This is the complete list of members for hal::Sequence, including all inherited members.
getArrayIndex() const =0 | hal::Sequence | pure virtual |
getBottomSegmentArrayIndex() const =0 | hal::Sequence | pure virtual |
getBottomSegmentEndIterator() const =0 | hal::SegmentedSequence | pure virtual |
getBottomSegmentIterator(hal_index_t position=0)=0 | hal::SegmentedSequence | pure virtual |
getBottomSegmentIterator(hal_index_t position=0) const =0 | hal::SegmentedSequence | pure virtual |
getColumnIterator(const std::set< const Genome * > *targets=NULL, hal_size_t maxInsertLength=0, hal_index_t position=0, hal_index_t lastPosition=NULL_INDEX, bool noDupes=false, bool noAncestors=false, bool reverseStrand=false) const =0 | hal::SegmentedSequence | pure virtual |
getDNAEndIterator() const =0 | hal::SegmentedSequence | pure virtual |
getDNAIterator(hal_index_t position=0)=0 | hal::SegmentedSequence | pure virtual |
getDNAIterator(hal_index_t position=0) const =0 | hal::SegmentedSequence | pure virtual |
getEndPosition() const =0 | hal::Sequence | pure virtual |
getFullName() const =0 | hal::Sequence | pure virtual |
getGappedBottomSegmentIterator(hal_index_t i, hal_size_t childIdx, hal_size_t gapThreshold, bool atomic=false) const =0 | hal::SegmentedSequence | pure virtual |
getGappedTopSegmentIterator(hal_index_t i, hal_size_t gapThreshold, bool atomic=false) const =0 | hal::SegmentedSequence | pure virtual |
getGenome() const =0 | hal::Sequence | pure virtual |
getGenome()=0 | hal::Sequence | pure virtual |
getName() const =0 | hal::Sequence | pure virtual |
getNumBottomSegments() const =0 | hal::SegmentedSequence | pure virtual |
getNumTopSegments() const =0 | hal::SegmentedSequence | pure virtual |
getRearrangement(hal_index_t position, hal_size_t gapLengthThreshold, double nThreshold, bool atomic=false) const =0 | hal::SegmentedSequence | pure virtual |
getSequenceLength() const =0 | hal::SegmentedSequence | pure virtual |
getStartPosition() const =0 | hal::Sequence | pure virtual |
getString(std::string &outString) const =0 | hal::SegmentedSequence | pure virtual |
getSubString(std::string &outString, hal_size_t start, hal_size_t length) const =0 | hal::SegmentedSequence | pure virtual |
getTopSegmentArrayIndex() const =0 | hal::Sequence | pure virtual |
getTopSegmentEndIterator() const =0 | hal::SegmentedSequence | pure virtual |
getTopSegmentIterator(hal_index_t position=0)=0 | hal::SegmentedSequence | pure virtual |
getTopSegmentIterator(hal_index_t position=0) const =0 | hal::SegmentedSequence | pure virtual |
setString(const std::string &inString)=0 | hal::SegmentedSequence | pure virtual |
setSubString(const std::string &inString, hal_size_t start, hal_size_t length)=0 | hal::SegmentedSequence | pure virtual |
~SegmentedSequence()=0 | hal::SegmentedSequence | inlineprotectedpure virtual |
~Sequence()=0 | hal::Sequence | inlineprotectedpure virtual |