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hierarchichalalignmentformatapi
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hal::TopSegment Class Referenceabstract

#include <halTopSegment.h>

Inheritance diagram for hal::TopSegment:
hal::Segment hal::TopSegmentIterator

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
 
- Public Member Functions inherited from hal::Segment
virtual void setArrayIndex (Genome *genome, hal_index_t arrayIndex)=0
 
virtual void setArrayIndex (const Genome *genome, hal_index_t arrayIndex) const =0
 
virtual const GenomegetGenome () const =0
 
virtual GenomegetGenome ()=0
 
virtual const SequencegetSequence () const =0
 
virtual SequencegetSequence ()=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 >
 

Detailed Description

Interface for a top segment of DNA

Member Function Documentation

virtual hal_index_t hal::TopSegment::getBottomParseIndex ( ) const
pure virtual

Get the index of the bottom segment in genome that contains the start coordinate of this top segment

virtual hal_offset_t hal::TopSegment::getBottomParseOffset ( ) const
pure virtual

Get the offset in the bottom parse segment that aligns with the start coordinate of this segment

virtual hal_index_t hal::TopSegment::getLeftParentIndex ( ) const
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)

virtual hal_index_t hal::TopSegment::getNextParalogyIndex ( ) const
pure virtual

Get index of the next paralogous segment in the genome

virtual hal_index_t hal::TopSegment::getParentIndex ( ) const
pure virtual

Get index of the homologous segmenet in the ancestral genome

virtual bool hal::TopSegment::getParentReversed ( ) const
pure virtual

Check whether segment is mapped to parent's reverse complement

virtual hal_index_t hal::TopSegment::getRightParentIndex ( ) const
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)

virtual bool hal::TopSegment::isCanonicalParalog ( ) const
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.

virtual void hal::TopSegment::setBottomParseIndex ( hal_index_t  botParseIdx)
pure virtual

Set the index of the bototm segment in the genome that contains the start coordinate of this top segment

Parameters
botParseIndxindex to set
virtual void hal::TopSegment::setNextParalogyIndex ( hal_index_t  parIdx)
pure virtual

Set index of the next paralogous segment in the genome

Parameters
parIdxof next segment in same genome that is homologous to this segment
virtual void hal::TopSegment::setParentIndex ( hal_index_t  parIdx)
pure virtual

Set the index of the homologous segment in the ancestra genome

Parameters
parIdxparent index to set
virtual void hal::TopSegment::setParentReversed ( bool  isReversed)
pure virtual

Set whether segment is mapped to parent's reverse complement

Parameters
isReversedFlag

The documentation for this class was generated from the following file: