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hal::SegmentedSequence Member List

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

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
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
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
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
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