70 virtual void getString(std::string& outString)
const = 0;
75 virtual void setCoordinates(hal_index_t startPos, hal_size_t length) = 0;
82 virtual bool leftOf(hal_index_t genomePos)
const = 0;
86 virtual bool rightOf(hal_index_t genomePos)
const = 0;
90 virtual bool overlaps(hal_index_t genomePos)
const = 0;
94 virtual bool isFirst()
const = 0;
98 virtual bool isLast()
const = 0;
109 virtual bool isTop()
const = 0;
129 std::set<MappedSegmentConstPtr>& outSegments,
131 const std::set<const Genome*>* genomesOnPath = NULL,
133 hal_size_t minLength = 0)
const = 0;
136 virtual void print(std::ostream& os)
const = 0;
139 friend class counted_ptr<Segment>;
140 friend class counted_ptr<const Segment>;
141 virtual ~Segment() = 0;
144 inline Segment::~Segment() {}
146 inline std::ostream& operator<<(std::ostream& os,
const Segment& s)
virtual hal_index_t getArrayIndex() const =0
Definition: halSegment.h:21
Definition: halGenome.h:24
virtual bool rightOf(hal_index_t genomePos) const =0
virtual hal_index_t getEndPosition() const =0
virtual const Sequence * getSequence() const =0
virtual bool leftOf(hal_index_t genomePos) const =0
virtual bool isFirst() const =0
virtual bool isTop() const =0
virtual void setArrayIndex(Genome *genome, hal_index_t arrayIndex)=0
virtual bool isLast() const =0
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
virtual void getString(std::string &outString) const =0
virtual void setCoordinates(hal_index_t startPos, hal_size_t length)=0
virtual const Genome * getGenome() const =0
virtual bool isMissingData(double nThreshold) const =0
virtual hal_index_t getStartPosition() const =0
virtual void print(std::ostream &os) const =0
Definition: halSequence.h:20
virtual bool overlaps(hal_index_t genomePos) const =0
virtual hal_size_t getLength() const =0