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hierarchichalalignmentformatapi
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hal::DNAIterator Class Referenceabstract

#include <halDNAIterator.h>

Public Member Functions

virtual char getChar () const =0
 
virtual void setChar (char c)=0
 
virtual void toLeft () const =0
 
virtual void toRight () const =0
 
virtual void jumpTo (hal_size_t index) const =0
 
virtual void toReverse () const =0
 
virtual bool getReversed () const =0
 
virtual void setReversed (bool reversed) const =0
 
virtual const GenomegetGenome () const =0
 
virtual GenomegetGenome ()=0
 
virtual const SequencegetSequence () const =0
 
virtual SequencegetSequence ()=0
 
virtual hal_index_t getArrayIndex () const =0
 
virtual bool equals (DNAIteratorConstPtr &other) const =0
 
virtual bool leftOf (DNAIteratorConstPtr &other) const =0
 

Friends

class counted_ptr< DNAIterator >
 
class counted_ptr< const DNAIterator >
 

Detailed Description

Interface for general dna iterator

Member Function Documentation

virtual bool hal::DNAIterator::equals ( DNAIteratorConstPtr &  other) const
pure virtual

Compare (array indexes) of two iterators

virtual hal_index_t hal::DNAIterator::getArrayIndex ( ) const
pure virtual

Get the index of the base in the dna array

virtual char hal::DNAIterator::getChar ( ) const
pure virtual

Get the DNA character at this position (if revsersed is set the reverse compelement is returned

virtual const Genome* hal::DNAIterator::getGenome ( ) const
pure virtual

Get the containing (read-only) genome

virtual Genome* hal::DNAIterator::getGenome ( )
pure virtual

Get the containing genome

virtual bool hal::DNAIterator::getReversed ( ) const
pure virtual

Check whether iterator is on base's complement

virtual const Sequence* hal::DNAIterator::getSequence ( ) const
pure virtual

Get the containing (read-only) sequence

virtual Sequence* hal::DNAIterator::getSequence ( )
pure virtual

Get the containing sequence

virtual void hal::DNAIterator::jumpTo ( hal_size_t  index) const
pure virtual

Jump to any point on the genome (can lead to inefficient paging from disk if used irresponsibly)

Parameters
indexposition in array to jump to
virtual bool hal::DNAIterator::leftOf ( DNAIteratorConstPtr &  other) const
pure virtual

Compare (array indexes) of two iterators

virtual void hal::DNAIterator::setChar ( char  c)
pure virtual

Set the DNA character at this position (if revsersed is set the reverse compelement is stored

Parameters
cDNA character to set
virtual void hal::DNAIterator::setReversed ( bool  reversed) const
pure virtual

Set the iterator's reverse complement status

virtual void hal::DNAIterator::toLeft ( ) const
pure virtual

Move to previous position (equiv. to toRight if reversed)

virtual void hal::DNAIterator::toReverse ( ) const
pure virtual

switch to base's reverse complement

virtual void hal::DNAIterator::toRight ( ) const
pure virtual

Move to next position (equiv. to toLeft if reversed)


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