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NCBI C++ ToolKit: include/objtools/readers/agp_seq_entry.hpp Source File

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fSetSeqGap = (1 << 0),

fForceLocalId = (1 << 1)

x_FinishedBioseq(

);

x_SetSeqGap( objects::CSeq_gap & out_gap_info );

@ eAgpVersion_auto

auto-detect using the first gap line

Detects scaffolds, object boundaries, errors that involve 2 consecutive lines, and is intended as a s...

virtual int Finalize()

This is called at the end of the file, usually automatically but can be called manually if the automa...

virtual void OnGapOrComponent()

This class is used to turn an AGP file into a vector of Seq-entry's.

vector< CRef< objects::CSeq_entry > > m_entries

Holds the results.

vector< CRef< objects::CSeq_entry > > TSeqEntryRefVec

This is the way the results will be returned Each Seq-entry contains just one Bioseq,...

TSeqEntryRefVec & GetResult(void)

This gets the results found, but don't call before finalizing.

CAgpToSeqEntry(const CAgpToSeqEntry &)

CRef< objects::CBioseq > m_bioseq

This is the bioseq currently being built.

static const char * str(char *buf, int n)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_XOBJREAD_EXPORT

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