AlignedRegion Class Reference

represents a region in a sequence alignment More...

#include <aligned_region.hh>

Public Types

typedef AlignedColumnIterator iterator

Public Member Functions

 AlignedRegion (const AlignmentHandle &aln, int start, int end, int master=-1)
int GetEnd () const
int GetStart () const
int GetMaster () const
void SetMaster (int master)
void Delete ()
void Replace (const AlignedRegion &aln_r)
void ShiftLeft (int n)
void ShiftRight (int n)
int GetLength () const
AlignmentHandle GetAlignmentHandle () const
AlignedColumn operator[] (int index) const
AlignedColumnIterator begin ()
AlignedColumnIterator end ()
bool operator== (const AlignedRegion &rhs) const
bool operator!= (const AlignedRegion &rhs) const

Detailed Description

represents a region in a sequence alignment

The region covers the half-closed interval start/stop.

You should never need to construct an aligned region manually. Use one of the helper methods of AlignmentHandle.

Definition at line 38 of file aligned_region.hh.

Member Typedef Documentation

Definition at line 40 of file aligned_region.hh.

Constructor & Destructor Documentation

AlignedRegion ( const AlignmentHandle aln,
int  start,
int  end,
int  master = -1 

Member Function Documentation

AlignedColumnIterator begin (  ) 

iterator pointing at start of aligned region

void Delete (  ) 

delete interval and update length of AlignedRegion

AlignedColumnIterator end (  ) 

iterator pointing at end of aligned region.

AlignmentHandle GetAlignmentHandle (  )  const

retrieve alignment handle for aligned region

int GetEnd (  )  const

get end of aligned region

int GetLength (  )  const

length of the aligned region

See also:
int GetMaster (  )  const
int GetStart (  )  const

get start of aligned region

bool operator!= ( const AlignedRegion rhs  )  const
bool operator== ( const AlignedRegion rhs  )  const
AlignedColumn operator[] ( int  index  )  const

get aligned column at given index

The indices range from 0 to GetLength()-1.

void Replace ( const AlignedRegion aln_r  ) 

replace region with content of AlignedRegion and set length to length of aln_r

void SetMaster ( int  master  ) 
void ShiftLeft ( int  n  ) 

shift the aligned region of the master sequence to the left by n characters.

void ShiftRight ( int  n  ) 

shift the aligned region of the master sequence to the right by n characters.

See also:

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