SNPStringKernel.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) 2009-2010 Soeren Sonnenburg
00008  * Copyright (C) 2009-2010 Berlin Institute of Technology
00009  */
00010 
00011 #ifndef _SNPSTRINGKERNEL_H___
00012 #define _SNPSTRINGKERNEL_H___
00013 
00014 #include "lib/common.h"
00015 #include "kernel/StringKernel.h"
00016 
00017 namespace shogun
00018 {
00036 class CSNPStringKernel: public CStringKernel<char>
00037 {
00038     public:
00046         CSNPStringKernel(int32_t size, int32_t degree, int32_t win_len, bool inhomogene);
00047 
00056         CSNPStringKernel(
00057             CStringFeatures<char>* l, CStringFeatures<char>* r,
00058             int32_t degree, int32_t win_len, bool inhomogene);
00059 
00060         virtual ~CSNPStringKernel();
00061 
00068         virtual bool init(CFeatures* l, CFeatures* r);
00069 
00071         virtual void cleanup();
00072 
00077         virtual EKernelType get_kernel_type()
00078         {
00079             return K_POLYMATCH;
00080         }
00081 
00082         void set_minor_base_string(const char* str)
00083         {
00084             m_str_min=strdup(str);
00085         }
00086 
00087         void set_major_base_string(const char* str)
00088         {
00089             m_str_maj=strdup(str);
00090         }
00091 
00092         char* get_minor_base_string()
00093         {
00094             return m_str_min;
00095         }
00096 
00097         char* get_major_base_string()
00098         {
00099             return m_str_maj;
00100         }
00101 
00102         void obtain_base_strings();
00103 
00108         virtual const char* get_name() const { return "SNPStringKernel"; }
00109 
00110     protected:
00119         virtual float64_t compute(int32_t idx_a, int32_t idx_b);
00120 
00121     protected:
00123         int32_t m_degree;
00125         int32_t m_win_len;
00126 
00128         bool m_inhomogene;
00129 
00132         int32_t m_str_len;
00133 
00135         char* m_str_min;
00137         char* m_str_maj;
00138 };
00139 }
00140 #endif /* _SNPSTRINGKERNEL_H___ */
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