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IntronList.h
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1 /*
2  * This program is free software; you can redistribute it and/or modify
3  * it under the terms of the GNU General Public License as published by
4  * the Free Software Foundation; either version 3 of the License, or
5  * (at your option) any later version.
6  *
7  * Written (W) 2009 Jonas Behr
8  * Copyright (C) 2009 Fraunhofer Institute FIRST and Max-Planck-Society
9  */
10 
11 #ifndef __INTRON_LIST__
12 #define __INTRON_LIST__
13 
14 #include <shogun/lib/config.h>
15 
16 #include <shogun/lib/common.h>
17 #include <shogun/base/SGObject.h>
18 
19 namespace shogun
20 {
22 class CIntronList : public CSGObject
23 {
24  public:
25 
28  CIntronList();
29 
30  virtual ~CIntronList();
31 
37  void init_list(int32_t* all_pos, int32_t len);
38 
46  void read_introns(int32_t* start_pos, int32_t* end_pos, int32_t* quality, int32_t len);
47 
54  void get_intron_support(int32_t* values, int32_t from_pos, int32_t to_pos);
55 
59  virtual const char* get_name() const { return "IntronList"; }
60  protected:
62  int32_t m_length;
63 
65  int32_t* m_all_pos;
66 
71  int32_t** m_intron_list;
72 
76  int32_t** m_quality_list;
77 };
78 }
79 #endif

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