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hierarchichalalignmentformatapi
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halGappedSegmentIterator.h
1 /*
2  * Copyright (C) 2012 by Glenn Hickey (hickey@soe.ucsc.edu)
3  *
4  * Released under the MIT license, see LICENSE.txt
5  */
6 
7 #ifndef _HALGAPPEDSEGMENTITERATOR_H
8 #define _HALGAPPEDSEGMENTITERATOR_H
9 
10 #include "halSegmentIterator.h"
11 
12 namespace hal {
13 
22 class GappedSegmentIterator : virtual public SegmentIterator
23 {
24 public:
25 
29  virtual hal_size_t getGapThreshold() const = 0;
30 
36  virtual bool getAtomic() const = 0;
37 
40  virtual hal_size_t getChildIndex() const = 0;
41 
44  virtual hal_size_t getNumSegments() const = 0;
45 
48  virtual hal_size_t getNumGaps() const = 0;
49 
52  virtual hal_size_t getNumGapBases() const = 0;
53 
55  virtual hal_index_t getLeftArrayIndex() const = 0;
56 
58  virtual hal_index_t getRightArrayIndex() const = 0;
59 
60 protected:
61  friend class counted_ptr<GappedSegmentIterator>;
62  friend class counted_ptr<const GappedSegmentIterator>;
63  virtual ~GappedSegmentIterator() = 0;
64 };
65 
66 inline GappedSegmentIterator::~GappedSegmentIterator() {}
67 
68 }
69 #endif
virtual hal_size_t getChildIndex() const =0
virtual hal_size_t getNumSegments() const =0
Definition: halSegmentIterator.h:20
virtual hal_index_t getLeftArrayIndex() const =0
virtual bool getAtomic() const =0
virtual hal_size_t getNumGapBases() const =0
virtual hal_index_t getRightArrayIndex() const =0
virtual hal_size_t getGapThreshold() const =0
virtual hal_size_t getNumGaps() const =0
Definition: halGappedSegmentIterator.h:22