bpp-seq-omics  2.4.1
Public Member Functions | Static Public Attributes | Protected Member Functions | Protected Attributes | Private Member Functions | Private Attributes | List of all members
bpp::WindowSplitMafIterator Class Reference

Splits block into windows of given sizes. More...

#include <Bpp/Seq/Io/Maf/WindowSplitMafIterator.h>

+ Inheritance diagram for bpp::WindowSplitMafIterator:
+ Collaboration diagram for bpp::WindowSplitMafIterator:

Public Member Functions

 WindowSplitMafIterator (MafIterator *iterator, size_t windowSize, size_t windowStep, short splitOption=CENTER, bool keepSmallBlocks=false)
 
void setLogStream (std::shared_ptr< OutputStream > logstream)
 
void addIterationListener (IterationListener *listener)
 
MafBlock * nextBlock ()
 Get the next available alignment block. More...
 
bool isVerbose () const
 
void setVerbose (bool yn)
 

Static Public Attributes

static const short RAGGED_LEFT = 0
 
static const short RAGGED_RIGHT = 1
 
static const short CENTER = 2
 
static const short ADJUST = 3
 

Protected Member Functions

virtual void fireIterationStartSignal_ ()
 
virtual void fireIterationMoveSignal_ (const MafBlock &currentBlock)
 
virtual void fireIterationStopSignal_ ()
 

Protected Attributes

MafIterator * iterator_
 
MafBlock * currentBlock_
 
std::shared_ptr< OutputStream > logstream_
 
std::vector< IterationListener * > iterationListeners_
 
bool started_
 
bool verbose_
 

Private Member Functions

MafBlock * analyseCurrentBlock_ ()
 

Private Attributes

size_t windowSize_
 
size_t windowStep_
 
short align_
 
std::deque< MafBlock * > blockBuffer_
 
bool keepSmallBlocks_
 

Detailed Description

Splits block into windows of given sizes.

Definition at line 55 of file WindowSplitMafIterator.h.

Constructor & Destructor Documentation

◆ WindowSplitMafIterator()

bpp::WindowSplitMafIterator::WindowSplitMafIterator ( MafIterator *  iterator,
size_t  windowSize,
size_t  windowStep,
short  splitOption = CENTER,
bool  keepSmallBlocks = false 
)
inline

Definition at line 72 of file WindowSplitMafIterator.h.

References ADJUST, CENTER, RAGGED_LEFT, RAGGED_RIGHT, and bpp::TextTools::toString().

Member Function Documentation

◆ addIterationListener()

void bpp::AbstractMafIterator::addIterationListener ( IterationListener *  listener)
inlinevirtualinherited

Implements bpp::MafIterator.

Definition at line 99 of file MafIterator.h.

References bpp::AbstractMafIterator::iterationListeners_.

◆ analyseCurrentBlock_()

MafBlock * WindowSplitMafIterator::analyseCurrentBlock_ ( )
privatevirtual

Implements bpp::AbstractMafIterator.

Definition at line 55 of file WindowSplitMafIterator.cpp.

References bpp::MafBlock::addSequence(), bpp::MafBlock::getNumberOfSequences(), bpp::MafBlock::getNumberOfSites(), bpp::MafBlock::getPass(), bpp::MafBlock::getScore(), bpp::MafBlock::getSequence(), bpp::MafBlock::setPass(), bpp::MafBlock::setScore(), and bpp::MafSequence::subSequence().

◆ fireIterationMoveSignal_()

void AbstractMafIterator::fireIterationMoveSignal_ ( const MafBlock &  currentBlock)
protectedvirtualinherited

Definition at line 57 of file MafIterator.cpp.

Referenced by bpp::AbstractMafIterator::nextBlock().

◆ fireIterationStartSignal_()

void AbstractMafIterator::fireIterationStartSignal_ ( )
protectedvirtualinherited

Definition at line 51 of file MafIterator.cpp.

Referenced by bpp::AbstractMafIterator::nextBlock().

◆ fireIterationStopSignal_()

void AbstractMafIterator::fireIterationStopSignal_ ( )
protectedvirtualinherited

Definition at line 63 of file MafIterator.cpp.

Referenced by bpp::AbstractMafIterator::nextBlock().

◆ isVerbose()

bool bpp::AbstractMafIterator::isVerbose ( ) const
inlinevirtualinherited

Implements bpp::MafIterator.

Definition at line 116 of file MafIterator.h.

References bpp::AbstractMafIterator::verbose_.

◆ nextBlock()

MafBlock* bpp::AbstractMafIterator::nextBlock ( )
inlinevirtualinherited

Get the next available alignment block.

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

Implements bpp::MafIterator.

Definition at line 103 of file MafIterator.h.

References bpp::AbstractMafIterator::analyseCurrentBlock_(), bpp::AbstractMafIterator::fireIterationMoveSignal_(), bpp::AbstractMafIterator::fireIterationStartSignal_(), bpp::AbstractMafIterator::fireIterationStopSignal_(), and bpp::AbstractMafIterator::started_.

◆ setLogStream()

void bpp::AbstractFilterMafIterator::setLogStream ( std::shared_ptr< OutputStream >  logstream)
inlineinherited

Definition at line 178 of file MafIterator.h.

