#include <halDNAIterator.h>
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class | counted_ptr< DNAIterator > |
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class | counted_ptr< const DNAIterator > |
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Interface for general dna iterator
virtual bool hal::DNAIterator::equals |
( |
DNAIteratorConstPtr & |
other | ) |
const |
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pure virtual |
Compare (array indexes) of two iterators
virtual hal_index_t hal::DNAIterator::getArrayIndex |
( |
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const |
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pure virtual |
Get the index of the base in the dna array
virtual char hal::DNAIterator::getChar |
( |
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const |
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pure virtual |
Get the DNA character at this position (if revsersed is set the reverse compelement is returned
virtual const Genome* hal::DNAIterator::getGenome |
( |
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const |
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pure virtual |
Get the containing (read-only) genome
virtual Genome* hal::DNAIterator::getGenome |
( |
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pure virtual |
Get the containing genome
virtual bool hal::DNAIterator::getReversed |
( |
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const |
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pure virtual |
Check whether iterator is on base's complement
virtual const Sequence* hal::DNAIterator::getSequence |
( |
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const |
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pure virtual |
Get the containing (read-only) sequence
virtual Sequence* hal::DNAIterator::getSequence |
( |
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pure virtual |
Get the containing sequence
virtual void hal::DNAIterator::jumpTo |
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hal_size_t |
index | ) |
const |
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pure virtual |
Jump to any point on the genome (can lead to inefficient paging from disk if used irresponsibly)
- Parameters
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index | position in array to jump to |
virtual bool hal::DNAIterator::leftOf |
( |
DNAIteratorConstPtr & |
other | ) |
const |
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pure virtual |
Compare (array indexes) of two iterators
virtual void hal::DNAIterator::setChar |
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char |
c | ) |
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pure virtual |
Set the DNA character at this position (if revsersed is set the reverse compelement is stored
- Parameters
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virtual void hal::DNAIterator::setReversed |
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bool |
reversed | ) |
const |
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pure virtual |
Set the iterator's reverse complement status
virtual void hal::DNAIterator::toLeft |
( |
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const |
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pure virtual |
Move to previous position (equiv. to toRight if reversed)
virtual void hal::DNAIterator::toReverse |
( |
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const |
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pure virtual |
switch to base's reverse complement
virtual void hal::DNAIterator::toRight |
( |
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const |
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pure virtual |
Move to next position (equiv. to toLeft if reversed)
The documentation for this class was generated from the following file: