halapi
hierarchichalalignmentformatapi
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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