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halGappedSegmentIterator.h
/*
* Copyright (C) 2012 by Glenn Hickey (hickey@soe.ucsc.edu)
*
* Released under the MIT license, see LICENSE.txt
*/
#ifndef _HALGAPPEDSEGMENTITERATOR_H
#define _HALGAPPEDSEGMENTITERATOR_H
#include "halSegmentIterator.h"
namespace hal {
class GappedSegmentIterator : virtual public SegmentIterator
{
public:
virtual hal_size_t getGapThreshold() const = 0;
virtual bool getAtomic() const = 0;
virtual hal_size_t getChildIndex() const = 0;
virtual hal_size_t getNumSegments() const = 0;
virtual hal_size_t getNumGaps() const = 0;
virtual hal_size_t getNumGapBases() const = 0;
virtual hal_index_t getLeftArrayIndex() const = 0;
virtual hal_index_t getRightArrayIndex() const = 0;
protected:
friend class counted_ptr<GappedSegmentIterator>;
friend class counted_ptr<const GappedSegmentIterator>;
virtual ~GappedSegmentIterator() = 0;
};
inline GappedSegmentIterator::~GappedSegmentIterator() {}
}
#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