRef<objects::CSeq_id> id);
200 NCBI_UNIT_TEST_UTIL_EXPORT CRef<objects::CSeq_loc> MakeMixLoc (CRef<objects::CSeq_id> id);
201 NCBI_UNIT_TEST_UTIL_EXPORT CRef<objects::CSeq_feat> MakeIntronForMixLoc (CRef<objects::CSeq_id> id);
208 NCBI_UNIT_TEST_UTIL_EXPORT CRef<objects::CSeq_feat> AddMiscFeature(CRef<objects::CSeq_entry> entry);
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/igblast/ |
| H A D | igblast.hpp | 221 CRef<CIgAnnotation> m_Annotation;
236 CRef<CScope> scope) in CIgBlast()
258 CRef<CScope> scope) in CIgBlast()
274 CRef<CSearchResultSet> Run();
288 CRef<CBlastQueryVector> m_Query;
289 CRef<IQueryFactory> m_Subject;
290 CRef<CLocalDbAdapter> m_LocalDb;
291 CRef<CSearchDatabase> m_RemoteDb;
292 CRef<CBlastOptionsHandle> m_Options;
296 CRef<CScope> m_Scope;
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/igblast/ |
| H A D | igblast.hpp | 221 CRef<CIgAnnotation> m_Annotation;
236 CRef<CScope> scope) in CIgBlast()
258 CRef<CScope> scope) in CIgBlast()
274 CRef<CSearchResultSet> Run();
288 CRef<CBlastQueryVector> m_Query;
289 CRef<IQueryFactory> m_Subject;
290 CRef<CLocalDbAdapter> m_LocalDb;
291 CRef<CSearchDatabase> m_RemoteDb;
292 CRef<CBlastOptionsHandle> m_Options;
296 CRef<CScope> m_Scope;
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/hgvs/ |
| H A D | semantic_actions.cpp | 8 CRef<T> MakeResult(CRef<T> result) in BEGIN_SCOPE()
14 CRef<T> CreateResultIfNull(CRef<T> result) in CreateResultIfNull()
137 void AssignAaInterval(CRef<CAaSite> start, CRef<CAaSite>& stop, CRef<CAaInterval>& result) in AssignAaInterval()
200 void AssignAaSSR(CRef<CAaLocation> aa_loc, CRef<CCount> count, CRef<CSimpleVariant>& result) in AssignAaSSR()
221 void AssignAaInsertionSize(CRef<CAaInterval> aa_interval, CRef<CCount> seq_size, CRef<CSimpleVarian… in AssignAaInsertionSize()
252 void AssignAaDelinsSize(CRef<CAaLocation> aa_loc, CRef<CCount> seq_size, CRef<CSimpleVariant>& resu… in AssignAaDelinsSize()
263 void AssignFuzzy(CRef<T> input, CRef<T>& result) in AssignFuzzy()
389 void AssignNtSiteRange(CRef<CNtSite> start, CRef<CNtSite> stop, CRef<CNtLocation>& result) in AssignNtSiteRange()
402 void AssignNtInterval(CRef<CNtLocation> start, CRef<CNtLocation> stop, CRef<CNtLocation>& result) in AssignNtInterval()
502 void AssignNtSSR(CRef<CNtLocation> nt_loc, CRef<CCount> count, CRef<CSimpleVariant>& result) in AssignNtSSR()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/structure/cd_utils/ |
| H A D | cuCdUpdater.hpp | 61 TGi refresh(CRef< CSeq_align> seqAlign, CRef< CSeq_entry > seqEntry);
160 CRef< CSeq_entry > seqEntry);
162 CRef<CSeq_entry>& seqEntry);
172 static TGi getGi(CRef<CBioseq> bioseq);
179 …static bool reformatBioseq(CRef< CBioseq > bioseq, CRef< CSeq_entry > seqEntry, CEntrez2Client& cl…
184 static int SplitBioseqByBlastDefline (CRef< CBioseq > handle, vector< CRef<CBioseq> >& bioseqs);
188 CRef< CSeq_entry > seqEntry);
194 CRef< CSeq_entry > seqEntry);
197 bool findSeq(CRef<CSeq_id> seqID, vector< CRef< CBioseq > >& bioseqs, CRef<CSeq_entry>& seqEntry);
210 CRef< CSeq_id > m_masterPdb;
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| H A D | cuSequence.hpp | 57 bool SeqIdsMatch(const CRef< CSeq_id>& id1, const CRef< CSeq_id>& id2);
65 int GetCDDPssmIdFromSeqId(const CRef< CSeq_id >& id);
114 bool IsConsensus(const CRef< CSeq_id >& seqId);
