This is the complete list of members for hal::BottomSegment, including all inherited members.
counted_ptr< BottomSegment > (defined in hal::BottomSegment) | hal::BottomSegment | friend |
counted_ptr< const BottomSegment > (defined in hal::BottomSegment) | hal::BottomSegment | friend |
getArrayIndex() const =0 | hal::Segment | pure virtual |
getChildIndex(hal_size_t i) const =0 | hal::BottomSegment | pure virtual |
getChildIndexG(const Genome *childGenome) const =0 | hal::BottomSegment | pure virtual |
getChildReversed(hal_size_t i) const =0 | hal::BottomSegment | pure virtual |
getEndPosition() const =0 | hal::Segment | pure virtual |
getGenome() const =0 | hal::Segment | pure virtual |
getGenome()=0 | hal::Segment | pure virtual |
getLeftChildIndex(hal_size_t i) const =0 | hal::BottomSegment | 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 |
getNumChildren() const =0 | hal::BottomSegment | pure virtual |
getRightChildIndex(hal_size_t i) const =0 | hal::BottomSegment | 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 |
getTopParseIndex() const =0 | hal::BottomSegment | pure virtual |
getTopParseOffset() const =0 | hal::BottomSegment | pure virtual |
hasChild(hal_size_t child) const =0 | hal::BottomSegment | pure virtual |
hasChildG(const Genome *childGenome) const =0 | hal::BottomSegment | pure virtual |
hasParseUp() const =0 | hal::BottomSegment | 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 |
setChildIndex(hal_size_t i, hal_index_t childIndex)=0 | hal::BottomSegment | pure virtual |
setChildReversed(hal_size_t child, bool isReversed)=0 | hal::BottomSegment | pure virtual |
setCoordinates(hal_index_t startPos, hal_size_t length)=0 | hal::Segment | pure virtual |
setTopParseIndex(hal_index_t parseIndex)=0 | hal::BottomSegment | pure virtual |
~BottomSegment()=0 (defined in hal::BottomSegment) | hal::BottomSegment | inlineprotectedpure virtual |
~Segment()=0 (defined in hal::Segment) | hal::Segment | inlineprotectedpure virtual |