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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
hal::GappedSegmentIterator::getChildIndex
virtual hal_size_t getChildIndex() const =0
hal::GappedSegmentIterator::getNumSegments
virtual hal_size_t getNumSegments() const =0
hal::SegmentIterator
Definition: halSegmentIterator.h:20
hal::GappedSegmentIterator::getLeftArrayIndex
virtual hal_index_t getLeftArrayIndex() const =0
hal::GappedSegmentIterator::getAtomic
virtual bool getAtomic() const =0
hal::GappedSegmentIterator::getNumGapBases
virtual hal_size_t getNumGapBases() const =0
hal::GappedSegmentIterator::getRightArrayIndex
virtual hal_index_t getRightArrayIndex() const =0
hal::GappedSegmentIterator::getGapThreshold
virtual hal_size_t getGapThreshold() const =0
hal::GappedSegmentIterator::getNumGaps
virtual hal_size_t getNumGaps() const =0
hal::GappedSegmentIterator
Definition: halGappedSegmentIterator.h:22