bpp-seq-omics  2.4.1
bpp::OrderFilterMafIterator Class Reference

This iterator check that blocks are ordered according to a reference sequence. More...

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

+ Inheritance diagram for bpp::OrderFilterMafIterator:
+ Collaboration diagram for bpp::OrderFilterMafIterator:

Public Member Functions

 OrderFilterMafIterator (MafIterator *iterator, const std::string &reference, bool unsortedBlockDiscarded=true, bool unsortedBlockThrowsException=false, bool overlappingBlockDiscarded=true, bool overlappingBlockThrowsException=false)
 Build a new OrderFilterMafIterator object. More...
 
MafBlockanalyseCurrentBlock_ ()
 
void setLogStream (std::shared_ptr< OutputStream > logstream)
 
void addIterationListener (IterationListener *listener)
 
MafBlocknextBlock ()
 Get the next available alignment block. More...
 
bool isVerbose () const
 
void setVerbose (bool yn)
 

Protected Member Functions

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

Protected Attributes

MafIteratoriterator_
 
MafBlockcurrentBlock_
 
std::shared_ptr< OutputStreamlogstream_
 
std::vector< IterationListener * > iterationListeners_
 
bool started_
 
bool verbose_
 

Private Member Functions

 OrderFilterMafIterator (const OrderFilterMafIterator &iterator)
 
OrderFilterMafIteratoroperator= (const OrderFilterMafIterator &iterator)
 
bool parseBlock_ (const MafBlock &block)
 

Private Attributes

std::string refSpecies_
 
std::string currentChr_
 
size_t previousBlockStart_
 
size_t previousBlockStop_
 
bool unsortedBlockDiscarded_
 
bool unsortedBlockThrowsException_
 
bool overlappingBlockDiscarded_
 
bool overlappingBlockThrowsException_
 

Detailed Description

This iterator check that blocks are ordered according to a reference sequence.

The occurrence of overlapping or unordered blocks result in an error message. Alternatively, conflicting blocks can be discarded.

Definition at line 58 of file OrderFilterMafIterator.h.

Constructor & Destructor Documentation

◆ OrderFilterMafIterator() [1/2]

bpp::OrderFilterMafIterator::OrderFilterMafIterator ( MafIterator iterator,
const std::string &  reference,
bool  unsortedBlockDiscarded = true,
bool  unsortedBlockThrowsException = false,
bool  overlappingBlockDiscarded = true,
bool  overlappingBlockThrowsException = false 
)
inline

Build a new OrderFilterMafIterator object.

Parameters
iteratorThe input iterator.
referenceThe species to use as a reference for coordinates.
unsortedBlockDiscardedTell is unsorted blocks should be discarded
unsortedBlockThrowsExceptionTell is unsorted blocks should throw an exception
overlappingBlockDiscardedTell is overlapping blocks should be discarded
overlappingBlockThrowsExceptionTell is overlapping blocks should throw an exception

Definition at line 82 of file OrderFilterMafIterator.h.

◆ OrderFilterMafIterator() [2/2]

bpp::OrderFilterMafIterator::OrderFilterMafIterator ( const OrderFilterMafIterator iterator)
inlineprivate

Definition at line 100 of file OrderFilterMafIterator.h.

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* bpp::OrderFilterMafIterator::analyseCurrentBlock_ ( )
inlinevirtual

◆ 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_.

◆ operator=()

◆ parseBlock_()

◆ 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

◆ currentBlock_

◆ currentChr_

std::string bpp::OrderFilterMafIterator::currentChr_
private

Definition at line 63 of file OrderFilterMafIterator.h.

Referenced by operator=().

◆ iterationListeners_

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

Definition at line 89 of file MafIterator.h.

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

◆ iterator_

◆ logstream_

◆ overlappingBlockDiscarded_

bool bpp::OrderFilterMafIterator::overlappingBlockDiscarded_
private

Definition at line 68 of file OrderFilterMafIterator.h.

Referenced by operator=().

◆ overlappingBlockThrowsException_

bool bpp::OrderFilterMafIterator::overlappingBlockThrowsException_
private

Definition at line 69 of file OrderFilterMafIterator.h.

Referenced by operator=().

◆ previousBlockStart_

size_t bpp::OrderFilterMafIterator::previousBlockStart_
private

Definition at line 64 of file OrderFilterMafIterator.h.

Referenced by operator=().

◆ previousBlockStop_

size_t bpp::OrderFilterMafIterator::previousBlockStop_
private

Definition at line 65 of file OrderFilterMafIterator.h.

Referenced by operator=().

◆ refSpecies_

std::string bpp::OrderFilterMafIterator::refSpecies_
private

Definition at line 62 of file OrderFilterMafIterator.h.

Referenced by operator=().

◆ started_

bool bpp::AbstractMafIterator::started_
protectedinherited

Definition at line 90 of file MafIterator.h.

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

◆ unsortedBlockDiscarded_

bool bpp::OrderFilterMafIterator::unsortedBlockDiscarded_
private

Definition at line 66 of file OrderFilterMafIterator.h.

Referenced by operator=().

◆ unsortedBlockThrowsException_

bool bpp::OrderFilterMafIterator::unsortedBlockThrowsException_
private

Definition at line 67 of file OrderFilterMafIterator.h.

Referenced by operator=().

◆ verbose_

bool bpp::AbstractMafIterator::verbose_
protectedinherited

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