#include <corelib/ncbistd.hpp>#include <serial/serial.hpp>#include <serial/objistr.hpp>#include <serial/objostr.hpp>#include <objects/seqfeat/SeqFeatData.hpp>#include <objects/seqfeat/Cdregion.hpp>#include <objects/seqloc/Na_strand.hpp>#include <objects/seqloc/Seq_interval.hpp>#include <objects/seqloc/Seq_loc.hpp>#include <util/strsearch.hpp>#include <objects/seq/seq_id_mapper.hpp>#include <util/range_coll.hpp>#include <objmgr/feat_ci.hpp>#include <objmgr/bioseq_ci.hpp>#include <objmgr/scope.hpp>#include <objmgr/util/seq_loc_util.hpp>#include <objmgr/util/create_defline.hpp>
Include dependency graph for sequence.hpp:
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Classes | |
| class | CGetOverlappingFeaturesPlugin |
| class | CSeqIdFromHandleException |
| class | CFastaOstream |
| FASTA-format output; see also ReadFasta in <objtools/readers/fasta.hpp> More... | |
| struct | CFastaOstream::SGapModText |
| This indicates the text of the modifiers of a gap. More... | |
| class | CCdregion_translate |
| Public interface for coding region translation function Uses CTrans_table in <objects/seqfeat/Genetic_code_table.hpp> for rapid translation from a given genetic code, allowing all of the iupac nucleotide ambiguity characters. More... | |
| class | CSeqTranslator |
| struct | SRelLoc |
| Location relative to a base Seq-loc: one (usually) or more ranges of offsets. More... | |
| class | CSeqSearch |
| ============================================================================// Sequence Search // ============================================================================// More... | |
| class | CSeqSearch::CPatternInfo |
| Holds information associated with a pattern, such as the name of the restriction enzyme, location of cut site etc. More... | |
| class | CSeqSearch::IClient |
| Client interface: ================== A class that uses the SeqSearch facility should implement the Client interface and register itself with the search utility to be notified of matches detection. More... | |
| class | CSequenceAmbigTrimmer |
| This trims ambiguous bases from the start and/or end of sequences, using customizable rules. More... | |
| struct | CSequenceAmbigTrimmer::STrimRule |
| For example, if bases_to_check is 10 and max_bases_allowed_to_be_ambig is 5, then on each iteration we check the 10 terminal bases and trim off those 10 if there are more than 5 ambiguous bases there. More... | |
| struct | CSequenceAmbigTrimmer::SAmbigCount |
| This holds the output of x_CountAmbigInRange. More... | |
| class | CBioseqGaps_CI |
| This iterates over the runs of Ns of each sequence. More... | |
| struct | CBioseqGaps_CI::Params |
| The params that control the behavior of CBioseqGaps_CI. More... | |
| struct | CBioseqGaps_CI::SCurrentGapInfo |
| This indicates the state of the iterator right now. More... | |
Functions | |
FindLatestSequence | |
Walk the replace history to find the latest revision of a sequence | |
| 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) |
Sequences | |
Searching for bioseqs etc. | |
| const CBioseq * | GetNucleotideParent (const CBioseq &product, CScope *scope) |
| Get the encoding nucleotide sequnce of a protein. More... | |
| CBioseq_Handle | GetNucleotideParent (const CBioseq_Handle &product) |
| CBioseq_Handle | GetParentForPart (const CBioseq_Handle &part) |
| Get the parent bioseq for a part of a segmented bioseq. More... | |
| const COrg_ref & | GetOrg_ref (const CBioseq_Handle &handle) |
| Return the org-ref associated with a given sequence. 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... | |
| 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) |
| const CBioSource * | GetBioSource (const CBioseq &bioseq) |
| Retrieve the BioSource object for a given bioseq handle. More... | |
| const CBioSource * | GetBioSource (const CBioseq_Handle &handle) |
