include/algo/align/util/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/Dense_seg.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Na_strand.hpp>
#include <algorithm>
#include <numeric>
#include <vector>

Include dependency graph for compartment_finder.hpp:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Classes
class	CCompartmentFinder< THit >
class	CCompartmentFinder< THit >::CCompartment
	Individual compartment representation. More...
struct	CCompartmentFinder< THit >::SHitStatus
class	CCompartmentAccessor< THit >
class	CQueryMatchAccumulator< THit >
Defines
#define	ALGO_ALIGN_COMPARTMENT_FINDER_USE_FULL_XFILTERING
Functions
const double	kPenaltyPerIntronBase (-2e-5)
	IMPLEMENTATION.
const double	kPenaltyPerIntronPos (-1e-9)
template<class THit>
double	GetTotalMatches (const typename CCompartmentFinder< THit >::THitRefs &hitrefs0)

---

Define Documentation

#define ALGO_ALIGN_COMPARTMENT_FINDER_USE_FULL_XFILTERING

---

Function Documentation

template<class THit> double GetTotalMatches (  const typename CCompartmentFinder< THit >::THitRefs &  hitrefs0  )

Definition at line 538 of file compartment_finder.hpp.

const double kPenaltyPerIntronBase (  -2e-  5  )

IMPLEMENTATION.

const double kPenaltyPerIntronPos (  -1e-  9  )

---