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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 =0 | hal::MappedSegment | pure virtual
copy() const =0 | hal::MappedSegment | pure virtual
counted_ptr< const MappedSegment > (defined in hal::MappedSegment) | hal::MappedSegment | friend
counted_ptr< MappedSegment > (defined in hal::MappedSegment) | hal::MappedSegment | friend
equals(const MappedSegmentConstPtr &other) const =0 | hal::MappedSegment | pure virtual
flip() const =0 | hal::MappedSegment | pure virtual
fullReverse() const =0 | hal::MappedSegment | pure virtual
getArrayIndex() const =0 | hal::Segment | 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
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
getReversed() const =0 | hal::SlicedSegment | pure virtual
getSequence() const =0 | hal::Segment | pure virtual
getSequence()=0 | hal::Segment | pure virtual
getSource() const =0 | hal::MappedSegment | 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
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
lessThan(const MappedSegmentConstPtr &other) const =0 | hal::MappedSegment | pure virtual
lessThanBySource(const MappedSegmentConstPtr &other) const =0 | hal::MappedSegment | pure virtual
overlaps(hal_index_t genomePos) const =0 | hal::Segment | pure virtual
print(std::ostream &os) const =0 | hal::MappedSegment | 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
setCoordinates(hal_index_t startPos, hal_size_t length)=0 | hal::Segment | pure virtual
slice(hal_offset_t startOffset=0, hal_offset_t endOffset=0) const =0 | hal::SlicedSegment | pure virtual
toReverse() const =0 | hal::SlicedSegment | pure virtual
toReverseInPlace() const =0 | hal::SlicedSegment | pure virtual
~MappedSegment()=0 (defined in hal::MappedSegment) | hal::MappedSegment | inline protected pure virtual
~Segment()=0 (defined in hal::Segment) | hal::Segment | inline protected pure virtual
~SlicedSegment()=0 (defined in hal::SlicedSegment) | hal::SlicedSegment | inline protected pure virtual