halapi
hierarchichalalignmentformatapi
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hal::Genome Member List

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

containsDNAArray() const =0hal::Genomepure virtual
getAlignment() const =0hal::Genomepure virtual
getBottomSegmentEndIterator() const =0hal::SegmentedSequencepure virtual
getBottomSegmentIterator(hal_index_t position=0)=0hal::SegmentedSequencepure virtual
getBottomSegmentIterator(hal_index_t position=0) const =0hal::SegmentedSequencepure virtual
getChild(hal_size_t childIdx)=0hal::Genomepure virtual
getChild(hal_size_t childIdx) const =0hal::Genomepure virtual
getChildIndex(const Genome *child) const =0hal::Genomepure 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 =0hal::SegmentedSequencepure virtual
getDNAEndIterator() const =0hal::SegmentedSequencepure virtual
getDNAIterator(hal_index_t position=0)=0hal::SegmentedSequencepure virtual
getDNAIterator(hal_index_t position=0) const =0hal::SegmentedSequencepure virtual
getGappedBottomSegmentIterator(hal_index_t i, hal_size_t childIdx, hal_size_t gapThreshold, bool atomic=false) const =0hal::SegmentedSequencepure virtual
getGappedTopSegmentIterator(hal_index_t i, hal_size_t gapThreshold, bool atomic=false) const =0hal::SegmentedSequencepure virtual
getMetaData()=0hal::Genomepure virtual
getMetaData() const =0hal::Genomepure virtual
getName() const =0hal::Genomepure virtual
getNumBottomSegments() const =0hal::SegmentedSequencepure virtual
getNumChildren() const =0hal::Genomepure virtual
getNumSequences() const =0hal::Genomepure virtual
getNumTopSegments() const =0hal::SegmentedSequencepure virtual
getParent()=0hal::Genomepure virtual
getParent() const =0hal::Genomepure virtual
getRearrangement(hal_index_t position, hal_size_t gapLengthThreshold, double nThreshold, bool atomic=false) const =0hal::SegmentedSequencepure virtual
getSequence(const std::string &name)=0hal::Genomepure virtual
getSequence(const std::string &name) const =0hal::Genomepure virtual
getSequenceBySite(hal_size_t position)=0hal::Genomepure virtual
getSequenceBySite(hal_size_t position) const =0hal::Genomepure virtual
getSequenceEndIterator() const =0hal::Genomepure virtual
getSequenceIterator(hal_index_t position=0)=0hal::Genomepure virtual
getSequenceIterator(hal_index_t position=0) const =0hal::Genomepure virtual
getSequenceLength() const =0hal::SegmentedSequencepure virtual
getString(std::string &outString) const =0hal::SegmentedSequencepure virtual
getSubString(std::string &outString, hal_size_t start, hal_size_t length) const =0hal::SegmentedSequencepure virtual
getTopSegmentEndIterator() const =0hal::SegmentedSequencepure virtual
getTopSegmentIterator(hal_index_t position=0)=0hal::SegmentedSequencepure virtual
getTopSegmentIterator(hal_index_t position=0) const =0hal::SegmentedSequencepure virtual
setDimensions(const std::vector< hal::Sequence::Info > &sequenceDimensions, bool storeDNAArrays=true)=0hal::Genomepure virtual
setString(const std::string &inString)=0hal::SegmentedSequencepure virtual
setSubString(const std::string &inString, hal_size_t start, hal_size_t length)=0hal::SegmentedSequencepure virtual
updateBottomDimensions(const std::vector< hal::Sequence::UpdateInfo > &sequenceDimensions)=0hal::Genomepure virtual
updateTopDimensions(const std::vector< hal::Sequence::UpdateInfo > &sequenceDimensions)=0hal::Genomepure virtual
~Genome()=0hal::Genomeinlineprotectedpure virtual
~SegmentedSequence()=0hal::SegmentedSequenceinlineprotectedpure virtual