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NCBI C++ ToolKit: include/objtools/alnmgr/aln_builders.hpp File Reference

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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().

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().

Merge two pariwise alignments.

Parameters

existing Source and destination pairwise alignment. addition Alignment to be added to to first one. flags Merge options.

Definition at line 49 of file aln_builders.cpp.

References CAlignRangeCollectionList< TAlnRange >::AddInsertions(), CAlignRangeCollectionList< TAlnRange >::fAllowAbutting, CAlignRangeCollectionList< TAlnRange >::fAllowMixedDir, CAlignRangeCollectionList< TAlnRange >::fAllowOverlap, CAlnUserOptions::fIgnoreInsertions, flags, CPairwiseAln::GetFirstId(), CAlignRangeCollectionList< TAlnRange >::GetInsertions(), CAlignRangeCollectionList< TAlnRange >::GetPolicyFlags(), CPairwiseAln::GetSecondId(), CAlignRangeCollectionList< TAlnRange >::insert(), ITERATE, and SubtractAlnRngCollections().

Referenced by BuildAln().

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