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Public Types | Public Member Functions
AlignedRegion Class Reference

#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

iterator pointing at start of aligned region

void Delete ( )

delete interval and update length of AlignedRegion

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
AlignmentHandle::GetLength()
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

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