This is the complete list of members for hal::TopSegmentIterator, including all inherited members.
copy()=0 | hal::TopSegmentIterator | pure virtual |
copy() const =0 | hal::TopSegmentIterator | pure virtual |
copy(TopSegmentIteratorConstPtr ts) const =0 | hal::TopSegmentIterator | pure virtual |
counted_ptr< const TopSegmentIterator > (defined in hal::TopSegmentIterator) | hal::TopSegmentIterator | friend |
counted_ptr< TopSegmentIterator > (defined in hal::TopSegmentIterator) | hal::TopSegmentIterator | friend |
equals(TopSegmentIteratorConstPtr other) const =0 | hal::TopSegmentIterator | pure virtual |
getArrayIndex() const =0 | hal::Segment | pure virtual |
getBottomParseIndex() const =0 | hal::TopSegment | pure virtual |
getBottomParseOffset() const =0 | hal::TopSegment | 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 |
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 |
getReversed() const =0 | hal::SlicedSegment | pure virtual |
getRightParentIndex() const =0 | hal::TopSegment | 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 |
getTopSegment()=0 | hal::TopSegmentIterator | pure virtual |
getTopSegment() const =0 | hal::TopSegmentIterator | 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 |
slice(hal_offset_t startOffset=0, hal_offset_t endOffset=0) const =0 | hal::SlicedSegment | pure virtual |
toChild(BottomSegmentIteratorConstPtr bs, hal_size_t child) const =0 | hal::TopSegmentIterator | pure virtual |
toChildG(BottomSegmentIteratorConstPtr bs, const Genome *childGenome) const =0 | hal::TopSegmentIterator | pure virtual |
toLeft(hal_index_t leftCutoff=NULL_INDEX) const =0 | hal::SegmentIterator | pure virtual |
toNextParalogy() const =0 | hal::TopSegmentIterator | pure virtual |
toParseUp(BottomSegmentIteratorConstPtr bs) const =0 | hal::TopSegmentIterator | 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 |
~Segment()=0 (defined in hal::Segment) | hal::Segment | inlineprotectedpure virtual |
~SegmentIterator()=0 (defined in hal::SegmentIterator) | hal::SegmentIterator | inlineprotectedpure virtual |
~SlicedSegment()=0 (defined in hal::SlicedSegment) | hal::SlicedSegment | inlineprotectedpure virtual |
~TopSegment()=0 (defined in hal::TopSegment) | hal::TopSegment | inlineprotectedpure virtual |
~TopSegmentIterator()=0 (defined in hal::TopSegmentIterator) | hal::TopSegmentIterator | inlineprotectedpure virtual |