halapi
hierarchichalalignmentformatapi
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hal::MappedSegment Member List

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

canMergeRightWith(const MappedSegmentConstPtr &next, const std::set< hal_index_t > *cutSet=NULL, const std::set< hal_index_t > *sourceCutSet=NULL) const =0hal::MappedSegmentpure virtual
copy() const =0hal::MappedSegmentpure virtual
counted_ptr< const MappedSegment > (defined in hal::MappedSegment)hal::MappedSegmentfriend
counted_ptr< MappedSegment > (defined in hal::MappedSegment)hal::MappedSegmentfriend
equals(const MappedSegmentConstPtr &other) const =0hal::MappedSegmentpure virtual
flip() const =0hal::MappedSegmentpure virtual
fullReverse() const =0hal::MappedSegmentpure virtual
getArrayIndex() const =0hal::Segmentpure virtual
getEndOffset() const =0hal::SlicedSegmentpure virtual
getEndPosition() const =0hal::Segmentpure virtual
getGenome() const =0hal::Segmentpure virtual
getGenome()=0hal::Segmentpure 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
getReversed() const =0hal::SlicedSegmentpure virtual
getSequence() const =0hal::Segmentpure virtual
getSequence()=0hal::Segmentpure virtual
getSource() const =0hal::MappedSegmentpure virtual
getStartOffset() const =0hal::SlicedSegmentpure virtual
getStartPosition() const =0hal::Segmentpure virtual
getString(std::string &outString) const =0hal::Segmentpure 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
lessThan(const MappedSegmentConstPtr &other) const =0hal::MappedSegmentpure virtual
lessThanBySource(const MappedSegmentConstPtr &other) const =0hal::MappedSegmentpure virtual
overlaps(hal_index_t genomePos) const =0hal::Segmentpure virtual
print(std::ostream &os) const =0hal::MappedSegmentpure 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
slice(hal_offset_t startOffset=0, hal_offset_t endOffset=0) const =0hal::SlicedSegmentpure virtual
toReverse() const =0hal::SlicedSegmentpure virtual
toReverseInPlace() const =0hal::SlicedSegmentpure virtual
~MappedSegment()=0 (defined in hal::MappedSegment)hal::MappedSegmentinlineprotectedpure virtual
~Segment()=0 (defined in hal::Segment)hal::Segmentinlineprotectedpure virtual
~SlicedSegment()=0 (defined in hal::SlicedSegment)hal::SlicedSegmentinlineprotectedpure virtual