src/algo/align/splign/splign.cpp File Reference

#include <ncbi_pch.hpp>
#include "splign_util.hpp"
#include "messages.hpp"
#include <algo/align/util/hit_comparator.hpp>
#include <algo/align/util/compartment_finder.hpp>
#include <algo/align/nw/nw_band_aligner.hpp>
#include <algo/align/nw/nw_spliced_aligner16.hpp>
#include <algo/align/nw/nw_formatter.hpp>
#include <algo/align/nw/align_exception.hpp>
#include <algo/align/splign/splign.hpp>
#include <algo/sequence/orf.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/util/seq_loc_util.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqalign/Spliced_seg.hpp>
#include <objects/seqalign/Spliced_exon.hpp>
#include <objects/seqalign/Spliced_exon_chunk.hpp>
#include <objects/seqalign/Product_pos.hpp>
#include <objects/seqalign/Splice_site.hpp>
#include <objects/seqalign/Score.hpp>
#include <objects/seqalign/Score_set.hpp>
#include <objects/general/Object_id.hpp>
#include <math.h>
#include <algorithm>

Include dependency graph for splign.cpp:

Go to the source code of this file.

Namespaces
namespace	splign_local
Functions
const Uint4	kNonCoveredEndThreshold (55)
const double	kPower (2.5)
const size_t	kMinTermExonSize (28)
const double	kMinTermExonIdty (0.9)
const CSplign::THit::TCoord	kMaxCoord (numeric_limits< CSplign::THit::TCoord >::max())
template<typename T>
void	splign_local::ElemToBuffer (const T &n, char *&p)
template<>
void	splign_local::ElemToBuffer (const string &s, char *&p)
template<typename T>
void	splign_local::ElemFromBuffer (T &n, const char *&p)
template<>
void	splign_local::ElemFromBuffer (string &s, const char *&p)
bool	IsConsDonor (const objects::CSpliced_exon &exon)
bool	IsConsAcceptor (const objects::CSpliced_exon &exon)
const int	kFrame_not_set (-10)
const int	kFrame_end (-5)
const int	kFrame_lost (-20)
Variables
static const char	s_kGap [] = "<GAP>"

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Function Documentation

bool IsConsAcceptor (  const objects::CSpliced_exon &  exon  )

Definition at line 2268 of file splign.cpp. References USING_SCOPE.

bool IsConsDonor (  const objects::CSpliced_exon &  exon  )

Definition at line 2260 of file splign.cpp. References USING_SCOPE.

const int @1::kFrame_end (  -  5  )  [static]

const int @1::kFrame_lost (  -  20  )  [static]

const int @1::kFrame_not_set (  -  10  )  [static]

const CSplign::THit::TCoord @0::kMaxCoord (  numeric_limits< CSplign::THit::TCoord >::  max()  )  [static]

Referenced by CSplign::AlignSingleCompartment(), and CSplign::GetCds().

const double @0::kMinTermExonIdty (  0.  9  )  [static]

Referenced by CSplign::x_ProcessTermSegm().

const size_t @0::kMinTermExonSize (  28   )  [static]

Referenced by CSplign::x_ProcessTermSegm().

const Uint4 @0::kNonCoveredEndThreshold (  55   )  [static]

Referenced by CSplign::x_GetGenomicExtent().

const double @0::kPower (  2.  5  )  [static]

Referenced by CSplign::x_GetGenomicExtent().

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Variable Documentation

const char s_kGap[] = "<GAP>" [static]

Definition at line 1449 of file splign.cpp.

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