7 #ifndef _HALSEGMENTEDSEQUENCE_H
8 #define _HALSEGMENTEDSEQUENCE_H
43 hal_index_t position = 0) = 0;
48 hal_index_t position = 0)
const = 0;
56 hal_index_t position = 0) = 0;
61 hal_index_t position = 0)
const = 0;
70 hal_index_t position = 0) = 0;
75 hal_index_t position = 0)
const = 0;
91 const std::set<const Genome*>* targets = NULL,
92 hal_size_t maxInsertLength = 0,
93 hal_index_t position = 0,
94 hal_index_t lastPosition = NULL_INDEX,
96 bool noAncestors =
false,
97 bool reverseStrand =
false)
const = 0;
101 virtual void getString(std::string& outString)
const = 0;
105 virtual void setString(
const std::string& inString) = 0;
112 virtual void getSubString(std::string& outString, hal_size_t start,
113 hal_size_t length)
const = 0;
121 hal_size_t length) = 0;
134 hal_size_t gapLengthThreshold,
136 bool atomic =
false)
const = 0;
144 hal_index_t i, hal_size_t gapThreshold,
bool atomic =
false)
const = 0;
152 hal_index_t i, hal_size_t childIdx, hal_size_t gapThreshold,
153 bool atomic =
false)
const = 0;
virtual TopSegmentIteratorConstPtr getTopSegmentEndIterator() const =0
virtual RearrangementPtr getRearrangement(hal_index_t position, hal_size_t gapLengthThreshold, double nThreshold, bool atomic=false) const =0
virtual void setSubString(const std::string &inString, hal_size_t start, hal_size_t length)=0
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
virtual BottomSegmentIteratorPtr getBottomSegmentIterator(hal_index_t position=0)=0
virtual TopSegmentIteratorPtr getTopSegmentIterator(hal_index_t position=0)=0
virtual hal_size_t getNumBottomSegments() const =0
virtual void setString(const std::string &inString)=0
virtual ~SegmentedSequence()=0
Definition: halSegmentedSequence.h:161
virtual void getString(std::string &outString) const =0
virtual hal_size_t getSequenceLength() const =0
virtual GappedBottomSegmentIteratorConstPtr getGappedBottomSegmentIterator(hal_index_t i, hal_size_t childIdx, hal_size_t gapThreshold, bool atomic=false) const =0
Definition: halSegmentedSequence.h:23
virtual BottomSegmentIteratorConstPtr getBottomSegmentEndIterator() const =0
virtual DNAIteratorConstPtr getDNAEndIterator() const =0
virtual hal_size_t getNumTopSegments() const =0
virtual GappedTopSegmentIteratorConstPtr getGappedTopSegmentIterator(hal_index_t i, hal_size_t gapThreshold, bool atomic=false) const =0
virtual void getSubString(std::string &outString, hal_size_t start, hal_size_t length) const =0
virtual DNAIteratorPtr getDNAIterator(hal_index_t position=0)=0