All Classes Namespaces Functions Pages
hal::GappedTopSegmentIterator Member List

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

adjacentTo(GappedTopSegmentIteratorConstPtr other) const =0 | hal::GappedTopSegmentIterator | pure virtual
copy()=0 | hal::GappedTopSegmentIterator | pure virtual
copy() const =0 | hal::GappedTopSegmentIterator | pure virtual
copy(GappedTopSegmentIteratorConstPtr ts) const =0 | hal::GappedTopSegmentIterator | pure virtual
counted_ptr< const GappedTopSegmentIterator > (defined in hal::GappedTopSegmentIterator) | hal::GappedTopSegmentIterator | friend
counted_ptr< GappedTopSegmentIterator > (defined in hal::GappedTopSegmentIterator) | hal::GappedTopSegmentIterator | friend
equals(GappedTopSegmentIteratorConstPtr other) const =0 | hal::GappedTopSegmentIterator | pure virtual
getArrayIndex() const =0 | hal::Segment | pure virtual
getAtomic() const =0 | hal::GappedSegmentIterator | pure virtual
getChildIndex() const =0 | hal::GappedSegmentIterator | pure virtual
getEndOffset() const =0 | hal::SlicedSegment | pure virtual
getEndPosition() const =0 | hal::Segment | pure virtual
getGapThreshold() const =0 | hal::GappedSegmentIterator | pure virtual
getGenome() const =0 | hal::Segment | pure virtual
getGenome()=0 | hal::Segment | pure virtual
getLeft() const =0 | hal::GappedTopSegmentIterator | pure virtual
getLeftArrayIndex() const =0 | hal::GappedSegmentIterator | 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
getNumGapBases() const =0 | hal::GappedSegmentIterator | pure virtual
getNumGaps() const =0 | hal::GappedSegmentIterator | pure virtual
getNumSegments() const =0 | hal::GappedSegmentIterator | pure virtual
getParentReversed() const =0 | hal::GappedTopSegmentIterator | pure virtual
getReversed() const =0 | hal::SlicedSegment | pure virtual
getRight() const =0 | hal::GappedTopSegmentIterator | pure virtual
getRightArrayIndex() const =0 | hal::GappedSegmentIterator | 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
hasNextParalogy() const =0 | hal::GappedTopSegmentIterator | pure virtual
hasParent() const =0 | hal::GappedTopSegmentIterator | pure virtual
isCanonicalParalog() const =0 | hal::GappedTopSegmentIterator | 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
setCoordinates(hal_index_t startPos, hal_size_t length)=0 | hal::Segment | pure virtual
setLeft(TopSegmentIteratorConstPtr ts) const =0 | hal::GappedTopSegmentIterator | pure virtual
slice(hal_offset_t startOffset=0, hal_offset_t endOffset=0) const =0 | hal::SlicedSegment | pure virtual
toChild(GappedBottomSegmentIteratorConstPtr bs) const =0 | hal::GappedTopSegmentIterator | pure virtual
toLeft(hal_index_t leftCutoff=NULL_INDEX) const =0 | hal::SegmentIterator | pure virtual
toNextParalogy() const =0 | hal::GappedTopSegmentIterator | 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
~GappedSegmentIterator()=0 (defined in hal::GappedSegmentIterator) | hal::GappedSegmentIterator | inlineprotectedpure virtual
~GappedTopSegmentIterator()=0 (defined in hal::GappedTopSegmentIterator) | hal::GappedTopSegmentIterator | inlineprotectedpure 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