src/algo/gnomon/chainer.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbienv.hpp>
#include <corelib/ncbiargs.hpp>
#include <algo/gnomon/chainer.hpp>
#include <algo/gnomon/id_handler.hpp>
#include <util/sequtil/sequtil_manip.hpp>
#include <algo/gnomon/gnomon_model.hpp>
#include <algo/gnomon/gnomon.hpp>
#include <map>
#include <sstream>
#include <objects/general/Object_id.hpp>

Include dependency graph for chainer.cpp:

Go to the source code of this file.

Classes
class	CChainer::CChainerImpl
struct	SChainMember
class	CChain
struct	LeftOrder
struct	RightOrder
struct	NumOrder
struct	ScoreOrder
class	CChainMembers
class	CModelCompare
struct	AlignSeqOrder
struct	LeftEndOrder
struct	RightEndOrder
struct	OverlapsSameAccessionAlignment
struct	ConnectsParalogs
struct	SFShiftsCluster
struct	ProjectCDS
struct	TrimAlignment
struct	DoNotBelieveShortPolyATail
struct	DoNotBelieveFrameShiftsWithoutCdsEvidence
Typedefs
typedef map< int, CAlignModel * >	TOrigAligns
typedef vector< SChainMember * >	TContained
typedef set< const CGeneModel * >	TEvidence
Enumerations
enum	{ eCDS, eLeftUTR, eRightUTR }
Functions
static bool	s_ByExonNumberAndLocation (const CGeneModel &a, const CGeneModel &b)
static bool	s_ScoreOrder (const CGeneModel &a, const CGeneModel &b)
template<class C>
void	uniq (C &container)
pair< string, int >	GetAccVer (const string &ident)
static int	s_ExonLen (const CGeneModel &a)
static bool	s_ByAccVerLen (const CAlignModel &a, const CAlignModel &b)
string	FindMultiplyIncluded (CAlignModel &algn, TAlignModelList &clust)
double	InframeFraction (const CGeneModel &a, TSignedSeqPos left, TSignedSeqPos right)
int	EffectiveExonLength (const CModelExon &e, const CAlignMap &alignmap, bool snap_to_codons)

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Typedef Documentation

typedef vector<SChainMember*> TContained

Definition at line 143 of file chainer.cpp.

typedef set<const CGeneModel*> TEvidence

Definition at line 145 of file chainer.cpp.

typedef map<int,CAlignModel*> TOrigAligns

Definition at line 55 of file chainer.cpp.

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Enumeration Type Documentation

anonymous enum

Enumerator: eCDS  eLeftUTR  eRightUTR  Definition at line 137 of file chainer.cpp.

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Function Documentation

int EffectiveExonLength (  const CModelExon &  e, const CAlignMap &  alignmap, bool  snap_to_codons )

Definition at line 2422 of file chainer.cpp. References CAlignMap::FShiftedLen(), COpenRange< Position >::GetLength(), and CAlignMap::ShrinkToRealPoints(). Referenced by CutShortPartialExons::operator()().

string FindMultiplyIncluded (  CAlignModel &  algn, TAlignModelList &  clust )

Definition at line 1432 of file chainer.cpp. References CGeneModel::AlignLen(), CGeneModel::Continuous(), CGeneModel::eProt, CGeneModel::IdenticalAlign(), CGeneModel::isCompatible(), len, NON_CONST_ITERATE, CGeneModel::Strand(), CAlignModel::TargetAccession(), and CGeneModel::Type(). Referenced by ConnectsParalogs::operator()().

pair<string,int> GetAccVer (  const string &  ident  )

Definition at line 1271 of file chainer.cpp. References dot. Referenced by OverlapsSameAccessionAlignment::OverlapsSameAccessionAlignment(), and s_ByAccVerLen().

double InframeFraction (  const CGeneModel &  a, TSignedSeqPos  left, TSignedSeqPos  right )

Definition at line 1783 of file chainer.cpp. References CGeneModel::FrameShifts(), CGeneModel::GetAlignMap(), ITERATE, and len. Referenced by ProjectCDS::operator()().

static bool s_ByAccVerLen (  const CAlignModel &  a, const CAlignModel &  b )  [static]

Definition at line 1295 of file chainer.cpp. References NStr::CompareCase(), CGeneModel::ConfirmedStart(), GetAccVer(), CGeneModel::ID(), s_ExonLen(), and CAlignModel::TargetAccession(). Referenced by OverlapsSameAccessionAlignment::OverlapsSameAccessionAlignment().

static bool s_ByExonNumberAndLocation (  const CGeneModel &  a, const CGeneModel &  b )  [static]

Definition at line 270 of file chainer.cpp. References CGeneModel::Exons(), CGeneModel::ID(), CGeneModel::Limits(), and CGeneModel::Strand(). Referenced by CChainer::CChainerImpl::ScoreCDSes_FilterOutPoorAlignments().

static int s_ExonLen (  const CGeneModel &  a  )  [static]

Definition at line 1314 of file chainer.cpp. References CGeneModel::Exons(), ITERATE, and len. Referenced by s_ByAccVerLen().

static bool s_ScoreOrder (  const CGeneModel &  a, const CGeneModel &  b )  [static]

Definition at line 289 of file chainer.cpp. References CGeneModel::ID(), and CGeneModel::Score(). Referenced by CChainer::CChainerImpl::FilterOutInferiorProtAlignmentsWithIncompatibleFShifts().

template<class C> void uniq (  C &  container  )

Definition at line 298 of file chainer.cpp. Referenced by CChainer::CChainerImpl::CollectFShifts().

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