#include <algo/align/util/score_lookup.hpp>

Inheritance diagram for CScoreLookup:

Collaboration diagram for CScoreLookup:

Classes
class	IScore

Public Member Functions
	CScoreLookup ()

	CScoreLookup (enum blast::EProgram program_type)

	CScoreLookup (blast::CBlastOptionsHandle &options)

void	SetScope (objects::CScope &scope)
	CScoreLookup uses a scope internally. More...

objects::CScope &	GetScope ()

void	PrintDictionary (CNcbiOstream &)
	Print out the dictionary of recognized score names. More...

string	HelpText (const string &score_name)
	Help text for score. More...

IScore::EComplexity	Complexity (const string &score_name)

bool	IsIntegerScore (const objects::CSeq_align &align, const string &score_name)

double	GetScore (const objects::CSeq_align &align, const string &score_name)
	Get requested score for alignment. More...

void	UpdateState (const objects::CSeq_align &align)

Public Member Functions inherited from CScoreBuilder
	CScoreBuilder ()
	Default constructor. More...

	CScoreBuilder (enum blast::EProgram program_type)

	CScoreBuilder (blast::CBlastOptionsHandle &options)

	~CScoreBuilder ()
	Destructor. More...

void	SetGapOpen (int gapopen)

void	SetGapExtend (int gapextend)

void	AddScore (CScope &scope, CSeq_align &align, EScoreType score)
	deprecated: use CSeq_align::EScoreType directly More...

void	AddScore (CScope &scope, list< CRef< CSeq_align > > &aligns, EScoreType score)
	deprecated: use CSeq_align::EScoreType directly More...

double	ComputeScore (CScope &scope, const CSeq_align &align, const CRangeCollection< TSeqPos > &ranges, CSeq_align::EScoreType score)

double	ComputeScore (CScope &scope, const CSeq_align &align, CSeq_align::EScoreType score)

double	ComputeScore (CScope &scope, const CSeq_align &align, const TSeqRange &range, CSeq_align::EScoreType score)

void	AddScore (CScope &scope, CSeq_align &align, CSeq_align::EScoreType score)

void	AddScore (CScope &scope, list< CRef< CSeq_align > > &aligns, CSeq_align::EScoreType score)

int	GetBlastScore (CScope &scope, const CSeq_align &align)
	Compute the BLAST score of the alignment. More...

double	GetBlastBitScore (CScope &scope, const CSeq_align &align)
	Compute the BLAST bit score. More...

double	GetBlastEValue (CScope &scope, const CSeq_align &align)
	Compute the BLAST e-value. More...

void	AddTracebacks (CScope &scope, CSeq_align &align)

void	AddTracebacks (CScope &scope, list< CRef< CSeq_align > > &aligns)

string	GetTraceback (const CSeq_align &align, CSeq_align::TDim row)

string	GetTraceback (CScope &scope, const CSeq_align &align, CSeq_align::TDim row)

int	ComputeTieBreaker (const CSeq_align &align)

void	AddTieBreaker (CSeq_align &align)

void	SetEffectiveSearchSpace (Int8 searchsp)

Public Member Functions inherited from CScoreBuilderBase
	CScoreBuilderBase ()
	Default constructor. More...

virtual	~CScoreBuilderBase ()
	Destructor. More...

EErrorMode	GetErrorMode (void) const

void	SetErrorMode (EErrorMode mode)

void	AddScore (CScope &scope, CSeq_align &align, CSeq_align::EScoreType score)

void	AddScore (CScope &scope, list< CRef< CSeq_align > > &aligns, CSeq_align::EScoreType score)

double	ComputeScore (CScope &scope, const CSeq_align &align, CSeq_align::EScoreType score)

double	ComputeScore (CScope &scope, const CSeq_align &align, const TSeqRange &range, CSeq_align::EScoreType score)

void	AddSplignScores (const CSeq_align &align, CSeq_align::TScore &scores)
	Compute the six splign scores. More...

