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NCBI C++ ToolKit: src/objtools/readers/fasta_aln_builder.hpp Source File

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Helper class to build pairwise alignments, with double gaps automatically spliced out.

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

void x_EnsurePos(TSignedSeqPos &pos, TSignedSeqPos last_pos, TSeqPos alignment_pos)

EConstants

special position values

TSignedSeqPos m_LastReferencePos

void AddData(TSeqPos alignment_pos, TSignedSeqPos reference_pos, TSignedSeqPos other_pos)

TSeqPos m_LastAlignmentPos

CRef< CSeq_align > GetCompletedAlignment(void)

EState x_State(TSignedSeqPos reference_pos, TSignedSeqPos other_pos)

CFastaAlignmentBuilder(CRef< CSeq_id > reference_id, CRef< CSeq_id > other_id)

TSignedSeqPos m_LastOtherPos

#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.

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

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