CEquivRange Class Reference

Search Toolkit Book for CEquivRange

#include <algo/align/mergetree/equiv_range.hpp>

Collaboration diagram for CEquivRange:

Public Types
enum	ERelative {   eWtf = 0x00 , eIntersects = 0x01 , eInterQuery = 0x02 , eInterSubjt = 0x04 ,   eBefore = 0x10 , eAfter = 0x20 , eAbove = 0x40 , eUnder = 0x80 }

Public Member Functions
	CEquivRange ()
bool	Empty () const
bool	NotEmpty () const
bool	IntersectingWith (const CEquivRange &Other) const
bool	AbuttingWith (const CEquivRange &Other) const
ERelative	CalcRelative (const CEquivRange &Check) const
ERelative	CalcRelativeDuo (const CEquivRange &Check) const

Static Public Member Functions
static TSeqPos	Distance (const CEquivRange &A, const CEquivRange &B)
static TSeqPos	Distance (const TEquivList &A, const TEquivList &B)

Public Attributes
CRange< TSeqPos >	Query
CRange< TSeqPos >	Subjt
objects::ENa_strand	Strand
int	Intercept
int	Matches
int	MisMatches
vector< TSeqPos >	MisMatchSubjtPoints
int	AlignId
int	SegmtId
int	SplitId

Detailed Description

Definition at line 51 of file equiv_range.hpp.

Member Enumeration Documentation

ERelative

enum CEquivRange::ERelative

Enumerator
eWtf
eIntersects
eInterQuery
eInterSubjt
eBefore
eAfter
eAbove
eUnder

Definition at line 94 of file equiv_range.hpp.

Constructor & Destructor Documentation

CEquivRange()

CEquivRange::CEquivRange ( )

inline

Definition at line 54 of file equiv_range.hpp.

Member Function Documentation

AbuttingWith()

bool CEquivRange::AbuttingWith ( const CEquivRange &  Other ) const

inline

Definition at line 81 of file equiv_range.hpp.

References COpenRange< Position >::AbuttingWith(), Query, Strand, and Subjt.

Referenced by CEquivRangeBuilder::MergeAbuttings().

CalcRelative()

CEquivRange::ERelative CEquivRange::CalcRelative

(

const CEquivRange &

Check

)

const

Definition at line 170 of file equiv_range.cpp.

References eAbove, eAfter, eBefore, eIntersects, Empty(), eNa_strand_minus, eNa_strand_plus, ERR_POST, eUnder, eWtf, CRange_Base::GetFrom(), CRange_Base::GetTo(), Info(), IntersectingWith(), Query, Strand, and Subjt.

Referenced by CMergeTree::x_FindAfters(), CMergeTree::x_FindAfters_Up(), CMergeTree::x_FindBefores(), CMergeTree::x_FindBefores_Up_Iter(), and CMergeTree::x_FindBefores_Up_Recur().

CalcRelativeDuo()

CEquivRange::ERelative CEquivRange::CalcRelativeDuo

(

const CEquivRange &

Check

)

const

Definition at line 243 of file equiv_range.cpp.

References eAbove, eAfter, eBefore, eInterQuery, eIntersects, eInterSubjt, eNa_strand_minus, eNa_strand_plus, eUnder, eWtf, CRange_Base::GetFrom(), CRange_Base::GetTo(), COpenRange< Position >::IntersectingWith(), Query, Strand, and Subjt.

Distance() [1/2]

TSeqPos CEquivRange::Distance ( const CEquivRange &  A, const CEquivRange &  B  )

static

Definition at line 330 of file equiv_range.cpp.

References A, abs, B, D, COpenRange< Position >::Empty(), max(), and SD.

Referenced by CAlignDistGraph::AddAlignment(), CAlignDistGraph::x_CalculateAllDistances(), and CAlignDistGraph::x_CalculateOneDistance().

Distance() [2/2]

TSeqPos CEquivRange::Distance ( const TEquivList &  A, const TEquivList &  B  )

static

Definition at line 359 of file equiv_range.cpp.

References A, abs, B, BSR, D, COpenRange< Position >::Empty(), CRange_Base::GetFrom(), CRange_Base::GetTo(), COpenRange< Position >::IntersectionWith(), ITERATE, max(), and SD.

Empty()

bool CEquivRange::Empty ( ) const

inline

Definition at line 68 of file equiv_range.hpp.

References COpenRange< Position >::Empty(), Query, and Subjt.

Referenced by CalcRelative(), CEquivRangeBuilder::MergeAbuttings(), CMergeTree::x_FindAfters(), CMergeTree::x_FindAfters_Up(), CMergeTree::x_FindBefores(), CMergeTree::x_FindBefores_Up_Iter(), and CMergeTree::x_FindBefores_Up_Recur().

