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: 00040 CSNPStringKernel(void); 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 00085 void set_minor_base_string(const char* str) 00086 { 00087 m_str_min=strdup(str); 00088 } 00089 00090 void set_major_base_string(const char* str) 00091 { 00092 m_str_maj=strdup(str); 00093 } 00094 00095 char* get_minor_base_string() 00096 { 00097 return m_str_min; 00098 } 00099 00100 char* get_major_base_string() 00101 { 00102 return m_str_maj; 00103 } 00104 00105 void obtain_base_strings(); 00106 00111 virtual const char* get_name() const { return "SNPStringKernel"; } 00112 00113 protected: 00122 virtual float64_t compute(int32_t idx_a, int32_t idx_b); 00123 00124 protected: 00126 int32_t m_degree; 00128 int32_t m_win_len; 00129 00131 bool m_inhomogene; 00132 00135 int32_t m_str_len; 00136 00138 char* m_str_min; 00140 char* m_str_maj; 00141 }; 00142 } 00143 #endif /* _SNPSTRINGKERNEL_H___ */