Filter maf blocks to keep a subset of sequences, given their name. this filter can also be used to filter block which contain a certain set of sequences. More...
#include <Bpp/Seq/Io/Maf/SequenceFilterMafIterator.h>
Inheritance diagram for bpp::SequenceFilterMafIterator:
Collaboration diagram for bpp::SequenceFilterMafIterator:
Public Member Functions | |
| SequenceFilterMafIterator (MafIterator *iterator, const std::vector< std::string > &species, bool strict=false, bool keep=false, bool rmDuplicates=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) |
Protected Member Functions | |
| virtual void | fireIterationStartSignal_ () |
| virtual void | fireIterationMoveSignal_ (const MafBlock ¤tBlock) |
| 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 | |
| SequenceFilterMafIterator (const SequenceFilterMafIterator &iterator) | |
| SequenceFilterMafIterator & | operator= (const SequenceFilterMafIterator &iterator) |
| MafBlock * | analyseCurrentBlock_ () |
Private Attributes | |
| std::vector< std::string > | species_ |
| bool | strict_ |
| bool | keep_ |
| bool | rmDuplicates_ |
Detailed Description
Filter maf blocks to keep a subset of sequences, given their name. this filter can also be used to filter block which contain a certain set of sequences.
Typical usage:
- strict=yes, keep=no: extract the species from the list, only if all of them are present in a block.
- strict=no, keep=no: extract the species from the list, at least the one which are there.
- strict=yes, keep=yes: filter blocks to retain only the ones that contain at least all species from the list. Blocks that are empty after the filtering are removed.
Definition at line 62 of file SequenceFilterMafIterator.h.
Constructor & Destructor Documentation
◆ SequenceFilterMafIterator() [1/2]
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inline |
- Parameters
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iterator The input iterator. species The list of species names to be retained. strict If true, then block that do not contain all species will be discarded. keep If true, sequences not in the selection will be kept. rmDuplicates If true, block that contain more than one instance for at least one species will be discarded.
Definition at line 79 of file SequenceFilterMafIterator.h.
◆ SequenceFilterMafIterator() [2/2]
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inlineprivate |
Definition at line 88 of file SequenceFilterMafIterator.h.
Member Function Documentation
◆ addIterationListener()
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inlinevirtualinherited |
Implements bpp::MafIterator.
Definition at line 99 of file MafIterator.h.
References bpp::AbstractMafIterator::iterationListeners_.
◆ analyseCurrentBlock_()
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privatevirtual |
Implements bpp::AbstractMafIterator.
Definition at line 50 of file SequenceFilterMafIterator.cpp.
References bpp::VectorTools::contains(), bpp::MafBlock::getSequence(), and bpp::MafSequence::getSpecies().
◆ fireIterationMoveSignal_()
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protectedvirtualinherited |
Definition at line 57 of file MafIterator.cpp.
Referenced by bpp::AbstractMafIterator::nextBlock().
◆ fireIterationStartSignal_()
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protectedvirtualinherited |
Definition at line 51 of file MafIterator.cpp.
Referenced by bpp::AbstractMafIterator::nextBlock().
◆ fireIterationStopSignal_()
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protectedvirtualinherited |
Definition at line 63 of file MafIterator.cpp.
Referenced by bpp::AbstractMafIterator::nextBlock().
◆ isVerbose()
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inlinevirtualinherited |
Implements bpp::MafIterator.
Definition at line 116 of file MafIterator.h.
References bpp::AbstractMafIterator::verbose_.
◆ nextBlock()
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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=()
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inlineprivate |
Definition at line 96 of file SequenceFilterMafIterator.h.
References keep_, rmDuplicates_, species_, and strict_.
◆ setLogStream()
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inlineinherited |
Definition at line 178 of file MafIterator.h.
References bpp::AbstractFilterMafIterator::logstream_.
◆ setVerbose()
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inlinevirtualinherited |
Implements bpp::MafIterator.
Definition at line 117 of file MafIterator.h.
References bpp::AbstractMafIterator::verbose_.
Member Data Documentation
◆ currentBlock_
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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_
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protectedinherited |
Definition at line 89 of file MafIterator.h.
Referenced by bpp::AbstractMafIterator::addIterationListener().
◆ iterator_
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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=().
◆ keep_
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private |
Definition at line 68 of file SequenceFilterMafIterator.h.
Referenced by operator=().
◆ logstream_
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protectedinherited |
Definition at line 155 of file MafIterator.h.
Referenced by bpp::BlockLengthMafIterator::analyseCurrentBlock_(), bpp::BlockSizeMafIterator::analyseCurrentBlock_(), bpp::AbstractFilterMafIterator::operator=(), and bpp::AbstractFilterMafIterator::setLogStream().
◆ rmDuplicates_
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private |
Definition at line 69 of file SequenceFilterMafIterator.h.
Referenced by operator=().
◆ species_
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private |
Definition at line 66 of file SequenceFilterMafIterator.h.
Referenced by operator=().
◆ started_
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protectedinherited |
Definition at line 90 of file MafIterator.h.
Referenced by bpp::AbstractMafIterator::nextBlock().
◆ strict_
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private |
Definition at line 67 of file SequenceFilterMafIterator.h.
Referenced by operator=().
◆ verbose_
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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:
- Bpp/Seq/Io/Maf/SequenceFilterMafIterator.h
- Bpp/Seq/Io/Maf/SequenceFilterMafIterator.cpp
