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hal::BottomSegmentIterator Member List

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

copy()=0 | hal::BottomSegmentIterator | pure virtual
copy() const =0 | hal::BottomSegmentIterator | pure virtual
copy(BottomSegmentIteratorConstPtr bs) const =0 | hal::BottomSegmentIterator | pure virtual
counted_ptr< BottomSegmentIterator > (defined in hal::BottomSegmentIterator) | hal::BottomSegmentIterator | friend
counted_ptr< const BottomSegmentIterator > (defined in hal::BottomSegmentIterator) | hal::BottomSegmentIterator | friend
equals(BottomSegmentIteratorConstPtr other) const =0 | hal::BottomSegmentIterator | pure virtual
getArrayIndex() const =0 | hal::Segment | pure virtual
getBottomSegment()=0 | hal::BottomSegmentIterator | pure virtual
getBottomSegment() const =0 | hal::BottomSegmentIterator | 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
getEndOffset() const =0 | hal::SlicedSegment | 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
getReversed() const =0 | hal::SlicedSegment | 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
getStartOffset() const =0 | hal::SlicedSegment | 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
slice(hal_offset_t startOffset=0, hal_offset_t endOffset=0) const =0 | hal::SlicedSegment | pure virtual
toLeft(hal_index_t leftCutoff=NULL_INDEX) const =0 | hal::SegmentIterator | pure virtual
toParent(TopSegmentIteratorConstPtr ts) const =0 | hal::BottomSegmentIterator | pure virtual
toParseDown(TopSegmentIteratorConstPtr ts) const =0 | hal::BottomSegmentIterator | pure virtual
toReverse() const =0 | hal::SlicedSegment | pure virtual
toReverseInPlace() const =0 | hal::SlicedSegment | pure virtual
toRight(hal_index_t rightCutoff=NULL_INDEX) const =0 | hal::SegmentIterator | pure virtual
toSite(hal_index_t position, bool slice=true) const =0 | hal::SegmentIterator | pure virtual
~BottomSegment()=0 (defined in hal::BottomSegment) | hal::BottomSegment | inline protected pure virtual
~BottomSegmentIterator()=0 (defined in hal::BottomSegmentIterator) | hal::BottomSegmentIterator | inline protected pure virtual
~Segment()=0 (defined in hal::Segment) | hal::Segment | inline protected pure virtual
~SegmentIterator()=0 (defined in hal::SegmentIterator) | hal::SegmentIterator | inline protected pure virtual
~SlicedSegment()=0 (defined in hal::SlicedSegment) | hal::SlicedSegment | inline protected pure virtual