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inc/bottomSegment.h

    00001 /*
    00002  * Copyright (C) 2012 by Glenn Hickey (hickey@soe.ucsc.edu)
    00003  *
    00004  * Released under the MIT license, see LICENSE.txt
    00005  */
    00006
    00007 #ifndef _BOTTOMSEGMENT_H
    00008 #define _BOTTOMSEGMENT_H
    00009
    00010 #include "genomeSegment.h"
    00011
    00012 namespace hal {
    00013
    00017 class BottomSegment: public GenomeSegment<genidx_t, segidx_t>
    00018 {
    00019 public:
    00022         virtual int getNumChildren() const = 0;
    00024         virtual segidx_t getChildIndex(int i) const = 0;
    00026         virtual bool getReverseComp(int i) const = 0;
    00028         segidx_t getRepeatIndex() const;
    00029
    00030 protected:
    00031         segidx_t _repeatIndex;
    00032 };
    00033
    00034 }
    00035 #endif

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