#include <halTopSegment.h>
Public Member Functions | |
virtual hal_index_t | getParentIndex () const =0 |
virtual bool | hasParent () const =0 |
virtual void | setParentIndex (hal_index_t parIdx)=0 |
virtual bool | getParentReversed () const =0 |
virtual void | setParentReversed (bool isReversed)=0 |
virtual hal_index_t | getBottomParseIndex () const =0 |
virtual void | setBottomParseIndex (hal_index_t botParseIdx)=0 |
virtual hal_offset_t | getBottomParseOffset () const =0 |
virtual bool | hasParseDown () const =0 |
virtual hal_index_t | getNextParalogyIndex () const =0 |
virtual bool | hasNextParalogy () const =0 |
virtual void | setNextParalogyIndex (hal_index_t parIdx)=0 |
virtual hal_index_t | getLeftParentIndex () const =0 |
virtual hal_index_t | getRightParentIndex () const =0 |
virtual bool | isCanonicalParalog () 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< TopSegment > |
class | counted_ptr< const TopSegment > |
Interface for a top segment of DNA
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pure virtual |
Get the index of the bottom segment in genome that contains the start coordinate of this top segment
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pure virtual |
Get the offset in the bottom parse segment that aligns with the start coordinate of this segment
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pure virtual |
Get the index of the parent of the left neighbour of this segment in the genome (use isLeft first to check the left current segment is the first segment in a sequence)
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pure virtual |
Get index of the next paralogous segment in the genome
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pure virtual |
Get index of the homologous segmenet in the ancestral genome
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pure virtual |
Check whether segment is mapped to parent's reverse complement
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pure virtual |
Get the index of the parent of the right neighbour of this segment in the genome (use isRight right to check the left current segment is the last segment in a sequence)
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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 |
Set the index of the bototm segment in the genome that contains the start coordinate of this top segment
botParseIndx | index to set |
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pure virtual |
Set index of the next paralogous segment in the genome
parIdx | of next segment in same genome that is homologous to this segment |
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pure virtual |
Set the index of the homologous segment in the ancestra genome
parIdx | parent index to set |
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pure virtual |
Set whether segment is mapped to parent's reverse complement
isReversed | Flag |