References bpp::AbstractFilterMafIterator::logstream_.

◆ setVerbose()

void bpp::AbstractMafIterator::setVerbose ( bool  yn)
inlinevirtualinherited

Implements bpp::MafIterator.

Definition at line 117 of file MafIterator.h.

References bpp::AbstractMafIterator::verbose_.

Member Data Documentation

◆ ADJUST

const short WindowSplitMafIterator::ADJUST = 3
static

Definition at line 69 of file WindowSplitMafIterator.h.

Referenced by WindowSplitMafIterator().

◆ align_

short bpp::WindowSplitMafIterator::align_
private

Definition at line 61 of file WindowSplitMafIterator.h.

◆ blockBuffer_

std::deque<MafBlock*> bpp::WindowSplitMafIterator::blockBuffer_
private

Definition at line 62 of file WindowSplitMafIterator.h.

◆ CENTER

const short WindowSplitMafIterator::CENTER = 2
static

Definition at line 68 of file WindowSplitMafIterator.h.

Referenced by WindowSplitMafIterator().

◆ currentBlock_

MafBlock* bpp::AbstractFilterMafIterator::currentBlock_
protectedinherited

Definition at line 154 of file MafIterator.h.

Referenced by bpp::BlockLengthMafIterator::analyseCurrentBlock_(), bpp::BlockSizeMafIterator::analyseCurrentBlock_(), bpp::MafIteratorSynchronizer::analyseCurrentBlock_(), bpp::MsmcOutputMafIterator::analyseCurrentBlock_(), bpp::OrderFilterMafIterator::analyseCurrentBlock_(), bpp::OutputMafIterator::analyseCurrentBlock_(), bpp::PlinkOutputMafIterator::analyseCurrentBlock_(), bpp::SequenceStatisticsMafIterator::analyseCurrentBlock_(), bpp::TableOutputMafIterator::analyseCurrentBlock_(), bpp::VcfOutputMafIterator::analyseCurrentBlock_(), and bpp::AbstractFilterMafIterator::operator=().

◆ iterationListeners_

std::vector<IterationListener*> bpp::AbstractMafIterator::iterationListeners_
protectedinherited

Definition at line 89 of file MafIterator.h.

Referenced by bpp::AbstractMafIterator::addIterationListener().

◆ iterator_

MafIterator* bpp::AbstractFilterMafIterator::iterator_
protectedinherited

Definition at line 153 of file MafIterator.h.

Referenced by bpp::BlockLengthMafIterator::analyseCurrentBlock_(), bpp::BlockSizeMafIterator::analyseCurrentBlock_(), bpp::MafIteratorSynchronizer::analyseCurrentBlock_(), bpp::MsmcOutputMafIterator::analyseCurrentBlock_(), bpp::OrderFilterMafIterator::analyseCurrentBlock_(), bpp::OutputMafIterator::analyseCurrentBlock_(), bpp::PlinkOutputMafIterator::analyseCurrentBlock_(), bpp::SequenceStatisticsMafIterator::analyseCurrentBlock_(), bpp::TableOutputMafIterator::analyseCurrentBlock_(), bpp::VcfOutputMafIterator::analyseCurrentBlock_(), and bpp::AbstractFilterMafIterator::operator=().

◆ keepSmallBlocks_

bool bpp::WindowSplitMafIterator::keepSmallBlocks_
private

Definition at line 63 of file WindowSplitMafIterator.h.

◆ logstream_

std::shared_ptr<OutputStream> bpp::AbstractFilterMafIterator::logstream_
protectedinherited

Definition at line 155 of file MafIterator.h.

Referenced by bpp::BlockLengthMafIterator::analyseCurrentBlock_(), bpp::BlockSizeMafIterator::analyseCurrentBlock_(), bpp::AbstractFilterMafIterator::operator=(), and bpp::AbstractFilterMafIterator::setLogStream().

◆ RAGGED_LEFT

const short WindowSplitMafIterator::RAGGED_LEFT = 0
static

Definition at line 66 of file WindowSplitMafIterator.h.

Referenced by WindowSplitMafIterator().

◆ RAGGED_RIGHT

const short WindowSplitMafIterator::RAGGED_RIGHT = 1
static

Definition at line 67 of file WindowSplitMafIterator.h.

Referenced by WindowSplitMafIterator().

◆ started_

bool bpp::AbstractMafIterator::started_
protectedinherited

Definition at line 90 of file MafIterator.h.

Referenced by bpp::AbstractMafIterator::nextBlock().

◆ verbose_

bool bpp::AbstractMafIterator::verbose_
protectedinherited

Definition at line 91 of file MafIterator.h.

Referenced by bpp::AbstractMafIterator::isVerbose(), and bpp::AbstractMafIterator::setVerbose().

◆ windowSize_

size_t bpp::WindowSplitMafIterator::windowSize_
private

Definition at line 59 of file WindowSplitMafIterator.h.

◆ windowStep_

size_t bpp::WindowSplitMafIterator::windowStep_
private

Definition at line 60 of file WindowSplitMafIterator.h.

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