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NCBI C++ ToolKit: src/objmgr/util/sequence.cpp File Reference

const CBioSource * GetBioSource (const CBioseq &bioseq) Retrieve the BioSource object for a given bioseq handle. More...
const CBioSource * GetBioSource (const CBioseq_Handle &handle) CConstRef< CSeq_feat > GetSourceFeatForProduct (const CBioseq_Handle &bsh) TTaxId GetTaxIdForProduct (const CBioseq_Handle &bsh) void GetOrg_refForProduct (const CBioseq_Handle &bsh, const COrg_ref *pOrgRef) const COrg_ref * GetOrg_refForBioseq (const CBioseq_Handle &bsh) Find an Org-ref for the given Bioseq: If it's a protein then look on the source feature of the product. More...
const CBioSource * GetBioSourceForBioseq (const CBioseq_Handle &bsh) Find a BioSource for the given Bioseq: If it's a protein then look for the source feature of the product. More...
const COrg_ref * GetOrg_refOrNull (const CBioseq_Handle &handle) Return the pointer to org-ref associated with a given sequence or null if there is no org-ref associated with the sequence. More...
const COrg_ref & GetOrg_ref (const CBioseq_Handle &handle) Return the org-ref associated with a given sequence. More...
TTaxId GetTaxId (const CBioseq_Handle &handle) return the tax-id associated with a given sequence. More...
const CMolInfo * GetMolInfo (const CBioseq &bioseq) Retrieve the MolInfo object for a given bioseq handle. More...
const CMolInfo * GetMolInfo (const CBioseq_Handle &handle) CBioseq_Handle GetBioseqFromSeqLoc (const CSeq_loc &loc, CScope &scope, CScope::EGetBioseqFlag flag) Retrieve the Bioseq Handle from a location. More...
string GetProteinName (const CBioseq_Handle &seq) Return protein name from corresponding Prot-ref feature. More...
int Score_SeqIdHandle (const CSeq_id_Handle &idh) int BestRank_SeqIdHandle (const CSeq_id_Handle &idh) int WorstRank_SeqIdHandle (const CSeq_id_Handle &idh) int FastaAARank_SeqIdHandle (const CSeq_id_Handle &idh) int FastaNARank_SeqIdHandle (const CSeq_id_Handle &idh) CSeq_id_Handle x_GetId (const CScope::TIds &ids, EGetIdType type) CSeq_id_Handle GetId (const CBioseq &seq, EGetIdType type) Return a selected ID type from a Bioseq Arguments (except 'seq') and behavior is the same as of GetId(const CBioseq_Handle& seq, ...). More...
CSeq_id_Handle GetId (const CBioseq::TId &ids_in, EGetIdType type) Return a selected ID type from a set of Seq-ids Arguments (except 'id') and behavior is the same as of GetId(const CSeq_id& id, ...). More...
CSeq_id_Handle GetId (const CSeq_id &id, CScope &scope, EGetIdType type) Return a selected ID type for a seq-id. More...
CSeq_id_Handle GetId (const CSeq_id_Handle &idh, CScope &scope, EGetIdType type) Return a selected ID type for a seq-id handle. More...
CSeq_id_Handle GetId (const CBioseq_Handle &handle, EGetIdType type) Return a selected ID type for a given bioseq handle. More...
TGi GetGiForAccession (const string &acc, CScope &scope, EGetIdType flags) Given an accession string retrieve the GI id. More...
TGi GetGiForId (const objects::CSeq_id &id, CScope &scope, EGetIdType flags) Given a Seq-id retrieve the corresponding GI. More...
string GetAccessionForGi (TGi gi, CScope &scope, EAccessionVersion use_version, EGetIdType flags) Retrieve the accession for a given GI. More...
string GetAccessionForId (const objects::CSeq_id &id, CScope &scope, EAccessionVersion use_version, EGetIdType flags) Retrieve the accession string for a Seq-id. More...
CSeq_id_Handle x_FindLatestSequence (const CSeq_id_Handle &idh, CScope &scope, const CTime *tlim) CConstRef< CSeq_id > FindLatestSequence (const CSeq_id &id, CScope &scope) Given a seq-id check its replace history and try to find the latest revision. More...
