IntronList.h

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00001 /*
00002  * This program is free software; you can redistribute it and/or modify
00003  * it under the terms of the GNU General Public License as published by
00004  * the Free Software Foundation; either version 3 of the License, or
00005  * (at your option) any later version.
00006  *
00007  * Written (W) 2009 Jonas Behr
00008  * Copyright (C) 2009 Fraunhofer Institute FIRST and Max-Planck-Society
00009  */
00010 
00011 #ifndef __INTRON_LIST__
00012 #define __INTRON_LIST__
00013 
00014 #include "lib/common.h"
00015 #include "base/SGObject.h"
00016 
00017 namespace shogun
00018 {
00020 class CIntronList : public CSGObject 
00021 {
00022     public:
00023 
00026         CIntronList();
00027 
00028         virtual ~CIntronList();
00029 
00035         void init_list(int32_t* all_pos, int32_t len);  
00036 
00044         void read_introns(int32_t* start_pos, int32_t* end_pos, int32_t* quality, int32_t len);
00045 
00052         void get_intron_support(int32_t* values, int32_t from_pos, int32_t to_pos);
00053     
00057         inline virtual const char* get_name() const { return "IntronList"; }
00058     protected:
00060         int32_t m_length;
00061 
00063         int32_t* m_all_pos;
00064 
00069         int32_t** m_intron_list;
00070 
00074         int32_t** m_quality_list;
00075 };
00076 }
00077 #endif
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