bpp::AlignmentFilter2MafIterator Class Reference

Filter maf blocks to remove ambiguously aligned or non-informative regions. More...

#include <Bpp/Seq/Io/MafIterator.h>

Inheritance diagram for bpp::AlignmentFilter2MafIterator:
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List of all members.

Public Member Functions

 AlignmentFilter2MafIterator (MafIterator *iterator, const std::vector< std::string > &species, unsigned int windowSize, unsigned int step, unsigned int maxGap, unsigned int maxPos, bool keepTrashedBlocks)
MafBlocknextBlock () throw (Exception)
 Get the next available alignment block.
MafBlocknextRemovedBlock () throw (Exception)
 Get the next available removed alignment block.
void setLogStream (OutputStream *logstream)
bool verbose () const
void verbose (bool yn)

Protected Attributes

MafIteratoriterator_
OutputStreamlogstream_
bool verbose_

Private Attributes

std::vector< std::string > species_
unsigned int windowSize_
unsigned int step_
unsigned int maxGap_
unsigned int maxPos_
std::deque< MafBlock * > blockBuffer_
std::deque< MafBlock * > trashBuffer_
std::deque< std::vector< bool > > window_
bool keepTrashedBlocks_

Detailed Description

Filter maf blocks to remove ambiguously aligned or non-informative regions.

This iterators offers a different algorithm than AlignmentFilterMafIterator. It takes two parameters: g=maxGap and n=maxPos. windows with at more than n positions containing each of them more than g=maxPos gaps will be discarded. In addition, consecutives patterns are only counted once.

Definition at line 668 of file MafIterator.h.


Constructor & Destructor Documentation

bpp::AlignmentFilter2MafIterator::AlignmentFilter2MafIterator ( MafIterator iterator,
const std::vector< std::string > &  species,
unsigned int  windowSize,
unsigned int  step,
unsigned int  maxGap,
unsigned int  maxPos,
bool  keepTrashedBlocks 
) [inline]

Definition at line 684 of file MafIterator.h.


Member Function Documentation

MafBlock * AlignmentFilter2MafIterator::nextBlock (  )  throw (Exception) [virtual]
MafBlock* bpp::AlignmentFilter2MafIterator::nextRemovedBlock (  )  throw (Exception) [inline, virtual]

Get the next available removed alignment block.

Returns:
A maf alignment block, or a null pointer if no more block is available.

Implements bpp::MafTrashIterator.

Definition at line 700 of file MafIterator.h.

void bpp::AbstractFilterMafIterator::setLogStream ( OutputStream logstream  )  [inline, inherited]

Definition at line 341 of file MafIterator.h.

void bpp::AbstractFilterMafIterator::verbose ( bool  yn  )  [inline, inherited]

Definition at line 343 of file MafIterator.h.

bool bpp::AbstractFilterMafIterator::verbose (  )  const [inline, inherited]

Definition at line 342 of file MafIterator.h.


Member Data Documentation

Definition at line 678 of file MafIterator.h.

Referenced by nextBlock().

Definition at line 681 of file MafIterator.h.

Referenced by nextBlock().

Definition at line 676 of file MafIterator.h.

Referenced by nextBlock().

Definition at line 677 of file MafIterator.h.

Referenced by nextBlock().

std::vector<std::string> bpp::AlignmentFilter2MafIterator::species_ [private]

Definition at line 673 of file MafIterator.h.

Referenced by nextBlock().

Definition at line 675 of file MafIterator.h.

Referenced by nextBlock().

Definition at line 679 of file MafIterator.h.

Referenced by nextBlock().

bool bpp::AbstractFilterMafIterator::verbose_ [protected, inherited]
std::deque< std::vector<bool> > bpp::AlignmentFilter2MafIterator::window_ [private]

Definition at line 680 of file MafIterator.h.

Referenced by nextBlock().

Definition at line 674 of file MafIterator.h.

Referenced by nextBlock().


The documentation for this class was generated from the following files:
Generated on Wed Feb 29 14:50:40 2012 for bpp-seq by  doxygen 1.6.3