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 | inlineprotectedpure virtual |
~Segment()=0 (defined in hal::Segment) | hal::Segment | inlineprotectedpure virtual |
~SlicedSegment()=0 (defined in hal::SlicedSegment) | hal::SlicedSegment | inlineprotectedpure virtual |