NCBI C++ ToolKit
Functions
aln_builders.hpp File Reference
#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>
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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_alnsInput Alignments (will be sorted by score unless fSkipSortByScore is raised).
out_alnOuput anchored alignment.
optionsOptions for merging input alignments.
pseudo_seqidUser-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(), s_TranslateToAlnCoords(), CAnchoredAln::SetAnchorRow(), CAnchoredAln::SetPairwiseAlns(), SortAnchoredAlnVecByScore(), and x_AdjustAnchorDirection().

Referenced by BOOST_AUTO_TEST_CASE(), CBuildSparseAlnJob::Build(), BuildAlignDataSource(), CAlnSpanVertModel::CAlnSpanVertModel(), CAlnBuildApp::Run(), CAlnTestApp::Run(), CAlignCleanup::x_Cleanup_AnchoredAln(), CMergeAlignmentsJob::x_CreateProjectItems(), CTreeBuilderJob::x_CreateProjectItems(), and CValidError_align::x_ValidateAlignPercentIdentity().

◆ MergePairwiseAlns()

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

◆ SortAnchoredAlnVecByScore()

void SortAnchoredAlnVecByScore ( TAnchoredAlnVec anchored_aln_vec)

Sort anchored alignments by score.

See also
PScoreGreater

Definition at line 332 of file aln_builders.cpp.

References ct::sort().

Referenced by BuildAln().

Modified on Sun Feb 25 03:04:37 2024 by modify_doxy.py rev. 669887