IntersectingWith()

bool CEquivRange::IntersectingWith ( const CEquivRange &  Other ) const

inline

Definition at line 76 of file equiv_range.hpp.

References COpenRange< Position >::IntersectingWith(), Query, and Subjt.

Referenced by CalcRelative().

NotEmpty()

bool CEquivRange::NotEmpty ( ) const

inline

Definition at line 72 of file equiv_range.hpp.

References COpenRange< Position >::NotEmpty(), Query, and Subjt.

Referenced by CEquivRangeBuilder::SplitIntersections().

Member Data Documentation

AlignId

int CEquivRange::AlignId

Definition at line 64 of file equiv_range.hpp.

Referenced by CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CEquivRangeBuilder::Merge(), CEquivRangeBuilder::MergeAbuttings(), CEquivRangeBuilder::SliceOnQuery(), CEquivRangeBuilder::SliceOnSubjt(), CMergeTree::x_Dot_Nodes(), and CMergeTree::x_Search_Iter().

Intercept

int CEquivRange::Intercept

Definition at line 59 of file equiv_range.hpp.

Referenced by CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CEquivRangeBuilder::Merge(), CEquivRangeBuilder::SliceOnQuery(), and CEquivRangeBuilder::SliceOnSubjt().

Matches

int CEquivRange::Matches

Definition at line 60 of file equiv_range.hpp.

Referenced by CEquivRangeBuilder::CalcMatches(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CEquivRangeBuilder::Merge(), CEquivRangeBuilder::SliceOnQuery(), CEquivRangeBuilder::SliceOnSubjt(), CMergeTree::x_Dot_Nodes(), and CMergeTree::x_Search_Recur().

MisMatches

int CEquivRange::MisMatches

Definition at line 61 of file equiv_range.hpp.

Referenced by CEquivRangeBuilder::CalcMatches(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CEquivRangeBuilder::Merge(), CEquivRangeBuilder::SliceOnQuery(), CEquivRangeBuilder::SliceOnSubjt(), and CMergeTree::x_Search_Recur().

MisMatchSubjtPoints

vector<TSeqPos> CEquivRange::MisMatchSubjtPoints

Definition at line 62 of file equiv_range.hpp.

Referenced by CEquivRangeBuilder::CalcMatches(), CEquivRangeBuilder::Merge(), CEquivRangeBuilder::SliceOnQuery(), and CEquivRangeBuilder::SliceOnSubjt().

Query

CRange<TSeqPos> CEquivRange::Query

Definition at line 56 of file equiv_range.hpp.

Referenced by AbuttingWith(), CEquivRangeBuilder::CalcMatches(), CalcRelative(), CalcRelativeDuo(), Empty(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), IntersectingWith(), CEquivRangeBuilder::Merge(), NotEmpty(), CEquivRangeBuilder::SliceOnQuery(), CEquivRangeBuilder::SliceOnSubjt(), CEquivRangeBuilder::SplitIntersections(), CMergeTree::x_Dot_Nodes(), and CMergeTree::x_EvalGap().

SegmtId

int CEquivRange::SegmtId

Definition at line 65 of file equiv_range.hpp.

Referenced by CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CEquivRangeBuilder::Merge(), CEquivRangeBuilder::MergeAbuttings(), CEquivRangeBuilder::SliceOnQuery(), and CEquivRangeBuilder::SliceOnSubjt().

SplitId

int CEquivRange::SplitId

Definition at line 66 of file equiv_range.hpp.

Referenced by CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CEquivRangeBuilder::Merge(), CEquivRangeBuilder::SliceOnQuery(), CEquivRangeBuilder::SliceOnSubjt(), and CMergeTree::x_GetNode().

Strand

objects::ENa_strand CEquivRange::Strand

Definition at line 58 of file equiv_range.hpp.

Referenced by AbuttingWith(), CEquivRangeBuilder::CalcMatches(), CalcRelative(), CalcRelativeDuo(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CEquivRangeBuilder::Merge(), CEquivRangeBuilder::SliceOnQuery(), CEquivRangeBuilder::SliceOnSubjt(), and CMergeTree::x_Dot_Nodes().

Subjt

CRange<TSeqPos> CEquivRange::Subjt

Definition at line 57 of file equiv_range.hpp.

Referenced by AbuttingWith(), CEquivRangeBuilder::CalcMatches(), CalcRelative(), CalcRelativeDuo(), Empty(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), IntersectingWith(), CEquivRangeBuilder::Merge(), NotEmpty(), CEquivRangeBuilder::SliceOnQuery(), CEquivRangeBuilder::SliceOnSubjt(), CEquivRangeBuilder::SplitIntersections(), CMergeTree::x_Dot_Nodes(), and CMergeTree::x_EvalGap().

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

• include/algo/align/mergetree/equiv_range.hpp
• src/algo/align/mergetree/equiv_range.cpp