116 bool GetAccAndVersion(const CRef< CBioseq > bioseq, string& acc, int& version, CRef< CSeq_id>& seqI…
118 bool GetPDBBlockFromSeqEntry(CRef< CSeq_entry > seqEntry, CRef< CPDB_block >& pdbBlock);
120 bool checkAndFixPdbBioseq(CRef< CBioseq > bioseq);
127 bool CopyGiSeqId(const CRef<CBioseq>& bioseq, CRef<CSeq_id>& giSeqId, unsigned int nth = 1);
134 bool CopyPdbSeqId(const CRef<CBioseq>& bioseq, CRef<CSeq_id>& pdbSeqId, unsigned int nth = 1);
147 unsigned int CopySeqIdsOfType(const CRef< CSeq_entry >& seqEntry, CSeq_id::E_Choice choice, list< C…
152 bool CopyBioseqWithType(const CRef< CSeq_entry >& seqEntry, CSeq_id::E_Choice choice, CRef< CBioseq…
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| H A D | cuAlign.hpp | 54 bool GetSeqID(const CRef< CSeq_align >& seqAlign, CRef< CSeq_id >& SeqID, bool getSlave=true);
58 bool ChangeSeqIdInSeqAlign(CRef< CSeq_align>& sa, const CRef< CSeq_id >& newSeqId, bool onMaster);
73 int GetAlignedPositions(const CRef< CSeq_align >& align1, const CRef< CSeq_align >& align2, vector…
86 bool CheckSeqIdInDD(const CRef< CSeq_align >& seqAlign);
92 int GetBlockCount (const CRef< CSeq_align >& seqAlign);
112 void AddIntervalToDD(TDendiag * pDD,CRef<CSeq_id> seqID1, CRef<CSeq_id> seqID2,TSeqPos st1,TSeqPos …
117 bool GetFirstOrLastDenDiag(const CRef< CSeq_align >& seqAlign, bool firstOrLast, CRef<CDense_diag>&…
124 bool EraseRow(CRef< CSeq_annot >& seqAnnot, int row);
132 CRef< CSeq_align > ExtractFirstSeqAlign(CRef< CSeq_align > seqAlign);
140 CRef<CSeq_align> Denseg2DenseDiagList(const CRef<CSeq_align>& denseSegSeqAlign);
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| H A D | cuCdCore.hpp | 116 bool GetBioseqForRow(int rowId, CRef< CBioseq >& bioseq);
126 bool GetBioseqForIndex(int seqIndex, CRef< CBioseq >& bioseq) ;
130 bool CopyBioseqForSeqId(const CRef< CSeq_id>& seqId, CRef< CBioseq >& bioseq) const;
133 bool GetBioseqWithSeqId(const CRef< CSeq_id>& seqid, const CBioseq*& bioseq) const;
141 bool GetSeqIDFromAlignment(int RowIndex, CRef<CSeq_id>& SeqID) const;
193 const CRef< CSeq_align >& GetSeqAlign(int Row) const; // get the Rowth Seq-align
205 bool AddSeqAlign(CRef< CSeq_align > seqAlign);
206 bool AddPendingSeqAlign(CRef< CSeq_align > seqAlign);
207 bool AddSequence(CRef< CSeq_entry > seqAntry);
251 bool AddCddDescr(CRef< CCdd_descr >& descr);
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/unit_test/ |
| H A D | unit_test_autodef.cpp | 158 static CRef<CSeq_entry> BuildSequence() in BuildSequence()
166 CRef<CSeq_id> id(new CSeq_id()); in BuildSequence()
177 static CRef<CSeqdesc> AddSource (CRef<CSeq_entry> entry, string taxname) in AddSource()
509 CRef<CSeq_entry> FindNucInSeqEntry(CRef<CSeq_entry> entry) in FindNucInSeqEntry()
511 CRef<CSeq_entry> empty(NULL); in FindNucInSeqEntry()
528 static void AddFeat (CRef<CSeq_feat> feat, CRef<CSeq_entry> entry) in AddFeat()
530 CRef<CSeq_annot> annot; in AddFeat()
576 CRef<CSeq_id> pid(new CSeq_id()); in MakeProteinForNucProtSet()
636 CRef<CSeq_id> id(new CSeq_id()); in BuildNucProtSet()
1268 CRef<CSeq_feat> s_AddCDS(CRef<CSeq_entry> np, const string& name, TSeqPos from, TSeqPos to) in s_AddCDS()
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| H A D | unit_test_feature_propagate.cpp | 161 tuple<CRef<CSeq_entry>, CRef<CSeq_align>, CRef<CSeq_entry>, CRef<CSeq_entry>, CRef<CSeq_entry> > C… in CreateBioseqsAndAlign()
