mems::SuperInterval Class Reference

A class that stores an alignment and coordinate mapping between collinear segments of an ancestral genome and two descendant genomes. More...

#include <SuperInterval.h>

Collaboration diagram for mems::SuperInterval:

[legend]List of all members.

Public Member Functions
void	CropLeft (gnSeqI amount)
void	CropRight (gnSeqI amount)
virtual int64	LeftEnd () const
virtual gnSeqI	Length () const
	Returns the length.
bool	operator< (const SuperInterval &si) const
SuperInterval &	operator= (const SuperInterval &siv)
virtual void	SetLeftEnd (const int64 &left_end)
virtual void	SetLength (gnSeqI len)
	Sets the length of this match to.
	SuperInterval (const SuperInterval &siv)
	SuperInterval (const mems::Interval &reference_iv)
	Creates a new SuperInterval.
	SuperInterval ()
void	swap (SuperInterval &other)
void	ValidateSelf () const
	~SuperInterval ()
Public Attributes
size_t	c1_siv
	the index of the SuperInterval this is aligned to in c1
size_t	c2_siv
	the index of the SuperInterval this is aligned to in c2
size_t	parent_siv
	the index of the SuperInterval this is aligned to in the parent
mems::Interval	reference_iv
Protected Attributes
int64	left_end
int64	length

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Detailed Description

A class that stores an alignment and coordinate mapping between collinear segments of an ancestral genome and two descendant genomes.

Definition at line 16 of file SuperInterval.h.

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Constructor & Destructor Documentation

mems::SuperInterval::SuperInterval (   )

Definition at line 16 of file SuperInterval.cpp.

mems::SuperInterval::SuperInterval (  const mems::Interval &  reference_iv  )

Creates a new SuperInterval. Definition at line 24 of file SuperInterval.cpp. References mems::Interval.

mems::SuperInterval::SuperInterval (  const SuperInterval &  siv  )

Definition at line 34 of file SuperInterval.cpp.

mems::SuperInterval::~SuperInterval (   )  [inline]

Definition at line 27 of file SuperInterval.h.

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Member Function Documentation

void mems::SuperInterval::CropLeft (  gnSeqI  amount  )

Definition at line 62 of file SuperInterval.cpp. References mems::GenericInterval< GappedBaseImpl >::CropStart(), mems::debug_aligner, reference_iv, and ValidateSelf(). Referenced by mems::SuperIntervalManipulator::CropLeft().

void mems::SuperInterval::CropRight (  gnSeqI  amount  )

Definition at line 73 of file SuperInterval.cpp. References mems::GenericInterval< GappedBaseImpl >::CropEnd(), mems::debug_aligner, reference_iv, and ValidateSelf(). Referenced by mems::SuperIntervalManipulator::CropRight().

virtual int64 mems::SuperInterval::LeftEnd (   )  const [inline, virtual]

Definition at line 35 of file SuperInterval.h. Referenced by mems::ProgressiveAligner::extractAlignment(), mems::ProgressiveAligner::FixLeftEnds(), and mems::SuperIntervalManipulator::LeftEnd().

virtual gnSeqI mems::SuperInterval::Length (   )  const [inline, virtual]

Returns the length. Definition at line 30 of file SuperInterval.h. Referenced by mems::ProgressiveAligner::extractAlignment(), mems::ProgressiveAligner::FixLeftEnds(), mems::SuperIntervalManipulator::Length(), and ValidateSelf().

bool mems::SuperInterval::operator< (  const SuperInterval &  si  )  const [inline]

Definition at line 51 of file SuperInterval.h. References left_end.

SuperInterval & mems::SuperInterval::operator= (  const SuperInterval &  siv  )

Definition at line 43 of file SuperInterval.cpp. References c1_siv, c2_siv, left_end, length, parent_siv, and reference_iv.

virtual void mems::SuperInterval::SetLeftEnd (  const int64 &  left_end  )  [inline, virtual]

Definition at line 37 of file SuperInterval.h. Referenced by mems::makeAlignmentTree().

void mems::SuperInterval::SetLength (  gnSeqI  len  )  [virtual]

Sets the length of this match to. Parameters: len  Definition at line 57 of file SuperInterval.cpp. Referenced by mems::makeAlignmentTree().

void mems::SuperInterval::swap (  SuperInterval &  other  )  [inline]

Definition at line 55 of file SuperInterval.h. References c1_siv, c2_siv, left_end, length, parent_siv, reference_iv, std::swap(), and mems::GenericInterval< GappedBaseImpl >::swap(). Referenced by std::swap().

void mems::SuperInterval::ValidateSelf (   )  const

Definition at line 82 of file SuperInterval.cpp. References mems::GenericInterval< GappedBaseImpl >::GetAlignment(), mems::GenericInterval< GappedBaseImpl >::GetMatches(), Length(), and reference_iv. Referenced by CropLeft(), and CropRight().

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Member Data Documentation

size_t mems::SuperInterval::c1_siv

the index of the SuperInterval this is aligned to in c1 Definition at line 42 of file SuperInterval.h. Referenced by operator=(), and swap().

size_t mems::SuperInterval::c2_siv

the index of the SuperInterval this is aligned to in c2 Definition at line 44 of file SuperInterval.h. Referenced by operator=(), and swap().

int64 mems::SuperInterval::left_end [protected]

Definition at line 66 of file SuperInterval.h. Referenced by operator<(), operator=(), and swap().

int64 mems::SuperInterval::length [protected]

Definition at line 67 of file SuperInterval.h. Referenced by operator=(), and swap().

size_t mems::SuperInterval::parent_siv

the index of the SuperInterval this is aligned to in the parent Definition at line 46 of file SuperInterval.h. Referenced by operator=(), and swap().

mems::Interval mems::SuperInterval::reference_iv

Definition at line 39 of file SuperInterval.h. Referenced by CropLeft(), CropRight(), operator=(), swap(), and ValidateSelf().

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

• libMems/SuperInterval.h
• libMems/SuperInterval.cpp

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