#include <corelib/ncbistd.hpp>
#include <corelib/ncbiobj.hpp>
#include <objtools/alnmgr/pairwise_aln.hpp>
#include <objtools/alnmgr/aln_stats.hpp>
#include <objtools/alnmgr/aln_user_options.hpp>

Include dependency graph for aln_builders.hpp:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Go to the SVN repository for this file.

Functions
void	MergePairwiseAlns (CPairwiseAln &existing, const CPairwiseAln &addition, const CAlnUserOptions::TMergeFlags &flags)
	Merge two pariwise alignments. More...

void	SortAnchoredAlnVecByScore (TAnchoredAlnVec &anchored_aln_vec)
	Sort anchored alignments by score. More...

void	BuildAln (TAnchoredAlnVec &in_alns, CAnchoredAln &out_aln, const CAlnUserOptions &options, TAlnSeqIdIRef pseudo_seqid=TAlnSeqIdIRef())
	Build anchored alignment from a set of alignmnets. More...

Function Documentation

◆ BuildAln()

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

Build anchored alignment from a set of alignmnets.

The input alignments are merged (according to the options), a new pseudo-sequence is used to provide alignment coordinates.

Parameters

in_alns	Input Alignments (will be sorted by score unless fSkipSortByScore is raised).
out_aln	Ouput anchored alignment.
options	Options for merging input alignments.
pseudo_seqid	User-created seq-id of the pseudo alignment sequence. If null, a new local, time-stamped seq-id will be automatically generated.

Definition at line 549 of file aln_builders.cpp.

References _ASSERT, BuildAln(), CTime::eCurrent, CAlnUserOptions::eMergeAllSeqs, CRef< C, Locker >::Empty(), CAlnUserOptions::ePreserveRows, CAlnUserOptions::eQuerySeqMergeOnly, CAlnUserOptions::fAllowMixedStrand, CAlnUserOptions::fAnchorRowFirst, flags, CAlnUserOptions::fSkipSortByScore, CAlnUserOptions::fTruncateOverlaps, CAlnUserOptions::fUseAnchorAsAlnSeq, AutoPtr< X, Del >::get(), CAnchoredAln::GetAnchorRow(), CAnchoredAln::GetDim(), CAnchoredAln::GetId(), CAnchoredAln::GetPairwiseAlns(), ITERATE, CAlnUserOptions::m_MergeAlgo, CAlnUserOptions::m_MergeFlags, MergePairwiseAlns(), NCBI_THROW, NON_CONST_ITERATE, CRef< C, Locker >::Reset(), row, s_TranslateToAlnCoords(), CAnchoredAln::SetAnchorRow(), CAnchoredAln::SetPairwiseAlns(), SortAnchoredAlnVecByScore(), and x_AdjustAnchorDirection().