#include <corelib/ncbistd.hpp>#include <objects/seqalign/Seq_align.hpp>#include <objects/seqalign/Seq_align_set.hpp>
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Typedefs | |
| typedef int | TCompartOptions |
Enumerations | |
| enum | ECompartOptions { fCompart_SortByScore = 0x02 , fCompart_SortByPctIdent = 0x04 , fCompart_FilterByDiffLen = 0x08 , fCompart_AllowIntersectionsQuery = 0x10 , fCompart_AllowIntersectionsSubject = 0x20 , fCompart_AllowIntersectionsBoth = 0x40 , fCompart_AllowInconsistentIntersection = 0x80 , fCompart_AllowIntersections , fCompart_Defaults = 0 } |
Functions | |
| void | FindCompartments (const list< CRef< CSeq_align > > &aligns, list< CRef< CSeq_align_set > > &align_sets, TCompartOptions options=fCompart_Defaults, float diff_len_filter=3.0f) |
| void | JoinCompartment (const CRef< CSeq_align_set > &compartment, float gap_ratio, list< CRef< CSeq_align > > &aligns) |
Typedef Documentation
◆ TCompartOptions
| typedef int TCompartOptions |
Definition at line 57 of file genomic_compart.hpp.
Enumeration Type Documentation
◆ ECompartOptions
| enum ECompartOptions |
Definition at line 43 of file genomic_compart.hpp.
Function Documentation
◆ FindCompartments()
| void FindCompartments | ( | const list< CRef< CSeq_align > > & | aligns, |
| list< CRef< CSeq_align_set > > & | align_sets, | ||
| TCompartOptions | options = fCompart_Defaults, |
||
| float | diff_len_filter = 3.0f |
||
| ) |
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().
◆ JoinCompartment()
| void JoinCompartment | ( | const CRef< CSeq_align_set > & | compartment, |
| float | gap_ratio, | ||
| list< CRef< CSeq_align > > & | aligns | ||
| ) |
Definition at line 876 of file genomic_compart.cpp.
References CSeq_align_Base::eType_disc, CSeq_align_set_Base::Get(), ITERATE, len, CRef< C, Locker >::Reset(), CSeq_align_set_Base::Set(), CSeq_align_Base::SetSegs(), and CSeq_align_Base::SetType().
