sequtils.hpp File Reference

#include <corelib/ncbistd.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objmgr/bioseq_handle.hpp>

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Functions
Uint4	GetSequenceType (const CBioseq_Handle &bsh)
	Return a (corrected) set of flags identifying the sequence type. More...

Function Documentation

GetSequenceType()

Uint4 GetSequenceType

(

const CBioseq_Handle &

bsh

)

Return a (corrected) set of flags identifying the sequence type.

This function is intended to produce a set of corrected sequence types indicating chromsome / not chromosome, genomic/mRNA/protein.

The returned flags are a subset of CSeq_id::EAccessionInfo types:

CSeq_id::fAcc_prot CSeq_id::fAcc_nuc CSeq_id::eAcc_mrna CSeq_id::fAcc_genomic CSeq_id::eAcc_unknown

Parameters

bsh	Bioseq-handle of the sequence to report on

Returns

Set of bitwise flags corresponding to sequence subtypes as noted above

Definition at line 42 of file sequtils.cpp.

References CSeq_id::eAcc_division_mask, CSeq_id::eAcc_est, CSeq_id::eAcc_gpipe_mrna, CSeq_id::eAcc_mrna, CSeq_id::eAcc_refseq_chromosome, CSeq_id::eAcc_refseq_contig, CSeq_id::eAcc_refseq_genome, CSeq_id::eAcc_refseq_genomic, CSeq_id::eAcc_refseq_mrna, CSeq_id::eAcc_refseq_mrna_predicted, CSeq_id::eAcc_refseq_wgs_intermed, CSeq_id::eAcc_unknown, CMolInfo_Base::eBiomol_cRNA, CMolInfo_Base::eBiomol_genomic, CMolInfo_Base::eBiomol_mRNA, CMolInfo_Base::eBiomol_ncRNA, CMolInfo_Base::eBiomol_pre_RNA, CMolInfo_Base::eBiomol_scRNA, CMolInfo_Base::eBiomol_snoRNA, CMolInfo_Base::eBiomol_snRNA, CMolInfo_Base::eBiomol_tmRNA, CMolInfo_Base::eBiomol_tRNA, eGetId_Best, CSeq_id::fAcc_genomic, CSeq_id::fAcc_nuc, CSeq_id::fAcc_prot, GetId(), GetMolInfo(), CSeq_id_Handle::GetSeqId(), CSeq_id::IdentifyAccession(), and info.

Referenced by CObjectCoords::GetCoordinates(), s_ExtendEntriesFromAlignments(), CTableColumnTypeGuesser::x_GuessType(), and CReportEntry::x_SetId().