SHOGUN
v1.1.0
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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) 2010 Soeren Sonnenburg 00008 * Copyright (C) 2010 Berlin Institute of Technology 00009 */ 00010 00011 #ifndef _SNPFEATURES_H___ 00012 #define _SNPFEATURES_H___ 00013 00014 #include <shogun/lib/common.h> 00015 #include <shogun/features/DotFeatures.h> 00016 #include <shogun/features/StringFeatures.h> 00017 00018 namespace shogun 00019 { 00020 template <class ST> class CStringFeatures; 00021 00027 class CSNPFeatures : public CDotFeatures 00028 { 00029 public: 00031 CSNPFeatures(); 00032 00037 CSNPFeatures(CStringFeatures<uint8_t>* str); 00038 00040 CSNPFeatures(const CSNPFeatures & orig); 00041 00043 virtual ~CSNPFeatures(); 00044 00052 virtual int32_t get_dim_feature_space() const; 00053 00061 virtual float64_t dot(int32_t vec_idx1, CDotFeatures* df, 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, 00080 float64_t* vec2, int32_t vec2_len, bool abs_val=false); 00081 00087 virtual int32_t get_nnz_features_for_vector(int32_t num); 00088 00098 virtual void* get_feature_iterator(int32_t vector_index); 00099 00110 virtual bool get_next_feature(int32_t& index, float64_t& value, void* iterator); 00111 00117 virtual void free_feature_iterator(void* iterator); 00118 00123 virtual CFeatures* duplicate() const; 00124 00129 virtual EFeatureType get_feature_type(); 00130 00135 virtual EFeatureClass get_feature_class(); 00136 00141 virtual int32_t get_num_vectors() const; 00142 00147 virtual int32_t get_size(); 00148 00151 void set_normalization_const(float64_t n=0); 00152 00154 float64_t get_normalization_const(); 00155 00160 void set_minor_base_string(const char* str); 00161 00166 void set_major_base_string(const char* str); 00167 00172 char* get_minor_base_string(); 00173 00178 char* get_major_base_string(); 00179 00185 void obtain_base_strings(CSNPFeatures* snp=NULL); 00186 00188 virtual const char* get_name() const { return "SNPFeatures"; } 00189 00192 virtual SGMatrix<float64_t> get_histogram(bool normalize=true); 00193 00197 static SGMatrix<float64_t> get_2x3_table(CSNPFeatures* pos, CSNPFeatures* neg); 00198 00199 private: 00206 void find_minor_major_strings(uint8_t* minor, uint8_t* major); 00207 00208 protected: 00210 CStringFeatures<uint8_t>* strings; 00211 00213 int32_t string_length; 00215 int32_t num_strings; 00217 int32_t w_dim; 00218 00220 float64_t normalization_const; 00221 00223 uint8_t* m_str_min; 00225 uint8_t* m_str_maj; 00226 }; 00227 } 00228 #endif // _SNPFEATURES_H___