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virtual TopSegmentIteratorPtr | copy ()=0 |
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virtual TopSegmentIteratorConstPtr | copy () const =0 |
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virtual void | copy (TopSegmentIteratorConstPtr ts) const =0 |
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virtual void | toChild (BottomSegmentIteratorConstPtr bs, hal_size_t child) const =0 |
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virtual void | toChildG (BottomSegmentIteratorConstPtr bs, const Genome *childGenome) const =0 |
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virtual void | toParseUp (BottomSegmentIteratorConstPtr bs) const =0 |
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virtual TopSegment * | getTopSegment ()=0 |
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virtual const TopSegment * | getTopSegment () const =0 |
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virtual bool | equals (TopSegmentIteratorConstPtr other) const =0 |
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virtual void | toNextParalogy () const =0 |
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virtual hal_index_t | getParentIndex () const =0 |
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virtual bool | hasParent () const =0 |
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virtual void | setParentIndex (hal_index_t parIdx)=0 |
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virtual bool | getParentReversed () const =0 |
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virtual void | setParentReversed (bool isReversed)=0 |
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virtual hal_index_t | getBottomParseIndex () const =0 |
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virtual void | setBottomParseIndex (hal_index_t botParseIdx)=0 |
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virtual hal_offset_t | getBottomParseOffset () const =0 |
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virtual bool | hasParseDown () const =0 |
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virtual hal_index_t | getNextParalogyIndex () const =0 |
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virtual bool | hasNextParalogy () const =0 |
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virtual void | setNextParalogyIndex (hal_index_t parIdx)=0 |
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virtual hal_index_t | getLeftParentIndex () const =0 |
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virtual hal_index_t | getRightParentIndex () const =0 |
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virtual bool | isCanonicalParalog () const =0 |
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virtual void | setArrayIndex (Genome *genome, hal_index_t arrayIndex)=0 |
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virtual void | setArrayIndex (const Genome *genome, hal_index_t arrayIndex) const =0 |
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virtual const Genome * | getGenome () const =0 |
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virtual Genome * | getGenome ()=0 |
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virtual const Sequence * | getSequence () const =0 |
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virtual Sequence * | getSequence ()=0 |
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virtual hal_index_t | getStartPosition () const =0 |
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virtual hal_index_t | getEndPosition () const =0 |
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virtual hal_size_t | getLength () const =0 |
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virtual void | getString (std::string &outString) const =0 |
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virtual void | setCoordinates (hal_index_t startPos, hal_size_t length)=0 |
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virtual hal_index_t | getArrayIndex () const =0 |
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virtual bool | leftOf (hal_index_t genomePos) const =0 |
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virtual bool | rightOf (hal_index_t genomePos) const =0 |
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virtual bool | overlaps (hal_index_t genomePos) const =0 |
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virtual bool | isFirst () const =0 |
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virtual bool | isLast () const =0 |
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virtual bool | isMissingData (double nThreshold) const =0 |
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virtual bool | isTop () const =0 |
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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 |
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virtual void | print (std::ostream &os) const =0 |
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virtual void | toLeft (hal_index_t leftCutoff=NULL_INDEX) const =0 |
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virtual void | toRight (hal_index_t rightCutoff=NULL_INDEX) const =0 |
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virtual void | toSite (hal_index_t position, bool slice=true) const =0 |
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virtual void | toReverse () const =0 |
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virtual void | toReverseInPlace () const =0 |
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virtual hal_offset_t | getStartOffset () const =0 |
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virtual hal_offset_t | getEndOffset () const =0 |
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virtual void | slice (hal_offset_t startOffset=0, hal_offset_t endOffset=0) const =0 |
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virtual bool | getReversed () const =0 |
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Interface for top segment iterator exposes the top segment interface and some new methods for jumping around the genome. Always hidden in smart pointers in the public interface.