#include <halGappedTopSegmentIterator.h>
Public Member Functions | |
virtual GappedTopSegmentIteratorPtr | copy ()=0 |
virtual GappedTopSegmentIteratorConstPtr | copy () const =0 |
virtual void | copy (GappedTopSegmentIteratorConstPtr ts) const =0 |
virtual void | toChild (GappedBottomSegmentIteratorConstPtr bs) const =0 |
virtual bool | equals (GappedTopSegmentIteratorConstPtr other) const =0 |
virtual bool | adjacentTo (GappedTopSegmentIteratorConstPtr other) const =0 |
virtual bool | hasParent () const =0 |
virtual bool | hasNextParalogy () const =0 |
virtual void | toNextParalogy () const =0 |
virtual bool | getParentReversed () const =0 |
virtual TopSegmentIteratorConstPtr | getLeft () const =0 |
virtual TopSegmentIteratorConstPtr | getRight () const =0 |
virtual void | setLeft (TopSegmentIteratorConstPtr ts) const =0 |
virtual bool | isCanonicalParalog () 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< GappedTopSegmentIterator > |
class | counted_ptr< const GappedTopSegmentIterator > |
Interface for Gepped Top 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 |
Return the leftmost 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 |
Test if in reverse orientationt with respect to parent
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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 |
Test if iterator has a duplicate
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pure virtual |
Test if iterator has a parent
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pure virtual |
For every set of paralogous top segments in a given genome, we identify a unique segment as the canonical reference. This is the segment that will be traversed when disabling duplication edges when mapping via the column iterator or mappedSegment interface. It is also the segment that is connected from its parent's down edge.
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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 child of given iterator
bs | Move to child of this iterator |
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pure virtual |
Move to next paralogy