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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/genomic__compart_8cpp.html below:

NCBI C++ ToolKit: src/algo/align/util/genomic_compart.cpp File Reference

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bool  IsIntersectingQuery (const pair< TSeqRange, TSeqRange > &r1, const pair< TSeqRange, TSeqRange > &r2)   bool  IsIntersectingSubject (const pair< TSeqRange, TSeqRange > &r1, const pair< TSeqRange, TSeqRange > &r2)   bool  IsConsistent (const pair< TSeqRange, TSeqRange > &r1, const pair< TSeqRange, TSeqRange > &r2, ENa_strand s1, ENa_strand s2)   TSeqPos  Difference (const pair< TSeqRange, TSeqRange > &r1, const pair< TSeqRange, TSeqRange > &r2, ENa_strand s1, ENa_strand s2)   void  FindCompartments (const list< CRef< CSeq_align > > &aligns, list< CRef< CSeq_align_set > > &align_sets, TCompartOptions options, float diff_len_filter)   void  JoinCompartment (const CRef< CSeq_align_set > &compartment, float gap_ratio, list< CRef< CSeq_align > > &aligns)   ◆ TAlignRange ◆ TAlignRangeMultiSet ◆ TRange ◆ Difference() ◆ FindCompartments()

Definition at line 385 of file genomic_compart.cpp.

References set< Key, Compare >::begin(), count, Difference(), eNa_strand_minus, eNa_strand_plus, set< Key, Compare >::end(), fCompart_AllowInconsistentIntersection, fCompart_AllowIntersectionsBoth, fCompart_AllowIntersectionsQuery, fCompart_AllowIntersectionsSubject, fCompart_FilterByDiffLen, fCompart_SortByPctIdent, fCompart_SortByScore, CSeq_id_Handle::GetHandle(), hex(), i, set< Key, Compare >::insert(), int, IsConsistent(), IsIntersectingQuery(), IsIntersectingSubject(), ITERATE, kMax_Int, max(), min(), NON_CONST_ITERATE, r(), SCompartScore::Reset(), CRef< C, Locker >::Reset(), REVERSE_ITERATE, CSeq_align_set_Base::Set(), ct::sort(), swap(), SCompartScore::total_range, and SCompartScore::total_size.

Referenced by BOOST_AUTO_TEST_CASE(), CAdvancedAlignCleanup::GetGenomicCompartments(), CTestCompartApplication::Run(), CBLASTSeqToolJob::x_CreateProjectItems(), and CMergeAligner::x_MergeAlignments().

◆ IsConsistent() ◆ IsIntersectingQuery() ◆ IsIntersectingSubject() ◆ JoinCompartment()

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