|
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 BottomSegment * | getBottomSegment ()=0 |
|
virtual const BottomSegment * | getBottomSegment () const =0 |
|
virtual bool | equals (BottomSegmentIteratorConstPtr other) const =0 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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.