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hal::GappedBottomSegmentIterator Class Referenceabstract

#include <halGappedBottomSegmentIterator.h>

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

Public Member Functions

virtual
GappedBottomSegmentIteratorPtr 
copy ()=0
 
virtual
GappedBottomSegmentIteratorConstPtr 
copy () const =0
 
virtual void copy (GappedBottomSegmentIteratorConstPtr ts) const =0
 
virtual void toParent (GappedTopSegmentIteratorConstPtr ts) const =0
 
virtual bool equals (GappedBottomSegmentIteratorConstPtr other) const =0
 
virtual bool adjacentTo (GappedBottomSegmentIteratorConstPtr other) const =0
 
virtual bool hasChild () const =0
 
virtual bool getChildReversed () const =0
 
virtual
BottomSegmentIteratorConstPtr 
getLeft () const =0
 
virtual
BottomSegmentIteratorConstPtr 
getRight () const =0
 
virtual void setLeft (BottomSegmentIteratorConstPtr bs) const =0
 
- Public Member Functions inherited from hal::GappedSegmentIterator
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< GappedBottomSegmentIterator >
 
class counted_ptr< const GappedBottomSegmentIterator >
 

Detailed Description

Interface for Gepped Bottom Segment iterator. Only used internally and probably shouldn't be in public interface.

Member Function Documentation

virtual bool hal::GappedBottomSegmentIterator::adjacentTo ( GappedBottomSegmentIteratorConstPtr  other) const
pure virtual

Test if iterator abuts other iterator

virtual GappedBottomSegmentIteratorPtr hal::GappedBottomSegmentIterator::copy ( )
pure virtual

Return a copy of the iterator

virtual GappedBottomSegmentIteratorConstPtr hal::GappedBottomSegmentIterator::copy ( ) const
pure virtual

Return a copy of the iterator

virtual void hal::GappedBottomSegmentIterator::copy ( GappedBottomSegmentIteratorConstPtr  ts) const
pure virtual

Copy another iterator into the current iterator (more efficient than above methods since no new iterators are created

virtual bool hal::GappedBottomSegmentIterator::equals ( GappedBottomSegmentIteratorConstPtr  other) const
pure virtual

Test equality with other iterator

Parameters
other
virtual bool hal::GappedBottomSegmentIterator::getChildReversed ( ) const
pure virtual

Test if in reverse orientationt with respect to child

virtual BottomSegmentIteratorConstPtr hal::GappedBottomSegmentIterator::getLeft ( ) const
pure virtual

Return the rightmost segment of the iterator (note that moving the returned iterator will corrupt the current gapped iterator. this is a bug)

virtual BottomSegmentIteratorConstPtr hal::GappedBottomSegmentIterator::getRight ( ) const
pure virtual

Reset the gapped iterator.

Parameters
tsThis will be the left segment of the current iterator. The right segment will be extended as far as possible
virtual bool hal::GappedBottomSegmentIterator::hasChild ( ) const
pure virtual

Test if iterator has a child

virtual void hal::GappedBottomSegmentIterator::setLeft ( BottomSegmentIteratorConstPtr  bs) const
pure virtual

Reset the gapped iterator.

Parameters
tsThis will be the left segment of the current iterator. The right segment will be extended as far as possible
virtual void hal::GappedBottomSegmentIterator::toParent ( GappedTopSegmentIteratorConstPtr  ts) const
pure virtual

Move to parent


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