halapi
hierarchichalalignmentformatapi
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
 All Classes Functions Variables