nucprot.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <algo/align/prosplign/prosplign_exception.hpp>
#include "nucprot.hpp"
#include "intron.hpp"
#include "Info.hpp"
#include "BackAlignInfo.hpp"
#include "Ali.hpp"
#include "AlignInfo.hpp"
#include "scoring.hpp"
#include <util/tables/raw_scoremat.h>

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Functions
int	FrAlign (const CProSplignInterrupt &interrupt, CBackAlignInfo &bi, const PSEQ &pseq, const CNSeq &nseq, int g, int e, int f, const CProSplignScaledScoring &, const CSubstMatrix &matrix)
int	FindFGapIntronNog (const CProSplignInterrupt &interrupt, vector< pair< int, int > > &igi, const PSEQ &pseq, const CNSeq &nseq, bool &left_gap, bool &right_gap, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix)
int	FindIGapIntrons (const CProSplignInterrupt &interrupt, vector< pair< int, int > > &igi, const PSEQ &pseq, const CNSeq &nseq, int g, int e, int f, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix)
void	FrBackAlign (CBackAlignInfo &bi, CAli &ali)
int	FrAlignFNog1 (const CProSplignInterrupt &interrupt, CBackAlignInfo &bi, const PSEQ &pseq, const CNSeq &nseq, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix, bool left_gap, bool right_gap)
int	AlignFNog (const CProSplignInterrupt &interrupt, CTBackAlignInfo< CBMode > &bi, const PSEQ &pseq, const CNSeq &nseq, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix)
void	BackAlignNog (CTBackAlignInfo< CBMode > &bi, CAli &ali)

Variables
const int	infinity = numeric_limits<int>::min()/3

Function Documentation

AlignFNog()

int AlignFNog	(	const CProSplignInterrupt &	interrupt,
		CTBackAlignInfo< CBMode > &	bi,
		const PSEQ &	pseq,
		const CNSeq &	nseq,
		const CProSplignScaledScoring &	scoring,
		const CSubstMatrix &	matrix
	)

Definition at line 937 of file nucprot.cpp.

References CTBackAlignInfo< T >::b, bb, ch1, ch2, ch3, CProSplignInterrupt::CheckUserInterrupt(), f(), g(), CFIntron::GetH1len(), CFIntron::GetH2len(), CFIntron::GetH3len(), CFastIScore::GetScore(), CFIntron::GetVlen(), CFIntron::GetW1len(), CFIntron::GetW2len(), CFIntron::GetWlen(), CAlignRow::h1, CBestI::h1, CAlignRow::h2, CBestI::h2, CAlignRow::h3, CBestI::h3, i, infinity, CFastIScore::Init(), CFIntron::InitRowScores(), int, CAlignRow::m_w, max(), CTBackAlignInfo< T >::maxi, CTBackAlignInfo< T >::maxj, pb, CFastIScore::SetAmin(), CNSeq::size(), CProSplignScaledScoring::sm_If, CProSplignScaledScoring::sm_Ig, CProSplignScaledScoring::sm_Ine, CFIntron::Step(), swap(), CAlignRow::v, CBestI::v, v2, CAlignRow::w, CBestI::w, CBestI::w1, and CBestI::w2.

Referenced by COneStage::stage1().

BackAlignNog()

void BackAlignNog	(	CTBackAlignInfo< CBMode > &	bi,
		CAli &	ali
	)

Definition at line 1143 of file nucprot.cpp.

References CAliCreator::Add(), CTBackAlignInfo< T >::b, eD, eH1, eH2, eH3, eHP, eMP, eSP, eV, eVP, CAliCreator::Fini(), i, CTBackAlignInfo< T >::ilen, CTBackAlignInfo< T >::jlen, CTBackAlignInfo< T >::maxi, CTBackAlignInfo< T >::maxj, and NCBI_THROW.

Referenced by COneStage::stage2().

FindFGapIntronNog()

int FindFGapIntronNog	(	const CProSplignInterrupt &	interrupt,
		vector< pair< int, int > > &	igi,
		const PSEQ &	pseq,
		const CNSeq &	nseq,
		bool &	left_gap,
		bool &	right_gap,
		const CProSplignScaledScoring &	scoring,
		const CSubstMatrix &	matrix
	)

Definition at line 260 of file nucprot.cpp.

References _ASSERT, ch1, ch2, ch3, CProSplignInterrupt::CheckUserInterrupt(), CIgapIntronChain::Clear(), CFindGapIntronRow::ClearIIC(), CIgapIntronChain::Copy(), CIgapIntronChain::Creat(), CIgapIntronChain::Expand(), f(), g(), CFIntron::GetH1len(), CFIntron::GetH2len(), CFIntron::GetH3len(), CFastIScore::GetScore(), CFIntron::GetVlen(), CFIntron::GetW1len(), CFIntron::GetW2len(), CFIntron::GetWlen(), CAlignRow::h1, CBestI::h1, CFindGapIntronRow::h1is, CAlignRow::h2, CBestI::h2, CFindGapIntronRow::h2is, CAlignRow::h3, CBestI::h3, CFindGapIntronRow::h3is, i, infinity, CFastIScore::Init(), CFIntron::InitRowScores(), int, len, CIgapIntronChain::m_Top, CAlignRow::m_w, max(), CFastIScore::SetAmin(), CIgapIntronChain::SetPool(), CNSeq::size(), CProSplignScaledScoring::sm_If, CProSplignScaledScoring::sm_Ig, CProSplignScaledScoring::sm_Ine, CFIntron::Step(), swap(), tmp, CAlignRow::v, CBestI::v, v2, CFindGapIntronRow::vis, CAlignRow::w, CBestI::w, CBestI::w1, CBestI::w2, and CFindGapIntronRow::wis.

