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hierarchichalalignmentformatapi
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hal::BottomSegmentIterator Class Referenceabstract

#include <halBottomSegmentIterator.h>

Inheritance diagram for hal::BottomSegmentIterator:
hal::BottomSegment hal::SegmentIterator hal::Segment hal::SlicedSegment hal::Segment

Public Member Functions

virtual BottomSegmentIteratorPtr copy ()=0
 
virtual
BottomSegmentIteratorConstPtr 
copy () const =0
 
virtual void copy (BottomSegmentIteratorConstPtr bs) const =0
 
virtual void toParent (TopSegmentIteratorConstPtr ts) const =0
 
virtual void toParseDown (TopSegmentIteratorConstPtr ts) const =0
 
virtual BottomSegmentgetBottomSegment ()=0
 
virtual const BottomSegmentgetBottomSegment () const =0
 
virtual bool equals (BottomSegmentIteratorConstPtr other) const =0
 
- Public Member Functions inherited from hal::BottomSegment
virtual hal_size_t getNumChildren () const =0
 
virtual hal_index_t getChildIndex (hal_size_t i) const =0
 
virtual hal_index_t getChildIndexG (const Genome *childGenome) const =0
 
virtual bool hasChild (hal_size_t child) const =0
 
virtual bool hasChildG (const Genome *childGenome) const =0
 
virtual void setChildIndex (hal_size_t i, hal_index_t childIndex)=0
 
virtual bool getChildReversed (hal_size_t i) const =0
 
virtual void setChildReversed (hal_size_t child, bool isReversed)=0
 
virtual hal_index_t getTopParseIndex () const =0
 
virtual void setTopParseIndex (hal_index_t parseIndex)=0
 
virtual hal_offset_t getTopParseOffset () const =0
 
virtual bool hasParseUp () const =0
 
virtual hal_index_t getLeftChildIndex (hal_size_t i) const =0
 
virtual hal_index_t getRightChildIndex (hal_size_t i) 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
 
- 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
 

Friends

class counted_ptr< BottomSegmentIterator >
 
class counted_ptr< const BottomSegmentIterator >
 

Detailed Description

Interface for bottom segment iterator exposes the bottom segment interface and some new methods for jumping around the genome. Always hidden in smart pointers in the public interface.

Member Function Documentation

virtual BottomSegmentIteratorPtr hal::BottomSegmentIterator::copy ( )
pure virtual

Return a new copy of the iterator

virtual BottomSegmentIteratorConstPtr hal::BottomSegmentIterator::copy ( ) const
pure virtual

Return a new copy of the iterator

virtual void hal::BottomSegmentIterator::copy ( BottomSegmentIteratorConstPtr  bs) const
pure virtual

Copy an input iterator. More efficient than the above methods as no new iterator needs to be allocated

Parameters
tsIterator to copy
virtual bool hal::BottomSegmentIterator::equals ( BottomSegmentIteratorConstPtr  other) const
pure virtual

Test equality with other iterator (current implementation does not take into account reverse state or offsets – too review)

Parameters
otherIterator to test equality to
virtual BottomSegment* hal::BottomSegmentIterator::getBottomSegment ( )
pure virtual

DEPRECATED

virtual const BottomSegment* hal::BottomSegmentIterator::getBottomSegment ( ) const
pure virtual

DEPRECATED

virtual void hal::BottomSegmentIterator::toParent ( TopSegmentIteratorConstPtr  ts) const
pure virtual

Move the iterator to the parent segment of a given iterator

Parameters
tsIterator whose parent to move to
virtual void hal::BottomSegmentIterator::toParseDown ( TopSegmentIteratorConstPtr  ts) const
pure virtual

Move the iterator down to the bottom segment containg the start position of the given iterator in the same genome

Parameters
tsTop iterator to parse down on

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