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:

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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
SuperIntervaloperator= (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

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.


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.


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().


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().


The documentation for this class was generated from the following files:
Generated on Fri Mar 14 06:01:44 2008 for libMems by doxygen 1.3.6