void	AddSplignScores (CSeq_align &align)

double	GetPercentIdentity (CScope &scope, const CSeq_align &align, EPercentIdentityType type=eGapped)

double	GetPercentCoverage (CScope &scope, const CSeq_align &align, unsigned query=0)
	Compute percent coverage of the query (sequence 0) (range 0-100) More...

double	GetPercentIdentity (CScope &scope, const CSeq_align &align, const TSeqRange &range, EPercentIdentityType type=eGapped)
	Compute percent identity or coverage of the query within specified range. More...

double	GetPercentCoverage (CScope &scope, const CSeq_align &align, const TSeqRange &range, unsigned query=0)

double	GetPercentIdentity (CScope &scope, const CSeq_align &align, const CRangeCollection< TSeqPos > &ranges, EPercentIdentityType type=eGapped)
	Compute percent identity or coverage of the query within specified collection of ranges. More...

double	GetPercentCoverage (CScope &scope, const CSeq_align &align, const CRangeCollection< TSeqPos > &ranges, unsigned query=0)

int	GetIdentityCount (CScope &scope, const CSeq_align &align)
	Compute the number of identities in the alignment. More...

int	GetMismatchCount (CScope &scope, const CSeq_align &align)
	Compute the number of mismatches in the alignment. More...

void	GetMismatchCount (CScope &scope, const CSeq_align &align, int &identities, int &mismatches)

int	GetIdentityCount (CScope &scope, const CSeq_align &align, const TSeqRange &range)
	Compute identity and/or mismatch counts within specified range. More...

int	GetMismatchCount (CScope &scope, const CSeq_align &align, const TSeqRange &range)

void	GetMismatchCount (CScope &scope, const CSeq_align &align, const TSeqRange &range, int &identities, int &mismatches)

int	GetIdentityCount (CScope &scope, const CSeq_align &align, const CRangeCollection< TSeqPos > &ranges)
	Compute identity and/or mismatch counts within specified collection of ranges. More...

int	GetMismatchCount (CScope &scope, const CSeq_align &align, const CRangeCollection< TSeqPos > &ranges)

void	GetMismatchCount (CScope &scope, const CSeq_align &align, const CRangeCollection< TSeqPos > &ranges, int &identities, int &mismatches)

int	GetPositiveCount (CScope &scope, const CSeq_align &align)
	counts based on substitution matrix for protein alignments More...

int	GetNegativeCount (CScope &scope, const CSeq_align &align)

void	GetMatrixCounts (CScope &scope, const CSeq_align &align, int &positives, int &negatives)

int	GetGapCount (const CSeq_align &align)
	Compute the number of gaps in the alignment. More...

int	GetGapCount (const CSeq_align &align, const TSeqRange &range)

int	GetGapCount (const CSeq_align &align, const CRangeCollection< TSeqPos > &ranges)

int	GetGapBaseCount (const CSeq_align &align)
	Compute the number of gap bases in the alignment (= length of all gap segments) More...

int	GetGapBaseCount (const CSeq_align &align, const TSeqRange &range)

int	GetGapBaseCount (const CSeq_align &align, const CRangeCollection< TSeqPos > &ranges)

TSeqPos	GetAlignLength (const CSeq_align &align, bool ungapped=false)
	Compute the length of the alignment (= length of all segments, gaps + aligned) More...