Referenced by CTwoStageNew::stage1().

FindIGapIntrons()

int FindIGapIntrons	(	const CProSplignInterrupt &	interrupt,
		vector< pair< int, int > > &	igi,
		const PSEQ &	pseq,
		const CNSeq &	nseq,
		int	g,
		int	e,
		int	f,
		const CProSplignScaledScoring &	scoring,
		const CSubstMatrix &	matrix
	)

Definition at line 508 of file nucprot.cpp.

References CProSplignInterrupt::CheckUserInterrupt(), CAlignInfo::ClearIIC(), CIgapIntronChain::Copy(), CIgapIntronChain::Creat(), CIgapIntronChain::Expand(), f(), CAlignInfo::fh, CAlignInfo::fhis, CAlignInfo::fv, CAlignInfo::fvis, g(), CBestIntron::Getfh000(), CBestIntron::Getfv000(), CBestIntron::Getfv111(), CBestIntron::Geth000(), CBestIntron::Geth012(), CBestIntron::Geth021(), CBestIntron::Getv000(), CBestIntron::Getw000(), CBestIntron::Getw012(), CBestIntron::Getw021(), CBestIntron::GetW1(), CBestIntron::Getw111(), CBestIntron::GetW2(), CAlignInfo::h, CAlignInfo::his, i, infinity, int, CIgapIntronChain::m_Top, max(), CSubstMatrix::MultScore(), CBestIntron::NucStep(), CNSeq::size(), swap(), tmp, CAlignInfo::v, v2, CAlignInfo::vis, CAlignInfo::w, and CAlignInfo::wis.

Referenced by CTwoStageOld::stage1().

FrAlign()

int FrAlign	(	const CProSplignInterrupt &	interrupt,
		CBackAlignInfo &	bi,
		const PSEQ &	pseq,
		const CNSeq &	nseq,
		int	g,
		int	e,
		int	f,
		const CProSplignScaledScoring &	scoring,
		const CSubstMatrix &	matrix
	)

Definition at line 171 of file nucprot.cpp.

References CTBackAlignInfo< T >::b, b, CProSplignInterrupt::CheckUserInterrupt(), f(), g(), i, CTBackAlignInfo< T >::ilen, infinity, int, max(), CTBackAlignInfo< T >::maxi, CTBackAlignInfo< T >::maxj, CSubstMatrix::MultScore(), CNSeq::size(), swap(), CFrAlignRow::v, v2, and CFrAlignRow::w.

Referenced by CIntronlessOld::stage1(), and CTwoStageOld::stage2().

FrAlignFNog1()

int FrAlignFNog1	(	const CProSplignInterrupt &	interrupt,
		CBackAlignInfo &	bi,
		const PSEQ &	pseq,
		const CNSeq &	nseq,
		const CProSplignScaledScoring &	scoring,
		const CSubstMatrix &	matrix,
		bool	left_gap,
		bool	right_gap
	)

Definition at line 774 of file nucprot.cpp.

References _ASSERT, CTBackAlignInfo< T >::b, b, bb, CProSplignInterrupt::CheckUserInterrupt(), f(), g(), CProSplignScoring::GetFrameshiftOpeningCost(), CProSplignScoring::GetGapExtensionCost(), CProSplignScoring::GetGapOpeningCost(), CFastIScore::GetScore(), i, infinity, CFastIScore::Init(), int, max(), CTBackAlignInfo< T >::maxi, CTBackAlignInfo< T >::maxj, CSubstMatrix::MultScore(), pb, CFastIScore::SetAmin(), CNSeq::size(), swap(), CFrAlignRow::v, v2, and CFrAlignRow::w.

Referenced by CIntronlessNew::stage1(), and CTwoStageNew::stage2().

FrBackAlign()

void FrBackAlign	(	CBackAlignInfo &	bi,
		CAli &	ali
	)

Definition at line 684 of file nucprot.cpp.

References CAliCreator::Add(), CTBackAlignInfo< T >::b, b, eD, eH, eH1, eH2, eH3, eHP, eMP, eV, eVP, CAliCreator::Fini(), i, CTBackAlignInfo< T >::ilen, CTBackAlignInfo< T >::jlen, CTBackAlignInfo< T >::maxi, CTBackAlignInfo< T >::maxj, and NCBI_THROW.

Referenced by CTwoStageOld::stage2(), CTwoStageNew::stage2(), and CIntronless::stage2().

Variable Documentation

infinity

const int infinity = numeric_limits<int>::min()/3

Definition at line 52 of file nucprot.cpp.

Referenced by CScoreBuilderBase::AddScore(), AlignFNog(), BOOST_AUTO_TEST_CASE(), CAlignRow::CAlignRow(), CClusterer::ComputeClusters(), CScoreBuilder::ComputeScore(), FindFGapIntronNog(), FindIGapIntrons(), FrAlign(), FrAlignFNog1(), isFinite(), rapidjson::GenericReader< SourceEncoding, TargetEncoding, StackAllocator >::ParseNumber(), CTabularFormatter_EValue::Print(), CTabularFormatter_EValue_Mantissa::Print(), CTabularFormatter_EValue_Exponent::Print(), CFIntronDon::Reset(), and CFloatTextValidator::Validate().