NCBI C++ ToolKit
Classes | Macros | Functions | Variables
compartment_finder.hpp File Reference
#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 672 of file compartment_finder.hpp.

◆ USING_SCOPE()

USING_SCOPE ( objects  )

Variable Documentation

◆ kPenaltyPerIntronBase

const double kPenaltyPerIntronBase = -2e-5

IMPLEMENTATION.

Definition at line 591 of file compartment_finder.hpp.

Referenced by CCompartmentFinder< THit >::Run().

◆ kPenaltyPerIntronPos

const double kPenaltyPerIntronPos = -1e-9

Definition at line 594 of file compartment_finder.hpp.

Referenced by CCompartmentFinder< THit >::Run().

Modified on Thu Apr 11 15:03:09 2024 by modify_doxy.py rev. 669887