halapi
hierarchichalalignmentformatapi
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hal::TopSegmentIterator Member List

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

copy()=0hal::TopSegmentIteratorpure virtual
copy() const =0hal::TopSegmentIteratorpure virtual
copy(TopSegmentIteratorConstPtr ts) const =0hal::TopSegmentIteratorpure virtual
counted_ptr< const TopSegmentIterator > (defined in hal::TopSegmentIterator)hal::TopSegmentIteratorfriend
counted_ptr< TopSegmentIterator > (defined in hal::TopSegmentIterator)hal::TopSegmentIteratorfriend
equals(TopSegmentIteratorConstPtr other) const =0hal::TopSegmentIteratorpure virtual
getArrayIndex() const =0hal::Segmentpure virtual
getBottomParseIndex() const =0hal::TopSegmentpure virtual
getBottomParseOffset() const =0hal::TopSegmentpure virtual
getEndOffset() const =0hal::SlicedSegmentpure virtual
getEndPosition() const =0hal::Segmentpure virtual
getGenome() const =0hal::Segmentpure virtual
getGenome()=0hal::Segmentpure virtual
getLeftParentIndex() const =0hal::TopSegmentpure virtual
getLength() const =0hal::Segmentpure 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 =0hal::Segmentpure virtual
getNextParalogyIndex() const =0hal::TopSegmentpure virtual
getParentIndex() const =0hal::TopSegmentpure virtual
getParentReversed() const =0hal::TopSegmentpure virtual
getReversed() const =0hal::SlicedSegmentpure virtual
getRightParentIndex() const =0hal::TopSegmentpure virtual
getSequence() const =0hal::Segmentpure virtual
getSequence()=0hal::Segmentpure virtual
getStartOffset() const =0hal::SlicedSegmentpure virtual
getStartPosition() const =0hal::Segmentpure virtual
getString(std::string &outString) const =0hal::Segmentpure virtual
getTopSegment()=0hal::TopSegmentIteratorpure virtual
getTopSegment() const =0hal::TopSegmentIteratorpure virtual
hasNextParalogy() const =0 (defined in hal::TopSegment)hal::TopSegmentpure virtual
hasParent() const =0 (defined in hal::TopSegment)hal::TopSegmentpure virtual
hasParseDown() const =0 (defined in hal::TopSegment)hal::TopSegmentpure virtual
isCanonicalParalog() const =0hal::TopSegmentpure virtual
isFirst() const =0hal::Segmentpure virtual
isLast() const =0hal::Segmentpure virtual
isMissingData(double nThreshold) const =0hal::Segmentpure virtual
isTop() const =0hal::Segmentpure virtual
leftOf(hal_index_t genomePos) const =0hal::Segmentpure virtual
overlaps(hal_index_t genomePos) const =0hal::Segmentpure virtual
print(std::ostream &os) const =0hal::Segmentpure virtual
rightOf(hal_index_t genomePos) const =0hal::Segmentpure virtual
setArrayIndex(Genome *genome, hal_index_t arrayIndex)=0hal::Segmentpure virtual
setArrayIndex(const Genome *genome, hal_index_t arrayIndex) const =0hal::Segmentpure virtual
setBottomParseIndex(hal_index_t botParseIdx)=0hal::TopSegmentpure virtual
setCoordinates(hal_index_t startPos, hal_size_t length)=0hal::Segmentpure virtual
setNextParalogyIndex(hal_index_t parIdx)=0hal::TopSegmentpure virtual
setParentIndex(hal_index_t parIdx)=0hal::TopSegmentpure virtual
setParentReversed(bool isReversed)=0hal::TopSegmentpure virtual
slice(hal_offset_t startOffset=0, hal_offset_t endOffset=0) const =0hal::SlicedSegmentpure virtual
toChild(BottomSegmentIteratorConstPtr bs, hal_size_t child) const =0hal::TopSegmentIteratorpure virtual
toChildG(BottomSegmentIteratorConstPtr bs, const Genome *childGenome) const =0hal::TopSegmentIteratorpure virtual
toLeft(hal_index_t leftCutoff=NULL_INDEX) const =0hal::SegmentIteratorpure virtual
toNextParalogy() const =0hal::TopSegmentIteratorpure virtual
toParseUp(BottomSegmentIteratorConstPtr bs) const =0hal::TopSegmentIteratorpure virtual
toReverse() const =0hal::SlicedSegmentpure virtual
toReverseInPlace() const =0hal::SlicedSegmentpure virtual
toRight(hal_index_t rightCutoff=NULL_INDEX) const =0hal::SegmentIteratorpure virtual
toSite(hal_index_t position, bool slice=true) const =0hal::SegmentIteratorpure virtual
~Segment()=0 (defined in hal::Segment)hal::Segmentinlineprotectedpure virtual
~SegmentIterator()=0 (defined in hal::SegmentIterator)hal::SegmentIteratorinlineprotectedpure virtual
~SlicedSegment()=0 (defined in hal::SlicedSegment)hal::SlicedSegmentinlineprotectedpure virtual
~TopSegment()=0 (defined in hal::TopSegment)hal::TopSegmentinlineprotectedpure virtual
~TopSegmentIterator()=0 (defined in hal::TopSegmentIterator)hal::TopSegmentIteratorinlineprotectedpure virtual