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virtual SlicedSegmentConstPtr | getSource () const =0 |
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virtual bool | lessThan (const MappedSegmentConstPtr &other) const =0 |
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virtual bool | lessThanBySource (const MappedSegmentConstPtr &other) const =0 |
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virtual bool | equals (const MappedSegmentConstPtr &other) const =0 |
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virtual void | flip () const =0 |
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virtual void | fullReverse () const =0 |
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virtual MappedSegmentConstPtr | copy () const =0 |
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virtual bool | canMergeRightWith (const MappedSegmentConstPtr &next, const std::set< hal_index_t > *cutSet=NULL, const std::set< hal_index_t > *sourceCutSet=NULL) const =0 |
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virtual void | print (std::ostream &os) const =0 |
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virtual void | toReverse () const =0 |
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virtual void | toReverseInPlace () const =0 |
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virtual hal_offset_t | getStartOffset () const =0 |
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virtual hal_offset_t | getEndOffset () const =0 |
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virtual void | slice (hal_offset_t startOffset=0, hal_offset_t endOffset=0) const =0 |
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virtual bool | getReversed () const =0 |
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virtual void | setArrayIndex (Genome *genome, hal_index_t arrayIndex)=0 |
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virtual void | setArrayIndex (const Genome *genome, hal_index_t arrayIndex) const =0 |
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virtual const Genome * | getGenome () const =0 |
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virtual Genome * | getGenome ()=0 |
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virtual const Sequence * | getSequence () const =0 |
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virtual Sequence * | getSequence ()=0 |
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virtual hal_index_t | getStartPosition () const =0 |
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virtual hal_index_t | getEndPosition () const =0 |
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virtual hal_size_t | getLength () const =0 |
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virtual void | getString (std::string &outString) const =0 |
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virtual void | setCoordinates (hal_index_t startPos, hal_size_t length)=0 |
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virtual hal_index_t | getArrayIndex () const =0 |
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virtual bool | leftOf (hal_index_t genomePos) const =0 |
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virtual bool | rightOf (hal_index_t genomePos) const =0 |
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virtual bool | overlaps (hal_index_t genomePos) const =0 |
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virtual bool | isFirst () const =0 |
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virtual bool | isLast () const =0 |
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virtual bool | isMissingData (double nThreshold) const =0 |
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virtual bool | isTop () const =0 |
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virtual hal_size_t | getMappedSegments (std::set< MappedSegmentConstPtr > &outSegments, const Genome *tgtGenome, const std::set< const Genome * > *genomesOnPath=NULL, bool doDupes=true, hal_size_t minLength=0) const =0 |
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Interface for a mapped segement. A mapped segment keeps track of a homologous region in another genome (from which it was mapped). Mapped segments are used to keep pairwise alignment fragments across the tree as an alternative to the column iterator.