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hal::TopSegment Member List

This is the complete list of members for hal::TopSegment, including all inherited members.

counted_ptr< const TopSegment > (defined in hal::TopSegment) | hal::TopSegment | friend
counted_ptr< TopSegment > (defined in hal::TopSegment) | hal::TopSegment | friend
getArrayIndex() const =0 | hal::Segment | pure virtual
getBottomParseIndex() const =0 | hal::TopSegment | pure virtual
getBottomParseOffset() const =0 | hal::TopSegment | pure virtual
getEndPosition() const =0 | hal::Segment | pure virtual
getGenome() const =0 | hal::Segment | pure virtual
getGenome()=0 | hal::Segment | pure virtual
getLeftParentIndex() const =0 | hal::TopSegment | pure virtual
getLength() const =0 | hal::Segment | pure virtual
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 | hal::Segment | pure virtual
getNextParalogyIndex() const =0 | hal::TopSegment | pure virtual
getParentIndex() const =0 | hal::TopSegment | pure virtual
getParentReversed() const =0 | hal::TopSegment | pure virtual
getRightParentIndex() const =0 | hal::TopSegment | pure virtual
getSequence() const =0 | hal::Segment | pure virtual
getSequence()=0 | hal::Segment | pure virtual
getStartPosition() const =0 | hal::Segment | pure virtual
getString(std::string &outString) const =0 | hal::Segment | pure virtual
hasNextParalogy() const =0 (defined in hal::TopSegment) | hal::TopSegment | pure virtual
hasParent() const =0 (defined in hal::TopSegment) | hal::TopSegment | pure virtual
hasParseDown() const =0 (defined in hal::TopSegment) | hal::TopSegment | pure virtual
isCanonicalParalog() const =0 | hal::TopSegment | pure virtual
isFirst() const =0 | hal::Segment | pure virtual
isLast() const =0 | hal::Segment | pure virtual
isMissingData(double nThreshold) const =0 | hal::Segment | pure virtual
isTop() const =0 | hal::Segment | pure virtual
leftOf(hal_index_t genomePos) const =0 | hal::Segment | pure virtual
overlaps(hal_index_t genomePos) const =0 | hal::Segment | pure virtual
print(std::ostream &os) const =0 | hal::Segment | pure virtual
rightOf(hal_index_t genomePos) const =0 | hal::Segment | pure virtual
setArrayIndex(Genome *genome, hal_index_t arrayIndex)=0 | hal::Segment | pure virtual
setArrayIndex(const Genome *genome, hal_index_t arrayIndex) const =0 | hal::Segment | pure virtual
setBottomParseIndex(hal_index_t botParseIdx)=0 | hal::TopSegment | pure virtual
setCoordinates(hal_index_t startPos, hal_size_t length)=0 | hal::Segment | pure virtual
setNextParalogyIndex(hal_index_t parIdx)=0 | hal::TopSegment | pure virtual
setParentIndex(hal_index_t parIdx)=0 | hal::TopSegment | pure virtual
setParentReversed(bool isReversed)=0 | hal::TopSegment | pure virtual
~Segment()=0 (defined in hal::Segment) | hal::Segment | inlineprotectedpure virtual
~TopSegment()=0 (defined in hal::TopSegment) | hal::TopSegment | inlineprotectedpure virtual