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

This iterator outputs sequence states for selected species and positions. More...

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

+ Inheritance diagram for bpp::TableOutputMafIterator:
+ Collaboration diagram for bpp::TableOutputMafIterator:

Public Member Functions

 TableOutputMafIterator (MafIterator *iterator, std::ostream *out, const std::vector< std::string > &species, const std::string &reference)
 Build a new TableOutputMafIterator object. More...
 
MafBlock * analyseCurrentBlock_ ()
 
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)
 

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

 TableOutputMafIterator (const TableOutputMafIterator &iterator)
 
TableOutputMafIterator & operator= (const TableOutputMafIterator &iterator)
 
void writeBlock_ (std::ostream &out, const MafBlock &block)
 

Private Attributes

std::ostream * output_
 
std::vector< std::string > species_
 
std::string refSpecies_
 

Detailed Description

This iterator outputs sequence states for selected species and positions.

Definition at line 55 of file TableOutputMafIterator.h.

Constructor & Destructor Documentation

◆ TableOutputMafIterator() [1/2]

bpp::TableOutputMafIterator::TableOutputMafIterator ( MafIterator *  iterator,
std::ostream *  out,
const std::vector< std::string > &  species,
const std::string &  reference 
)
inline

Build a new TableOutputMafIterator object.

Parameters
iteratorThe input iterator.
outThe output stream where to write the table file.
speciesA list of species for which sequence content should be output (one column per selected species). In case one species is duplicated in a block, the first sequence will be used.
referenceThe species to use as a reference for coordinates. It does not have to be one of the selected species for output.

Definition at line 74 of file TableOutputMafIterator.h.

References output_.

◆ TableOutputMafIterator() [2/2]

bpp::TableOutputMafIterator::TableOutputMafIterator ( const TableOutputMafIterator &  iterator)
inlineprivate

Definition at line 90 of file TableOutputMafIterator.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::TableOutputMafIterator::analyseCurrentBlock_ ( )
inlinevirtual

Implements bpp::AbstractMafIterator.

Definition at line 107 of file TableOutputMafIterator.h.

References bpp::AbstractFilterMafIterator::currentBlock_, bpp::AbstractFilterMafIterator::iterator_, bpp::MafIterator::nextBlock(), output_, and writeBlock_().

◆ 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=()

TableOutputMafIterator& bpp::TableOutputMafIterator::operator= ( const TableOutputMafIterator &  iterator)
inlineprivate

Definition at line 97 of file TableOutputMafIterator.h.

References output_, refSpecies_, and species_.

◆ 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_.

◆ writeBlock_()

void TableOutputMafIterator::writeBlock_ ( std::ostream &  out,
const MafBlock &  block 
)
private

Definition at line 57 of file TableOutputMafIterator.cpp.

References bpp::MafSequence::getChromosome(), bpp::MafBlock::getNumberOfSites(), bpp::MafBlock::getSequenceForSpecies(), bpp::MafBlock::hasSequenceForSpecies(), bpp::SequenceWithAnnotation::toString(), and bpp::TextTools::toString().

Referenced by analyseCurrentBlock_().

Member Data Documentation

◆ 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_(), 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_(), analyseCurrentBlock_(), bpp::VcfOutputMafIterator::analyseCurrentBlock_(), and bpp::AbstractFilterMafIterator::operator=().

◆ 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().

◆ output_

std::ostream* bpp::TableOutputMafIterator::output_
private

Definition at line 59 of file TableOutputMafIterator.h.

Referenced by analyseCurrentBlock_(), operator=(), and TableOutputMafIterator().

◆ refSpecies_

std::string bpp::TableOutputMafIterator::refSpecies_
private

Definition at line 61 of file TableOutputMafIterator.h.

Referenced by operator=().

◆ species_

std::vector<std::string> bpp::TableOutputMafIterator::species_
private

Definition at line 60 of file TableOutputMafIterator.h.

Referenced by operator=().

◆ 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().

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