TSeqPos	GetAlignLength (const CSeq_align &align, const TSeqRange &range, bool ungapped=false)

TSeqPos	GetAlignLength (const CSeq_align &align, const CRangeCollection< TSeqPos > &ranges, bool ungapped=false)

void	SetSubstMatrix (const string &name)

Static Public Member Functions
static int	GetGeneId (const objects::CBioseq_Handle &bsh)

Private Types
typedef map< string, CIRef< IScore > >	TScoreDictionary

Private Member Functions
void	x_Init ()

void	x_PrintDictionaryEntry (CNcbiOstream &ostr, const string &score_name)

Private Attributes
CRef< objects::CScope >	m_Scope

TScoreDictionary	m_Scores

set< string >	m_ScoresUsed

Additional Inherited Members
Public Types inherited from CScoreBuilderBase
enum	EScoreType { eScore_Blast , eScore_Blast_BitScore , eScore_Blast_EValue , eScore_IdentityCount , eScore_MismatchCount , eScore_PercentIdentity , eScore_PercentCoverage }

enum	EErrorMode { eError_Silent , eError_Report , eError_Throw }
	Error handling while adding scores that are not implemented or unsupported (cannot be defined) for certain types of alignments. More...

enum	EPercentIdentityType { eGapped , eUngapped , eGBDNA }
	Compute percent identity (range 0-100) More...

Protected Member Functions inherited from CScoreBuilder
struct BlastScoreBlk *	GetBlastScoreBlkPtr ()

Detailed Description

Definition at line 48 of file score_lookup.hpp.

Member Typedef Documentation

◆ TScoreDictionary

typedef map<string, CIRef<IScore> > CScoreLookup::TScoreDictionary

private

Definition at line 115 of file score_lookup.hpp.

Constructor & Destructor Documentation

◆ CScoreLookup() [1/3]

CScoreLookup::CScoreLookup ( )

inline

Definition at line 72 of file score_lookup.hpp.

References x_Init().

◆ CScoreLookup() [2/3]

CScoreLookup::CScoreLookup ( enum blast::EProgram program_type )

inline

Definition at line 74 of file score_lookup.hpp.

References x_Init().

◆ CScoreLookup() [3/3]

CScoreLookup::CScoreLookup ( blast::CBlastOptionsHandle & options )

inline

Definition at line 77 of file score_lookup.hpp.

References x_Init().

Member Function Documentation

◆ Complexity()

CScoreLookup::IScore::EComplexity CScoreLookup::Complexity ( const string & score_name )

Definition at line 2386 of file score_lookup.cpp.

References CScoreLookup::IScore::eEasy, map_checker< Container >::end(), map_checker< Container >::find(), m_Scores, NCBI_THROW, and CSeq_align::ScoreNameMap().

◆ GetGeneId()

int CScoreLookup::GetGeneId ( const objects::CBioseq_Handle & bsh )

static

Definition at line 1708 of file score_lookup.cpp.

References CSeqFeatData_Base::e_Gene, eUnknown, CSeq_feat_Handle::GetData(), CGene_ref_Base::GetDb(), CSeqFeatData_Base::GetGene(), CObject_id_Base::GetId(), CSeq_feat_Handle::GetNamedDbxref(), CDbtag_Base::GetTag(), CGene_ref_Base::IsSetDb(), and NCBI_THROW.

Referenced by CScore_GeneID::Get().

◆ GetScope()

objects::CScope& CScoreLookup::GetScope ( void )

inline

Definition at line 85 of file score_lookup.hpp.

References m_Scope.

◆ GetScore()

double CScoreLookup::GetScore	(	const objects::CSeq_align &	align,
		const string &	score_name
	)

Get requested score for alignment.

Definition at line 2429 of file score_lookup.cpp.

References CScoreBuilder::ComputeScore(), map_checker< Container >::end(), map_checker< Container >::find(), CObjectManager::GetInstance(), set< Key, Compare >::insert(), CRef< C, Locker >::IsNull(), m_Scope, m_Scores, m_ScoresUsed, NCBI_THROW, CRef< C, Locker >::Reset(), and CSeq_align::ScoreNameMap().

Referenced by BOOST_AUTO_TEST_CASE().

◆ HelpText()

string CScoreLookup::HelpText ( const string & score_name )

Help text for score.

Definition at line 2367 of file score_lookup.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), CSeq_align::HelpText(), set< Key, Compare >::insert(), m_Scores, m_ScoresUsed, CSeq_align::ScoreNameMap(), and string.

