This is the complete list of members for hal::Genome, including all inherited members.
containsDNAArray() const =0 | hal::Genome | pure virtual |
getAlignment() const =0 | hal::Genome | 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 |
getChild(hal_size_t childIdx)=0 | hal::Genome | pure virtual |
getChild(hal_size_t childIdx) const =0 | hal::Genome | pure virtual |
getChildIndex(const Genome *child) const =0 | hal::Genome | 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 |
getMetaData()=0 | hal::Genome | pure virtual |
getMetaData() const =0 | hal::Genome | pure virtual |
getName() const =0 | hal::Genome | pure virtual |
getNumBottomSegments() const =0 | hal::SegmentedSequence | pure virtual |
getNumChildren() const =0 | hal::Genome | pure virtual |
getNumSequences() const =0 | hal::Genome | pure virtual |
getNumTopSegments() const =0 | hal::SegmentedSequence | pure virtual |
getParent()=0 | hal::Genome | pure virtual |
getParent() const =0 | hal::Genome | pure virtual |
getRearrangement(hal_index_t position, hal_size_t gapLengthThreshold, double nThreshold, bool atomic=false) const =0 | hal::SegmentedSequence | pure virtual |
getSequence(const std::string &name)=0 | hal::Genome | pure virtual |
getSequence(const std::string &name) const =0 | hal::Genome | pure virtual |
getSequenceBySite(hal_size_t position)=0 | hal::Genome | pure virtual |
getSequenceBySite(hal_size_t position) const =0 | hal::Genome | pure virtual |
getSequenceEndIterator() const =0 | hal::Genome | pure virtual |
getSequenceIterator(hal_index_t position=0)=0 | hal::Genome | pure virtual |
getSequenceIterator(hal_index_t position=0) const =0 | hal::Genome | 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 |
setDimensions(const std::vector< hal::Sequence::Info > &sequenceDimensions, bool storeDNAArrays=true)=0 | hal::Genome | 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 |
updateBottomDimensions(const std::vector< hal::Sequence::UpdateInfo > &sequenceDimensions)=0 | hal::Genome | pure virtual |
updateTopDimensions(const std::vector< hal::Sequence::UpdateInfo > &sequenceDimensions)=0 | hal::Genome | pure virtual |
~Genome()=0 | hal::Genome | inlineprotectedpure virtual |
~SegmentedSequence()=0 | hal::SegmentedSequence | inlineprotectedpure virtual |