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1 #ifndef OBJTOOLS_ALNMGR___ALN_BUILDERS__HPP 2 #define OBJTOOLS_ALNMGR___ALN_BUILDERS__HPP

void MergePairwiseAlns(CPairwiseAln &existing, const CPairwiseAln &addition, const CAlnUserOptions::TMergeFlags &flags)

Merge two pariwise alignments.

void SortAnchoredAlnVecByScore(TAnchoredAlnVec &anchored_aln_vec)

Sort anchored alignments by score.

void BuildAln(TAnchoredAlnVec &in_alns, CAnchoredAln &out_aln, const CAlnUserOptions &options, TAlnSeqIdIRef pseudo_seqid=TAlnSeqIdIRef())

Build anchored alignment from a set of alignmnets.

CIRef< IAlnSeqId > TAlnSeqIdIRef

Options for different alignment manager operations.

Query-anchored alignment can be 2 or multi-dimentional.

A pairwise aln is a collection of ranges for a pair of rows.

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_XALNMGR_EXPORT

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

vector< CRef< CAnchoredAln > > TAnchoredAlnVec

Collection of anchored alignments.

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