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virtual const std::string & | getName () const =0 |
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virtual void | setDimensions (const std::vector< hal::Sequence::Info > &sequenceDimensions, bool storeDNAArrays=true)=0 |
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virtual void | updateTopDimensions (const std::vector< hal::Sequence::UpdateInfo > &sequenceDimensions)=0 |
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virtual void | updateBottomDimensions (const std::vector< hal::Sequence::UpdateInfo > &sequenceDimensions)=0 |
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virtual hal_size_t | getNumSequences () const =0 |
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virtual Sequence * | getSequence (const std::string &name)=0 |
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virtual const Sequence * | getSequence (const std::string &name) const =0 |
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virtual Sequence * | getSequenceBySite (hal_size_t position)=0 |
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virtual const Sequence * | getSequenceBySite (hal_size_t position) const =0 |
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virtual SequenceIteratorPtr | getSequenceIterator (hal_index_t position=0)=0 |
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virtual SequenceIteratorConstPtr | getSequenceIterator (hal_index_t position=0) const =0 |
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virtual SequenceIteratorConstPtr | getSequenceEndIterator () const =0 |
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virtual MetaData * | getMetaData ()=0 |
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virtual const MetaData * | getMetaData () const =0 |
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virtual Genome * | getParent ()=0 |
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virtual const Genome * | getParent () const =0 |
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virtual Genome * | getChild (hal_size_t childIdx)=0 |
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virtual const Genome * | getChild (hal_size_t childIdx) const =0 |
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virtual hal_size_t | getNumChildren () const =0 |
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virtual hal_index_t | getChildIndex (const Genome *child) const =0 |
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virtual bool | containsDNAArray () const =0 |
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virtual const Alignment * | getAlignment () const =0 |
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virtual hal_size_t | getSequenceLength () const =0 |
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virtual hal_size_t | getNumTopSegments () const =0 |
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virtual hal_size_t | getNumBottomSegments () const =0 |
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virtual TopSegmentIteratorPtr | getTopSegmentIterator (hal_index_t position=0)=0 |
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virtual TopSegmentIteratorConstPtr | getTopSegmentIterator (hal_index_t position=0) const =0 |
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virtual TopSegmentIteratorConstPtr | getTopSegmentEndIterator () const =0 |
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virtual BottomSegmentIteratorPtr | getBottomSegmentIterator (hal_index_t position=0)=0 |
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virtual
BottomSegmentIteratorConstPtr | getBottomSegmentIterator (hal_index_t position=0) const =0 |
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virtual
BottomSegmentIteratorConstPtr | getBottomSegmentEndIterator () const =0 |
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virtual DNAIteratorPtr | getDNAIterator (hal_index_t position=0)=0 |
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virtual DNAIteratorConstPtr | getDNAIterator (hal_index_t position=0) const =0 |
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virtual DNAIteratorConstPtr | getDNAEndIterator () const =0 |
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virtual ColumnIteratorConstPtr | 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 |
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virtual void | getString (std::string &outString) const =0 |
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virtual void | setString (const std::string &inString)=0 |
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virtual void | getSubString (std::string &outString, hal_size_t start, hal_size_t length) const =0 |
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virtual void | setSubString (const std::string &inString, hal_size_t start, hal_size_t length)=0 |
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virtual RearrangementPtr | getRearrangement (hal_index_t position, hal_size_t gapLengthThreshold, double nThreshold, bool atomic=false) const =0 |
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virtual
GappedTopSegmentIteratorConstPtr | getGappedTopSegmentIterator (hal_index_t i, hal_size_t gapThreshold, bool atomic=false) const =0 |
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virtual
GappedBottomSegmentIteratorConstPtr | getGappedBottomSegmentIterator (hal_index_t i, hal_size_t childIdx, hal_size_t gapThreshold, bool atomic=false) const =0 |
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Interface for a genome within a hal alignment. The genome is comprised of a dna sequence, and two segment arrays (top and bottom) which are used to map between ancestral and descendant genomes. This data is all accessed through iterators.