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hal::GappedSegmentIterator Class Referenceabstract

#include <halGappedSegmentIterator.h>

Inheritance diagram for hal::GappedSegmentIterator:
hal::SegmentIterator hal::SlicedSegment hal::Segment hal::GappedBottomSegmentIterator hal::GappedTopSegmentIterator

Public Member Functions

virtual hal_size_t getGapThreshold () const =0
 
virtual bool getAtomic () const =0
 
virtual hal_size_t getChildIndex () const =0
 
virtual hal_size_t getNumSegments () const =0
 
virtual hal_size_t getNumGaps () const =0
 
virtual hal_size_t getNumGapBases () const =0
 
virtual hal_index_t getLeftArrayIndex () const =0
 
virtual hal_index_t getRightArrayIndex () const =0
 
- Public Member Functions inherited from hal::SegmentIterator
virtual void toLeft (hal_index_t leftCutoff=NULL_INDEX) const =0
 
virtual void toRight (hal_index_t rightCutoff=NULL_INDEX) const =0
 
virtual void toSite (hal_index_t position, bool slice=true) const =0
 
- Public Member Functions inherited from hal::SlicedSegment
virtual void toReverse () const =0
 
virtual void toReverseInPlace () const =0
 
virtual hal_offset_t getStartOffset () const =0
 
virtual hal_offset_t getEndOffset () const =0
 
virtual void slice (hal_offset_t startOffset=0, hal_offset_t endOffset=0) const =0
 
virtual bool getReversed () const =0
 
- Public Member Functions inherited from hal::Segment
virtual void setArrayIndex (Genome *genome, hal_index_t arrayIndex)=0
 
virtual void setArrayIndex (const Genome *genome, hal_index_t arrayIndex) const =0
 
virtual const GenomegetGenome () const =0
 
virtual GenomegetGenome ()=0
 
virtual const SequencegetSequence () const =0
 
virtual SequencegetSequence ()=0
 
virtual hal_index_t getStartPosition () const =0
 
virtual hal_index_t getEndPosition () const =0
 
virtual hal_size_t getLength () const =0
 
virtual void getString (std::string &outString) const =0
 
virtual void setCoordinates (hal_index_t startPos, hal_size_t length)=0
 
virtual hal_index_t getArrayIndex () const =0
 
virtual bool leftOf (hal_index_t genomePos) const =0
 
virtual bool rightOf (hal_index_t genomePos) const =0
 
virtual bool overlaps (hal_index_t genomePos) const =0
 
virtual bool isFirst () const =0
 
virtual bool isLast () const =0
 
virtual bool isMissingData (double nThreshold) const =0
 
virtual bool isTop () const =0
 
virtual hal_size_t getMappedSegments (std::set< MappedSegmentConstPtr > &outSegments, const Genome *tgtGenome, const std::set< const Genome * > *genomesOnPath=NULL, bool doDupes=true, hal_size_t minLength=0) const =0
 
virtual void print (std::ostream &os) const =0
 

Friends

class counted_ptr< GappedSegmentIterator >
 
class counted_ptr< const GappedSegmentIterator >
 

Detailed Description

Interface for general gappedSegment iterator. Behaves like a regular iterator, but operates on a linear sequence of segments that are consistent modulo gaps. Is only really used internally at the moment so I haven't spent the effort to make gapped iterators fully general (such as including the Top/Bottom Segment iterfaces)

Member Function Documentation

virtual bool hal::GappedSegmentIterator::getAtomic ( ) const
pure virtual

When the gap iterator is in atomic mode, it allows for now gaps. Also, it will not merge consistent segments together if they are adjacent and there are no gaps (something that could happen when the threshold is set to zero but atomic is false). This is mostly a hack to get the gapped iterator to behive as a single segment

virtual hal_size_t hal::GappedSegmentIterator::getChildIndex ( ) const
pure virtual

Gapped iterators are tied to a specific parent child pair. The child index is the index of the child genome within the parent

virtual hal_size_t hal::GappedSegmentIterator::getGapThreshold ( ) const
pure virtual

Get the gap length threshold. This is the maximum length (in sites) of an indel such that it can be considered a gap (and therefore ignored in the rearrangement analysis

virtual hal_index_t hal::GappedSegmentIterator::getLeftArrayIndex ( ) const
pure virtual

Get the Segment array index of the left segment of the iterator

virtual hal_size_t hal::GappedSegmentIterator::getNumGapBases ( ) const
pure virtual

Get the number of bases within gaps within segments that have been agglomerated together within the gapped iterator

virtual hal_size_t hal::GappedSegmentIterator::getNumGaps ( ) const
pure virtual

Get the number of gaps within segments that have been agglomerated together within the gapped iterator

virtual hal_size_t hal::GappedSegmentIterator::getNumSegments ( ) const
pure virtual

Get the number of segments that have been agglomerated together within the gapped iterator

virtual hal_index_t hal::GappedSegmentIterator::getRightArrayIndex ( ) const
pure virtual

Get the Segment array index of the right segment of the iterator


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