#include <halGappedBottomSegmentIterator.h>
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 |
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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 |
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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 |
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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 |
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virtual void | setArrayIndex (Genome *genome, hal_index_t arrayIndex)=0 |
virtual void | setArrayIndex (const Genome *genome, hal_index_t arrayIndex) const =0 |
virtual const Genome * | getGenome () const =0 |
virtual Genome * | getGenome ()=0 |
virtual const Sequence * | getSequence () const =0 |
virtual Sequence * | getSequence ()=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 > |
Interface for Gepped Bottom Segment iterator. Only used internally and probably shouldn't be in public interface.
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pure virtual |
Test if iterator abuts other iterator
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pure virtual |
Return a copy of the iterator
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pure virtual |
Return a copy of the iterator
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pure virtual |
Copy another iterator into the current iterator (more efficient than above methods since no new iterators are created
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pure virtual |
Test equality with other iterator
other |
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pure virtual |
Test if in reverse orientationt with respect to child
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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)
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pure virtual |
Reset the gapped iterator.
ts | This will be the left segment of the current iterator. The right segment will be extended as far as possible |
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pure virtual |
Test if iterator has a child
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pure virtual |
Reset the gapped iterator.
ts | This will be the left segment of the current iterator. The right segment will be extended as far as possible |
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pure virtual |
Move to parent