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hierarchichalalignmentformatapi
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hal::BottomSegment Class Referenceabstract

#include <halBottomSegment.h>

Inheritance diagram for hal::BottomSegment:
hal::Segment hal::BottomSegmentIterator

Public Member Functions

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
 
- 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< BottomSegment >
 
class counted_ptr< const BottomSegment >
 

Detailed Description

Interface for a bottom segment of DNA

Member Function Documentation

virtual hal_index_t hal::BottomSegment::getChildIndex ( hal_size_t  i) const
pure virtual

Get the index of a child segment (OR NULL_INDEX if none)

Parameters
iindex of child to query
virtual hal_index_t hal::BottomSegment::getChildIndexG ( const Genome childGenome) const
pure virtual

Get the index of a child segment (OR NULL_INDEX if none)

Parameters
childGenomegenome of child to query
virtual bool hal::BottomSegment::getChildReversed ( hal_size_t  i) const
pure virtual

Get whether descent segment for ith child is mapped to the reverse complement of this segment

Parameters
iindex of child to query
virtual hal_index_t hal::BottomSegment::getLeftChildIndex ( hal_size_t  i) const
pure virtual

Get the index of the child of the left neighbour of this segment in the genome (use isLeft first to check if the left neighbour is in the same sequence)

Parameters
iindex of child genome to query
virtual hal_size_t hal::BottomSegment::getNumChildren ( ) const
pure virtual

Get the number of child genomes (note this is a number of slots and that the current segment could actually have fewer children)

virtual hal_index_t hal::BottomSegment::getRightChildIndex ( hal_size_t  i) const
pure virtual

Get the right of the child of the left neighbour of this segment in the genome (use isRight first to check if the right neighbour is in the same sequence)

Parameters
iindex of child genome to query
virtual hal_index_t hal::BottomSegment::getTopParseIndex ( ) const
pure virtual

Get index of top segment in samge genome that contains this segment's start coordinate

virtual hal_offset_t hal::BottomSegment::getTopParseOffset ( ) const
pure virtual

Get offset in associated top segment of start coordinate of this segment

virtual bool hal::BottomSegment::hasChild ( hal_size_t  child) const
pure virtual

Test if child segment exists

Parameters
childindex of child genome
virtual bool hal::BottomSegment::hasChildG ( const Genome childGenome) const
pure virtual

Test if child segment exists

Parameters
childChild genome
virtual bool hal::BottomSegment::hasParseUp ( ) const
pure virtual

Test if there is a top parse segment in the genome that contains the start positon of the current iterator (should be true if not in root

virtual void hal::BottomSegment::setChildIndex ( hal_size_t  i,
hal_index_t  childIndex 
)
pure virtual

Set the index of a child segment (OR NULL_INDEX if none)

Parameters
iindex of child to set
childIndexindex of segment in child to set
virtual void hal::BottomSegment::setChildReversed ( hal_size_t  child,
bool  isReversed 
)
pure virtual

Set whether descent segment for ith child is mapped to the reverse complement of this segment

Parameters
iindex of child to set
isReverseflag
virtual void hal::BottomSegment::setTopParseIndex ( hal_index_t  parseIndex)
pure virtual

Set index of top segment in samge genome that contains this segment's start coordinate

Parameters
parParseIndexindex

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