260 CRef<CSeq_feat> CreateCds(CRef<CSeq_loc> main_loc, CRef<CSeq_entry> seq) in CreateCds()
268 void AddCodeBreak(CRef<CSeq_feat> cds, CRef<CSeq_loc> subloc) in AddCodeBreak()
275 CRef<CSeq_feat> CreateTrna(CRef<CSeq_loc> main_loc, CRef<CSeq_entry> seq) in CreateTrna()
283 void AddAnticodon(CRef<CSeq_feat> trna, CRef<CSeq_loc> subloc) in AddAnticodon()
305 CRef<CScope> scope; in TestCds()
351 CRef<CScope> scope; in TestCdsWithCodeBreak()
391 CRef<CScope> scope; in TestCdsFromLastBioseq()
435 CRef<CScope> scope; in TestCdsFromLastBioseqWithCodeBreak()
477 CRef<CScope> scope; in TestTrnaAnticodon()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/api/ |
| H A D | remote_blast.hpp | 119 CRemoteBlast(CRef<IQueryFactory> queries,
214 CRef<CSearchResultSet> GetResultSet();
430 CRef<objects::CBlast4_queries> GetQueries();
440 CRef<CBlastOptionsHandle> GetSearchOptions();
625 CRef<objects::CBlast4_reply>
630 CRef<objects::CBlast4_reply>
728 CRef<blast::CBlastOptionsHandle> m_CBOH;
773 CRef<objects::CBlast4_database> m_Dbs;
791 CRef<objects::CBlast4_queries> m_Queries;
794 CRef<objects::CBlast4_parameters> m_AlgoOpts;
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| H A D | deltablast.hpp | 75 CRef<CLocalDbAdapter> blastdb,
76 CRef<CLocalDbAdapter> domaindb,
92 CRef<CLocalDbAdapter> blastdb,
93 CRef<CLocalDbAdapter> domaindb,
115 CRef<CSearchResultSet> Run();
132 CRef<IQueryFactory> m_Queries;
135 CRef<CLocalDbAdapter> m_Subject;
138 CRef<CLocalDbAdapter> m_DomainDb;
144 CRef<CBlastRPSOptionsHandle> m_RpsOptions;
150 CRef<CSearchResultSet> m_DomainResults;
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| H A D | traceback_stage.hpp | 60 CBlastTracebackSearch(CRef<IQueryFactory> qf,
61 CRef<CBlastOptions> opts,
79 CRef<CSearchResultSet> Run();
96 void x_Init(CRef<IQueryFactory> qf,
97 CRef<CBlastOptions> opts,
100 CRef<TBlastHSPStream> hsps);
110 CRef<IQueryFactory> m_QueryFactory;
113 CRef<CBlastOptions> m_Options;
116 CRef<SInternalData> m_InternalData;
126 CRef<IBlastSeqInfoSrc> m_SeqInfoSrc;
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/api/ |
| H A D | remote_blast.hpp | 119 CRemoteBlast(CRef<IQueryFactory> queries,
214 CRef<CSearchResultSet> GetResultSet();
430 CRef<objects::CBlast4_queries> GetQueries();
440 CRef<CBlastOptionsHandle> GetSearchOptions();
625 CRef<objects::CBlast4_reply>
630 CRef<objects::CBlast4_reply>
728 CRef<blast::CBlastOptionsHandle> m_CBOH;
773 CRef<objects::CBlast4_database> m_Dbs;
791 CRef<objects::CBlast4_queries> m_Queries;
794 CRef<objects::CBlast4_parameters> m_AlgoOpts;
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| H A D | deltablast.hpp | 75 CRef<CLocalDbAdapter> blastdb,
76 CRef<CLocalDbAdapter> domaindb,
92 CRef<CLocalDbAdapter> blastdb,
93 CRef<CLocalDbAdapter> domaindb,
115 CRef<CSearchResultSet> Run();
132 CRef<IQueryFactory> m_Queries;
135 CRef<CLocalDbAdapter> m_Subject;
138 CRef<CLocalDbAdapter> m_DomainDb;
144 CRef<CBlastRPSOptionsHandle> m_RpsOptions;
150 CRef<CSearchResultSet> m_DomainResults;
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| H A D | traceback_stage.hpp | 60 CBlastTracebackSearch(CRef<IQueryFactory> qf,
61 CRef<CBlastOptions> opts,
79 CRef<CSearchResultSet> Run();
96 void x_Init(CRef<IQueryFactory> qf,
97 CRef<CBlastOptions> opts,
100 CRef<TBlastHSPStream> hsps);