Referenced by x_PrintDictionaryEntry().

◆ IsIntegerScore()

bool CScoreLookup::IsIntegerScore	(	const objects::CSeq_align &	align,
		const string &	score_name
	)

Definition at line 2403 of file score_lookup.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), CSeq_align::IsIntegerScore(), ITERATE, m_Scores, and CSeq_align::ScoreNameMap().

◆ PrintDictionary()

void CScoreLookup::PrintDictionary ( CNcbiOstream & ostr )

Print out the dictionary of recognized score names.

Definition at line 2353 of file score_lookup.cpp.

References ITERATE, m_Scores, CSeq_align::ScoreNameMap(), and x_PrintDictionaryEntry().

◆ SetScope()

void CScoreLookup::SetScope ( objects::CScope & scope )

inline

CScoreLookup uses a scope internally.

You can set a scope yourself; alternatively, the scope used internally will be a default scope

Definition at line 82 of file score_lookup.hpp.

References m_Scope, and CRef< C, Locker >::Reset().

Referenced by BOOST_AUTO_TEST_CASE().

◆ UpdateState()

void CScoreLookup::UpdateState ( const objects::CSeq_align & align )

Definition at line 2334 of file score_lookup.cpp.

References ITERATE, m_Scores, and m_ScoresUsed.

◆ x_Init()

void CScoreLookup::x_Init ( void )

private

Definition at line 2004 of file score_lookup.cpp.

References CScore_EdgeExonInfo::e3Prime, CScore_EdgeExonInfo::e5Prime, CScore_SymmetricOverlap::e_Avg, CScore_SymmetricOverlap::e_Min, CScore_CdsScore::eEnd, CScore_EdgeExonInfo::eLength, CScore_CdsScore::ePercentCoverage, CScore_CdsScore::ePercentIdentity, CScore_EdgeExonInfo::ePercentIdentity, CScore_CdsScore::eStart, map_checker< Container >::insert(), and m_Scores.

Referenced by CScoreLookup().

◆ x_PrintDictionaryEntry()

void CScoreLookup::x_PrintDictionaryEntry	(	CNcbiOstream &	ostr,
		const string &	score_name
	)

private

Definition at line 2341 of file score_lookup.cpp.

References HelpText(), i, ITERATE, tmp, and NStr::Wrap().

Referenced by PrintDictionary().

Member Data Documentation

◆ m_Scope

CRef<objects::CScope> CScoreLookup::m_Scope

private

Definition at line 113 of file score_lookup.hpp.

Referenced by GetScope(), GetScore(), and SetScope().

◆ m_Scores

TScoreDictionary CScoreLookup::m_Scores

private

Definition at line 116 of file score_lookup.hpp.

Referenced by Complexity(), GetScore(), HelpText(), IsIntegerScore(), PrintDictionary(), UpdateState(), and x_Init().

◆ m_ScoresUsed

set<string> CScoreLookup::m_ScoresUsed

private

Definition at line 118 of file score_lookup.hpp.

Referenced by GetScore(), HelpText(), and UpdateState().

The documentation for this class was generated from the following files:

include/algo/align/util/score_lookup.hpp
src/algo/align/util/score_lookup.cpp

Classes

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TScoreDictionary

Constructor & Destructor Documentation

◆ CScoreLookup() [1/3]

◆ CScoreLookup() [2/3]

◆ CScoreLookup() [3/3]

Member Function Documentation

◆ Complexity()

◆ GetGeneId()

◆ GetScope()

◆ GetScore()

◆ HelpText()

◆ IsIntegerScore()

◆ PrintDictionary()

◆ SetScope()

◆ UpdateState()

◆ x_Init()

◆ x_PrintDictionaryEntry()

Member Data Documentation

◆ m_Scope

◆ m_Scores

◆ m_ScoresUsed