bpp-seq-omics
2.4.1
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This iterator check that blocks are ordered according to a reference sequence. More...
#include <Bpp/Seq/Io/Maf/OrderFilterMafIterator.h>
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... | |
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 ¤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 | |
OrderFilterMafIterator (const OrderFilterMafIterator &iterator) | |
OrderFilterMafIterator & | operator= (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_ |
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.
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inline |
Build a new OrderFilterMafIterator object.
iterator | The input iterator. |
reference | The species to use as a reference for coordinates. |
unsortedBlockDiscarded | Tell is unsorted blocks should be discarded |
unsortedBlockThrowsException | Tell is unsorted blocks should throw an exception |
overlappingBlockDiscarded | Tell is overlapping blocks should be discarded |
overlappingBlockThrowsException | Tell is overlapping blocks should throw an exception |
Definition at line 82 of file OrderFilterMafIterator.h.
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inlineprivate |
Definition at line 100 of file OrderFilterMafIterator.h.
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inlinevirtualinherited |
Implements bpp::MafIterator.
Definition at line 99 of file MafIterator.h.
References bpp::AbstractMafIterator::iterationListeners_.
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inlinevirtual |
Implements bpp::AbstractMafIterator.
Definition at line 127 of file OrderFilterMafIterator.h.
References bpp::AbstractFilterMafIterator::currentBlock_, bpp::AbstractFilterMafIterator::iterator_, bpp::MafIterator::nextBlock(), and parseBlock_().
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protectedvirtualinherited |
Definition at line 57 of file MafIterator.cpp.
Referenced by bpp::AbstractMafIterator::nextBlock().
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protectedvirtualinherited |
Definition at line 51 of file MafIterator.cpp.
Referenced by bpp::AbstractMafIterator::nextBlock().
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protectedvirtualinherited |
Definition at line 63 of file MafIterator.cpp.
Referenced by bpp::AbstractMafIterator::nextBlock().
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inlinevirtualinherited |
Implements bpp::MafIterator.
Definition at line 116 of file MafIterator.h.
References bpp::AbstractMafIterator::verbose_.
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inlinevirtualinherited |
Get the next available alignment block.
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_.
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inlineprivate |
Definition at line 112 of file OrderFilterMafIterator.h.
References currentChr_, overlappingBlockDiscarded_, overlappingBlockThrowsException_, previousBlockStart_, previousBlockStop_, refSpecies_, unsortedBlockDiscarded_, and unsortedBlockThrowsException_.
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private |
Definition at line 57 of file OrderFilterMafIterator.cpp.
References bpp::MafSequence::getChromosome(), bpp::MafSequence::getDescription(), bpp::MafBlock::getSequenceForSpecies(), bpp::MafBlock::hasSequenceForSpecies(), bpp::MafSequence::start(), bpp::MafSequence::stop(), and bpp::TextTools::toString().
Referenced by analyseCurrentBlock_().
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inlineinherited |
Definition at line 178 of file MafIterator.h.
References bpp::AbstractFilterMafIterator::logstream_.
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inlinevirtualinherited |
Implements bpp::MafIterator.
Definition at line 117 of file MafIterator.h.
References bpp::AbstractMafIterator::verbose_.
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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_(), analyseCurrentBlock_(), bpp::OutputMafIterator::analyseCurrentBlock_(), bpp::PlinkOutputMafIterator::analyseCurrentBlock_(), bpp::SequenceStatisticsMafIterator::analyseCurrentBlock_(), bpp::TableOutputMafIterator::analyseCurrentBlock_(), bpp::VcfOutputMafIterator::analyseCurrentBlock_(), and bpp::AbstractFilterMafIterator::operator=().
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private |
Definition at line 63 of file OrderFilterMafIterator.h.
Referenced by operator=().
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protectedinherited |
Definition at line 89 of file MafIterator.h.
Referenced by bpp::AbstractMafIterator::addIterationListener().
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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_(), analyseCurrentBlock_(), bpp::OutputMafIterator::analyseCurrentBlock_(), bpp::PlinkOutputMafIterator::analyseCurrentBlock_(), bpp::SequenceStatisticsMafIterator::analyseCurrentBlock_(), bpp::TableOutputMafIterator::analyseCurrentBlock_(), bpp::VcfOutputMafIterator::analyseCurrentBlock_(), and bpp::AbstractFilterMafIterator::operator=().
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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().
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private |
Definition at line 68 of file OrderFilterMafIterator.h.
Referenced by operator=().
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private |
Definition at line 69 of file OrderFilterMafIterator.h.
Referenced by operator=().
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private |
Definition at line 64 of file OrderFilterMafIterator.h.
Referenced by operator=().
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private |
Definition at line 65 of file OrderFilterMafIterator.h.
Referenced by operator=().
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private |
Definition at line 62 of file OrderFilterMafIterator.h.
Referenced by operator=().
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protectedinherited |
Definition at line 90 of file MafIterator.h.
Referenced by bpp::AbstractMafIterator::nextBlock().
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private |
Definition at line 66 of file OrderFilterMafIterator.h.
Referenced by operator=().
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private |
Definition at line 67 of file OrderFilterMafIterator.h.
Referenced by operator=().
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protectedinherited |
Definition at line 91 of file MafIterator.h.
Referenced by bpp::AbstractMafIterator::isVerbose(), and bpp::AbstractMafIterator::setVerbose().