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