110 CRef<IQueryFactory> m_QueryFactory;
113 CRef<CBlastOptions> m_Options;
116 CRef<SInternalData> m_InternalData;
126 CRef<IBlastSeqInfoSrc> m_SeqInfoSrc;
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/sra/readers/sra/ |
| H A D | csraread.hpp | 742 CRef<CSeq_annot>
750 CRef<CSeq_annot>
761 CRef<CSeq_entry>
769 CRef<CSeq_entry>
777 CRef<CSeq_annot>
785 CRef<CSeq_annot>
793 CRef<CSeq_annot>
801 CRef<CSeq_annot>
809 CRef<CSeq_annot>
817 CRef<CSeq_annot>
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/igblast/ |
| H A D | igblastn.hpp | 44 CRef<CSearchResultSet> m_results;
45 CRef<CBlastQueryVector> m_queries;
46 CRef<CScope> m_scope;
75 CRef<CIgBlastArgs> igargs, in CIgWorker()
76 CRef<CBlastOptionsHandle> opts_hndl, in CIgWorker()
77 CRef<CLocalDbAdapter> blastdb, in CIgWorker()
78 CRef<CBlastInput> user_input, in CIgWorker()
103 CRef<CIgBlastnAppArgs> thm_CmdLineArgs;
112 CRef<CLocalDbAdapter> thm_blastdb;
113 CRef<CBlastInput> thm_input;
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/readers/ |
| H A D | bed_reader.hpp | 95 CRef<CSeq_id> m_pId;
140 CRef< CSeq_annot >
239 CRef<CSeq_feat>&,
242 CRef<CSeq_feat>&,
245 CRef<CSeq_feat>&,
248 CRef<CSeq_feat>&,
251 CRef<CSeq_feat>&,
254 CRef<CSeq_feat>&,
257 CRef<CSeq_feat>&,
260 CRef<CSeq_feat>&,
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/readers/ |
| H A D | bed_reader.hpp | 95 CRef<CSeq_id> m_pId;
239 CRef<CSeq_feat>&,
242 CRef<CSeq_feat>&,
245 CRef<CSeq_feat>&,
248 CRef<CSeq_feat>&,
251 CRef<CSeq_feat>&,
254 CRef<CSeq_feat>&,
257 CRef<CSeq_feat>&,
260 CRef<CSeq_feat>&,
264 CRef<CSeq_feat>&,
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/blast/ |
| H A D | Blast4_parameters.cpp | 56 CRef< CBlast4_parameter> p; in Add()
60 CRef< CBlast4_value> v(new CBlast4_value); in Add()
75 CRef< CBlast4_parameter> p; in Add()
79 CRef< CBlast4_value> v(new CBlast4_value); in Add()
95 CRef< CBlast4_parameter> p; in Add()
99 CRef< CBlast4_value> v(new CBlast4_value); in Add()
113 CRef< CBlast4_parameter> p; in Add()
132 CRef< CBlast4_parameter> p; in Add()
150 CRef< CBlast4_parameter> p; in Add()
168 CRef< CBlast4_parameter> p; in Add()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/blast/ |
| H A D | Blast4_parameters.cpp | 56 CRef< CBlast4_parameter> p; in Add()
60 CRef< CBlast4_value> v(new CBlast4_value); in Add()
75 CRef< CBlast4_parameter> p; in Add()
79 CRef< CBlast4_value> v(new CBlast4_value); in Add()
95 CRef< CBlast4_parameter> p; in Add()
99 CRef< CBlast4_value> v(new CBlast4_value); in Add()
113 CRef< CBlast4_parameter> p; in Add()
132 CRef< CBlast4_parameter> p; in Add()
150 CRef< CBlast4_parameter> p; in Add()
168 CRef< CBlast4_parameter> p; in Add()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/app/blast/ |
| H A D | psiblast_app.cpp | 110 CRef<CPssmWithParameters>
118 CRef<CPsiBlastAppArgs> m_CmdLineArgs;
168 CRef<CPssmWithParameters>
183 static CRef<IQueryFactory>
184 s_MakeQueryFactory(CRef<CPssmWithParameters> pssm,CRef<CBlastQueryVector> query) in s_MakeQueryFactory()
186 CRef<IQueryFactory> retval; in s_MakeQueryFactory()
234 CRef<CPsiBlast> psiblast; in x_RunLocalPsiBlastIterations()
345 CRef<CRemoteBlast> rmt_psiblast = in DoIterations()
442 CRef<CLocalDbAdapter> db_adapter; in Run()
451 CRef<CBlastInput> input; in Run()
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