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) 2010 Soeren Sonnenburg 00008 * Copyright (C) 2010 Berlin Institute of Technology 00009 */ 00010 00011 #ifndef _SNPFEATURES_H___ 00012 #define _SNPFEATURES_H___ 00013 00014 #include "lib/common.h" 00015 #include "features/DotFeatures.h" 00016 #include "features/StringFeatures.h" 00017 00018 namespace shogun 00019 { 00020 template <class ST> class CStringFeatures; 00021 00027 class CSNPFeatures : public CDotFeatures 00028 { 00029 public: 00030 00035 CSNPFeatures(CStringFeatures<uint8_t>* str); 00036 00038 CSNPFeatures(const CSNPFeatures & orig); 00039 00041 virtual ~CSNPFeatures(); 00042 00050 inline virtual int32_t get_dim_feature_space() 00051 { 00052 return w_dim; 00053 } 00054 00061 virtual float64_t dot(int32_t vec_idx1, int32_t vec_idx2); 00062 00069 virtual float64_t dense_dot(int32_t vec_idx1, const float64_t* vec2, int32_t vec2_len); 00070 00079 virtual void add_to_dense_vec(float64_t alpha, int32_t vec_idx1, float64_t* vec2, int32_t vec2_len, bool abs_val=false); 00080 00086 virtual inline int32_t get_nnz_features_for_vector(int32_t num) 00087 { 00088 return w_dim/3; 00089 } 00090 00100 virtual void* get_feature_iterator(int32_t vector_index); 00101 00112 virtual bool get_next_feature(int32_t& index, float64_t& value, void* iterator); 00113 00119 virtual void free_feature_iterator(void* iterator); 00120 00125 virtual CFeatures* duplicate() const; 00126 00131 inline virtual EFeatureType get_feature_type() 00132 { 00133 return F_UNKNOWN; 00134 } 00135 00140 inline virtual EFeatureClass get_feature_class() 00141 { 00142 return C_WD; 00143 } 00144 00149 inline virtual int32_t get_num_vectors() 00150 { 00151 return num_strings; 00152 } 00153 00158 inline virtual int32_t get_size() 00159 { 00160 return sizeof(float64_t); 00161 } 00162 00165 void set_normalization_const(float64_t n=0); 00166 00168 inline float64_t get_normalization_const() 00169 { 00170 return normalization_const; 00171 } 00172 00177 void set_minor_base_string(const char* str) 00178 { 00179 m_str_min=(uint8_t*) strdup(str); 00180 } 00181 00182 00187 void set_major_base_string(const char* str) 00188 { 00189 m_str_maj=(uint8_t*) strdup(str); 00190 } 00191 00192 00197 char* get_minor_base_string() 00198 { 00199 return (char*) m_str_min; 00200 } 00201 00202 00207 char* get_major_base_string() 00208 { 00209 return (char*) m_str_maj; 00210 } 00211 00213 void obtain_base_strings(); 00214 00215 00217 inline virtual const char* get_name() const { return "SNPFeatures"; } 00218 00219 protected: 00221 CStringFeatures<uint8_t>* strings; 00222 00224 int32_t string_length; 00226 int32_t num_strings; 00228 int32_t w_dim; 00229 00231 float64_t normalization_const; 00232 00234 uint8_t* m_str_min; 00236 uint8_t* m_str_maj; 00237 00238 }; 00239 } 00240 #endif // _SNPFEATURES_H___