#include <corelib/ncbi_limits.hpp>#include <algo/align/nw/align_exception.hpp>#include <algo/align/util/hit_filter.hpp>#include <objects/seqalign/Seq_align_set.hpp>#include <objects/seqalign/Seq_align.hpp>#include <objects/seqalign/Std_seg.hpp>#include <objects/seqalign/Dense_seg.hpp>#include <objects/seqloc/Seq_loc.hpp>#include <objects/seqloc/Na_strand.hpp>#include <objects/seq/Seq_literal.hpp>#include <objmgr/seq_map.hpp>#include <objmgr/scope.hpp>#include <objmgr/seq_map_ci.hpp>#include <algorithm>#include <numeric>#include <vector>
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Classes | |
| class | CGapInfo< THit > |
| class | CPrecalcGapInfo< THit > |
| class | CCompartmentFinder< THit > |
| class | CCompartmentFinder< THit >::CCompartment |
| Individual compartment representation. More... | |
| struct | CCompartmentFinder< THit >::SHitStatus |
| class | CCompartmentAccessor< THit > |
| class | CQueryMatchAccumulator< THit > |
Macros | |
| #define | ALGO_ALIGN_COMPARTMENT_FINDER_USE_FULL_XFILTERING |
Functions | |
| USING_SCOPE (objects) | |
| template<class THit > | |
| double | GetTotalMatches (const typename CCompartmentFinder< THit >::THitRefs &hitrefs0) |
Variables | |
| const double | kPenaltyPerIntronBase = -2e-5 |
| IMPLEMENTATION. More... | |
| const double | kPenaltyPerIntronPos = -1e-9 |
Macro Definition Documentation
◆ ALGO_ALIGN_COMPARTMENT_FINDER_USE_FULL_XFILTERING
| #define ALGO_ALIGN_COMPARTMENT_FINDER_USE_FULL_XFILTERING |
Function Documentation
◆ GetTotalMatches()
template<class THit >
| double GetTotalMatches | ( | const typename CCompartmentFinder< THit >::THitRefs & | hitrefs0 | ) |
Definition at line 674 of file compartment_finder.hpp.
◆ USING_SCOPE()
| USING_SCOPE | ( | objects | ) |
Referenced by CCompartmentAccessor< THit >::AsSeqAlignSet().
Variable Documentation
◆ kPenaltyPerIntronBase
| const double kPenaltyPerIntronBase = -2e-5 |
IMPLEMENTATION.
Definition at line 593 of file compartment_finder.hpp.
Referenced by CCompartmentFinder< THit >::Run().
◆ kPenaltyPerIntronPos
| const double kPenaltyPerIntronPos = -1e-9 |
Definition at line 596 of file compartment_finder.hpp.
Referenced by CCompartmentFinder< THit >::Run().
