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hierarchichalalignmentformatapi
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hal::GappedBottomSegmentIterator Member List

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

adjacentTo(GappedBottomSegmentIteratorConstPtr other) const =0hal::GappedBottomSegmentIteratorpure virtual
copy()=0hal::GappedBottomSegmentIteratorpure virtual
copy() const =0hal::GappedBottomSegmentIteratorpure virtual
copy(GappedBottomSegmentIteratorConstPtr ts) const =0hal::GappedBottomSegmentIteratorpure virtual
counted_ptr< const GappedBottomSegmentIterator > (defined in hal::GappedBottomSegmentIterator)hal::GappedBottomSegmentIteratorfriend
counted_ptr< GappedBottomSegmentIterator > (defined in hal::GappedBottomSegmentIterator)hal::GappedBottomSegmentIteratorfriend
equals(GappedBottomSegmentIteratorConstPtr other) const =0hal::GappedBottomSegmentIteratorpure virtual
getArrayIndex() const =0hal::Segmentpure virtual
getAtomic() const =0hal::GappedSegmentIteratorpure virtual
getChildIndex() const =0hal::GappedSegmentIteratorpure virtual
getChildReversed() const =0hal::GappedBottomSegmentIteratorpure virtual
getEndOffset() const =0hal::SlicedSegmentpure virtual
getEndPosition() const =0hal::Segmentpure virtual
getGapThreshold() const =0hal::GappedSegmentIteratorpure virtual
getGenome() const =0hal::Segmentpure virtual
getGenome()=0hal::Segmentpure virtual
getLeft() const =0hal::GappedBottomSegmentIteratorpure virtual
getLeftArrayIndex() const =0hal::GappedSegmentIteratorpure 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
getNumGapBases() const =0hal::GappedSegmentIteratorpure virtual
getNumGaps() const =0hal::GappedSegmentIteratorpure virtual
getNumSegments() const =0hal::GappedSegmentIteratorpure virtual
getReversed() const =0hal::SlicedSegmentpure virtual
getRight() const =0hal::GappedBottomSegmentIteratorpure virtual
getRightArrayIndex() const =0hal::GappedSegmentIteratorpure 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
hasChild() const =0hal::GappedBottomSegmentIteratorpure 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
setCoordinates(hal_index_t startPos, hal_size_t length)=0hal::Segmentpure virtual
setLeft(BottomSegmentIteratorConstPtr bs) const =0hal::GappedBottomSegmentIteratorpure virtual
slice(hal_offset_t startOffset=0, hal_offset_t endOffset=0) const =0hal::SlicedSegmentpure virtual
toLeft(hal_index_t leftCutoff=NULL_INDEX) const =0hal::SegmentIteratorpure virtual
toParent(GappedTopSegmentIteratorConstPtr ts) const =0hal::GappedBottomSegmentIteratorpure 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
~GappedBottomSegmentIterator()=0 (defined in hal::GappedBottomSegmentIterator)hal::GappedBottomSegmentIteratorinlineprotectedpure virtual
~GappedSegmentIterator()=0 (defined in hal::GappedSegmentIterator)hal::GappedSegmentIteratorinlineprotectedpure 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