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NCBI C++ ToolKit: include/objtools/edit/cds_fix.hpp Source File

s_SetCDSFrame(

& cds, ECdsFrame frame_type,

& scope);

ECdsFrame s_GetFrameFromName(

& name);

User-defined methods of the data storage class.

bool AddTerminalCodeBreak(CSeq_feat &cds, CScope &scope)

bool ExtendCDSToStopCodon(CSeq_feat &cds, CScope &scope)

ExtendCDSToStopCodon A function to extend a CDS location to the first in-frame stop codon in the prot...

CRef< CSeq_loc > GetLastCodonLoc(const CSeq_feat &cds, CScope &scope)

void ExtendStop(CSeq_loc &loc, TSeqPos len, CScope &scope)

bool AdjustProteinFeaturePartialsToMatchCDS(CSeq_feat &new_prot, const CSeq_feat &cds)

AdjustProteinFeaturePartialsToMatchCDS A function to change an existing MolInfo to match a coding reg...

bool SetTranslExcept(objects::CSeq_feat &cds, const string &comment, bool strict, bool extend, objects::CScope &scope)

CRef< CSeq_feat > MakemRNAforCDS(const CSeq_feat &cds, CScope &scope)

MakemRNAforCDS A function to create a CSeq_feat that represents the appropriate mRNA for a given CDS.

void AdjustCDSFrameForStartChange(CCdregion &cds, int change)

bool TruncateCDSAtStop(CSeq_feat &cds, CScope &scope)

TruncateCDSAtStop A function to truncate a CDS location after the first stop codon in the protein tra...

CRef< objects::CSeq_id > GetNewProtId(objects::CBioseq_Handle bsh, int &offset, string &id_label, bool general_only)

bool DoesCodingRegionHaveTerminalCodeBreak(const objects::CCdregion &cdr)

CRef< objects::CSeq_id > GetNewLocalProtId(const string &id_base, CScope &scope, int &offset)

vector< CRef< objects::CSeq_id > > GetNewProtIdFromExistingProt(objects::CBioseq_Handle bsh, int &offset, string &id_label)

bool IsGeneralIdProtPresent(objects::CSeq_entry_Handle tse)

CRef< CGenetic_code > GetGeneticCodeForBioseq(CBioseq_Handle bh)

GetGeneticCodeForBioseq A function to construct the appropriate CGenetic_code object to use when cons...

bool DemoteCDSToNucSeq(objects::CSeq_feat_Handle &orig_feat)

string GetIdHashOrValue(const string &base, int offset)

namespace ncbi::objects::

Include a standard set of the NCBI C++ Toolkit most basic headers.

unsigned int TSeqPos

Type for sequence locations and lengths.

NCBI_XOBJEDIT_EXPORT bool AdjustForCDSPartials(const CSeq_feat &cds, CSeq_entry_Handle seh)

AdjustForCDSPartials A function to make all of the necessary related changes to a Seq-entry after the...

NCBI_XOBJEDIT_EXPORT bool AdjustProteinMolInfoToMatchCDS(CMolInfo &molinfo, const CSeq_feat &cds)

AdjustProteinMolInfoToMatchCDS A function to change an existing MolInfo to match a coding region.

NCBI_XOBJEDIT_EXPORT 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.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_XOBJEDIT_EXPORT

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