CSeq_id_Handle FindLatestSequence (const CSeq_id_Handle &idh, CScope &scope) CConstRef< CSeq_id > FindLatestSequence (const CSeq_id &id, CScope &scope, const CTime &tlim) Check replace history up to the specified date. More...
CSeq_id_Handle FindLatestSequence (const CSeq_id_Handle &idh, CScope &scope, const CTime &tlim) CRef< CSeq_loc > SourceToProduct (const CSeq_feat &feat, const CSeq_loc &source_loc, TS2PFlags flags, CScope *scope, int *frame) CRef< CSeq_loc > ProductToSource (const CSeq_feat &feat, const CSeq_loc &prod_loc, TP2SFlags flags, CScope *scope) void GetOverlappingFeatures (const CSeq_loc &loc, CSeqFeatData::E_Choice feat_type, CSeqFeatData::ESubtype feat_subtype, EOverlapType overlap_type, TFeatScores &feats, CScope &scope, const TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin) Find all features overlapping the location. More...
CConstRef< CSeq_feat > GetBestOverlappingFeat (const CSeq_loc &loc, CSeqFeatData::E_Choice feat_type, EOverlapType overlap_type, CScope &scope, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin) See the note above on 'overlap_type' meaning. More...
CConstRef< CSeq_feat > GetBestOverlappingFeat (const CSeq_loc &loc, CSeqFeatData::ESubtype feat_type, EOverlapType overlap_type, CScope &scope, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin) See the note above on 'overlap_type' meaning. More...
CConstRef< CSeq_feat > GetmRNAforCDS (const CSeq_feat &cds, CScope &scope) GetmRNAforCDS A function to find a CSeq_feat representing the appropriate mRNA for a given CDS. More...
static CConstRef< CSeq_feat > x_GetBestOverlapForSNP (const CSeq_feat &snp_feat, CSeqFeatData::E_Choice type, CSeqFeatData::ESubtype subtype, CScope &scope, bool search_both_strands=true) CConstRef< CSeq_feat > GetBestOverlapForSNP (const CSeq_feat &snp_feat, CSeqFeatData::E_Choice type, CScope &scope, bool search_both_strands) Get the best overlapping feature for a SNP (variation) feature. More...
CConstRef< CSeq_feat > GetBestOverlapForSNP (const CSeq_feat &snp_feat, CSeqFeatData::ESubtype subtype, CScope &scope, bool search_both_strands) Get the best overlapping feature for a SNP (variation) More...
CConstRef< CSeq_feat > GetOverlappingGene (const CSeq_loc &loc, CScope &scope, ETransSplicing eTransSplicing) bool IsTransSpliced (const CSeq_feat &feat) bool IsPseudo (const CSeq_feat &feat, CScope &scope) Determines whether given feature is pseudo, using gene associated with feature if necessary Checks to see if a feature is pseudo. More...
CConstRef< CSeq_feat > GetLocalGeneByLocus (const string &locus, bool use_tag, CBioseq_Handle bsh) CConstRef< CSeq_feat > GetLocalGeneByXref (const CGene_ref &gene, CBioseq_Handle bsh) CConstRef< CSeq_feat > GetGeneForFeature (const CSeq_feat &feat, CScope &scope) Finds gene for feature, but obeys SeqFeatXref directives. More...
