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 <shogun/lib/common.h> 00015 #include <shogun/kernel/StringKernel.h> 00016 00017 namespace shogun 00018 { 00036 class CSNPStringKernel: public CStringKernel<char> 00037 { 00038 public: 00040 CSNPStringKernel(); 00041 00049 CSNPStringKernel(int32_t size, int32_t degree, int32_t win_len, bool inhomogene); 00050 00059 CSNPStringKernel( 00060 CStringFeatures<char>* l, CStringFeatures<char>* r, 00061 int32_t degree, int32_t win_len, bool inhomogene); 00062 00063 virtual ~CSNPStringKernel(); 00064 00071 virtual bool init(CFeatures* l, CFeatures* r); 00072 00074 virtual void cleanup(); 00075 00080 virtual EKernelType get_kernel_type() 00081 { 00082 return K_POLYMATCH; 00083 } 00084 00089 void set_minor_base_string(const char* str) 00090 { 00091 m_str_min=strdup(str); 00092 } 00093 00098 void set_major_base_string(const char* str) 00099 { 00100 m_str_maj=strdup(str); 00101 } 00102 00107 char* get_minor_base_string() 00108 { 00109 return m_str_min; 00110 } 00111 00116 char* get_major_base_string() 00117 { 00118 return m_str_maj; 00119 } 00120 00122 void obtain_base_strings(); 00123 00128 virtual const char* get_name() const { return "SNPStringKernel"; } 00129 00130 /* register the parameters 00131 */ 00132 virtual void register_params(); 00133 00134 protected: 00143 virtual float64_t compute(int32_t idx_a, int32_t idx_b); 00144 00145 protected: 00147 int32_t m_degree; 00149 int32_t m_win_len; 00150 00152 bool m_inhomogene; 00153 00156 int32_t m_str_len; 00157 00159 char* m_str_min; 00161 char* m_str_maj; 00162 00163 private: 00164 void init(); 00165 }; 00166 } 00167 #endif /* _SNPSTRINGKERNEL_H___ */