| CBioseq_Handle | GetBioseqFromSeqLoc (const CSeq_loc &loc, CScope &scope, CScope::EGetBioseqFlag flag=CScope::eGetBioseq_Loaded) |
| Retrieve the Bioseq Handle from a location. More... | |
| string | GetProteinName (const CBioseq_Handle &seq) |
| Return protein name from corresponding Prot-ref feature. More... | |
| CConstRef< CSeq_feat > | GetSourceFeatForProduct (const CBioseq_Handle &bsh) |
| TTaxId | GetTaxIdForProduct (const CBioseq_Handle &bsh) |
| void | GetOrg_refForProduct (const CBioseq_Handle &bsh, const COrg_ref *) |
| 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... | |
| void | ReverseComplement (CSeq_inst &seq, CScope *scope) |
| Reverse complement a Bioseq in place. More... | |
SeqIdConv | |
| enum | EAccessionVersion { eWithAccessionVersion , eWithoutAccessionVersion } |
| enum | EGetIdFlags { eGetId_ForceGi = 0x0000 , eGetId_ForceAcc = 0x0001 , eGetId_Best = 0x0002 , eGetId_HandleDefault = 0x0003 , eGetId_Seq_id_Score = 0x0004 , eGetId_Seq_id_BestRank = 0x0005 , eGetId_Seq_id_WorstRank = 0x0006 , eGetId_Seq_id_FastaAARank = 0x0007 , eGetId_Seq_id_FastaNARank = 0x0008 , eGetId_Canonical = eGetId_Seq_id_BestRank , eGetId_TypeMask = 0x00FF , eGetId_VerifyId = 0x0100 , eGetId_ThrowOnError = 0x0200 , eGetId_Default = eGetId_Best | eGetId_ThrowOnError } |
| Retrieve a particular seq-id from a given bioseq handle. More... | |
| typedef int | EGetIdType |
| TGi | GetGiForAccession (const string &acc, CScope &scope, EGetIdType flags=0) |
| Given an accession string retrieve the GI id. More... | |
| string | GetAccessionForGi (TGi gi, CScope &scope, EAccessionVersion use_version=eWithAccessionVersion, EGetIdType flags=0) |
| Retrieve the accession for a given GI. More... | |
| TGi | GetGiForId (const objects::CSeq_id &id, CScope &scope, EGetIdType flags=0) |
| Given a Seq-id retrieve the corresponding GI. More... | |
| string | GetAccessionForId (const objects::CSeq_id &id, CScope &scope, EAccessionVersion use_version=eWithAccessionVersion, EGetIdType flags=0) |
| Retrieve the accession string for a Seq-id. More... | |
| CSeq_id_Handle | GetId (const CBioseq_Handle &handle, EGetIdType type=eGetId_Default) |
| Return a selected ID type for a given bioseq handle. More... | |
| CSeq_id_Handle | GetId (const CSeq_id &id, CScope &scope, EGetIdType type=eGetId_Default) |
| Return a selected ID type for a seq-id. More... | |
| CSeq_id_Handle | GetId (const CSeq_id_Handle &id, CScope &scope, EGetIdType type=eGetId_Default) |
| Return a selected ID type for a seq-id handle. More... | |
| CSeq_id_Handle | GetId (const CBioseq::TId &id, EGetIdType type=eGetId_Default) |
| 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 CBioseq &seq, EGetIdType type=eGetId_Default) |
| Return a selected ID type from a Bioseq Arguments (except 'seq') and behavior is the same as of GetId(const CBioseq_Handle& seq, ...). More... | |
GetTitle | |
Get sequence's title (used in various flat-file formats.) Deprecated in favor of CDeflineGenerator. | |
| enum | EGetTitleFlags { fGetTitle_Reconstruct = 0x1 , fGetTitle_Organism = 0x2 , fGetTitle_AllProteins = 0x4 , fGetTitle_NoExpensive = 0x8 } |
| This function is here rather than in CBioseq because it may need to inspect other sequences. More... | |
| typedef int | TGetTitleFlags |
| NCBI_XOBJUTIL_EXPORT string | GetTitle (const CBioseq_Handle &hnd, TGetTitleFlags flags=0) |
| NCBI_XOBJUTIL_EXPORT bool | GetTitle (const CBioseq &seq, string *title_ptr, TGetTitleFlags flags=0) |
Source and Product | |
| enum | ES2PFlags { fS2P_NoMerge = 0x1 , fS2P_AllowTer = 0x2 } |
| enum | EP2SFlags { fP2S_Extend = 0x1 } |
| typedef int | TS2PFlags |
| typedef int | TP2SFlags |
| CRef< CSeq_loc > | SourceToProduct (const CSeq_feat &feat, const CSeq_loc &source_loc, TS2PFlags flags=0, CScope *scope=0, int *frame=0) |
| CRef< CSeq_loc > | ProductToSource (const CSeq_feat &feat, const CSeq_loc &prod_loc, TP2SFlags flags=0, CScope *scope=0) |