CConstRef< CSeq_feat > GetOverlappingmRNA (const CSeq_loc &loc, CScope &scope) CConstRef< CSeq_feat > GetOverlappingCDS (const CSeq_loc &loc, CScope &scope) CConstRef< CSeq_feat > GetOverlappingPub (const CSeq_loc &loc, CScope &scope) CConstRef< CSeq_feat > GetOverlappingSource (const CSeq_loc &loc, CScope &scope) CConstRef< CSeq_feat > GetOverlappingOperon (const CSeq_loc &loc, CScope &scope) CConstRef< CSeq_feat > GetBestMrnaForCds (const CSeq_feat &cds_feat, CScope &scope, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin) CConstRef< CSeq_feat > GetBestCdsForMrna (const CSeq_feat &mrna_feat, CScope &scope, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin) CConstRef< CSeq_feat > GetBestGeneForMrna (const CSeq_feat &mrna_feat, CScope &scope, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin) CConstRef< CSeq_feat > GetBestGeneForCds (const CSeq_feat &cds_feat, CScope &scope, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin) void GetMrnasForGene (const CSeq_feat &gene_feat, CScope &scope, list< CConstRef< CSeq_feat > > &mrna_feats, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin) void GetCdssForGene (const CSeq_feat &gene_feat, CScope &scope, list< CConstRef< CSeq_feat > > &cds_feats, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin) CConstRef< CSeq_feat > GetBestOverlappingFeat (const CSeq_feat &feat, CSeqFeatData::E_Choice feat_type, sequence::EOverlapType overlap_type, CScope &scope, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin) CConstRef< CSeq_feat > GetBestOverlappingFeat (const CSeq_feat &feat, CSeqFeatData::ESubtype subtype, sequence::EOverlapType overlap_type, CScope &scope, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin) CConstRef< CSeq_feat > GetBestGeneForMrna (const CSeq_feat &mrna_feat, const CTSE_Handle &tse, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin) CConstRef< CSeq_feat > GetBestGeneForCds (const CSeq_feat &cds_feat, const CTSE_Handle &tse, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin) CConstRef< CSeq_feat > GetBestMrnaForCds (const CSeq_feat &cds_feat, const CTSE_Handle &tse, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin) CConstRef< CSeq_feat > GetBestCdsForMrna (const CSeq_feat &mrna_feat, const CTSE_Handle &tse, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin) void GetMrnasForGene (const CSeq_feat &gene_feat, const CTSE_Handle &tse, list< CConstRef< CSeq_feat > > &mrna_feats, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin) void GetCdssForGene (const CSeq_feat &gene_feat, const CTSE_Handle &tse, list< CConstRef< CSeq_feat > > &cds_feats, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin) const CSeq_feat * GetCDSForProduct (const CBioseq &product, CScope *scope) Get the encoding CDS feature of a given protein sequence. More...
const CSeq_feat * GetCDSForProduct (const CBioseq_Handle &bsh) CMappedFeat GetMappedCDSForProduct (const CBioseq_Handle &bsh) const CSeq_feat * GetPROTForProduct (const CBioseq &product, CScope *scope) Get the mature peptide feature of a protein. More...
const CSeq_feat * GetPROTForProduct (const CBioseq_Handle &bsh) const CSeq_feat * GetmRNAForProduct (const CBioseq &product, CScope *scope) Get the encoding mRNA feature of a given mRNA (cDNA) bioseq. More...
const CSeq_feat * GetmRNAForProduct (const CBioseq_Handle &bsh) CMappedFeat GetMappedmRNAForProduct (const CBioseq_Handle &bsh) const CBioseq * GetNucleotideParent (const CBioseq &product, CScope *scope) Get the encoding nucleotide sequnce of a protein. More...
CBioseq_Handle GetNucleotideParent (const CBioseq_Handle &bsh) CBioseq_Handle GetParentForPart (const CBioseq_Handle &part) Get the parent bioseq for a part of a segmented bioseq. More...
static string s_FastaGetOriginalID (const CBioseq &seq) static bool s_ShouldUseOriginalID (const CBioseq &seq) static bool s_WriteGnlAndAcc (const CBioseq &bioseq, CNcbiOstream &ostr) template<class Container > void x_Translate (const Container &seq, string &prot, unsigned int frame, const CGenetic_code *code, bool is_5prime_complete, bool is_3prime_complete, bool include_stop, bool remove_trailing_X, bool *alt_start) static void AddAAToDeltaSeq (CRef< CBioseq > prot, char residue) static void AddGapToDeltaSeq (CRef< CBioseq >prot, bool unknown_length, TSeqPos add_len) DEFINE_STATIC_ARRAY_MAP (TComplement, sc_Complement, sc_comp_tbl) static char s_GetComplement (char c) static string s_GetReverseComplement (const string &sequence) void ReverseComplement (CSeq_inst &inst, CScope *scope) Reverse complement a Bioseq in place. More...

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