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 Soeren Sonnenburg 00008 * Copyright (C) 2009 Fraunhofer Institute FIRST and Max-Planck-Society 00009 */ 00010 00011 #ifndef _EXPLICITSPECFEATURES_H___ 00012 #define _EXPLICITSPECFEATURES_H___ 00013 00014 #include "lib/common.h" 00015 #include "lib/io.h" 00016 #include "features/DotFeatures.h" 00017 #include "features/StringFeatures.h" 00018 00019 template <class ST> class CStringFeatures; 00020 00025 class CExplicitSpecFeatures : public CDotFeatures 00026 { 00027 public: 00028 00034 CExplicitSpecFeatures(CStringFeatures<uint16_t>* str, bool normalize=true); 00035 00037 CExplicitSpecFeatures(const CExplicitSpecFeatures & orig); 00038 00040 virtual ~CExplicitSpecFeatures(); 00041 00046 virtual CFeatures* duplicate() const; 00047 00055 inline virtual int32_t get_dim_feature_space() 00056 { 00057 return spec_size; 00058 } 00059 00066 virtual float64_t dot(int32_t vec_idx1, int32_t vec_idx2); 00067 00074 virtual float64_t dense_dot(int32_t vec_idx1, const float64_t* vec2, int32_t vec2_len); 00075 00084 virtual void add_to_dense_vec(float64_t alpha, int32_t vec_idx1, float64_t* vec2, int32_t vec2_len, bool abs_val=false); 00085 00091 virtual inline int32_t get_nnz_features_for_vector(int32_t num) 00092 { 00093 SG_NOTIMPLEMENTED; 00094 return 0; 00095 } 00096 00101 inline virtual EFeatureType get_feature_type() 00102 { 00103 return F_UNKNOWN; 00104 } 00105 00110 inline virtual EFeatureClass get_feature_class() 00111 { 00112 return C_SPEC; 00113 } 00114 00119 inline virtual int32_t get_num_vectors() 00120 { 00121 return num_strings; 00122 } 00123 00128 inline virtual int32_t get_size() 00129 { 00130 return sizeof(float64_t); 00131 } 00132 00134 inline virtual const char* get_name() const { return "ExplicitSpecFeatures"; } 00135 00136 protected: 00141 void obtain_kmer_spectrum(CStringFeatures<uint16_t>* str); 00142 00144 void delete_kmer_spectrum(); 00145 00146 protected: 00148 bool use_normalization; 00150 int32_t num_strings; 00152 int32_t alphabet_size; 00153 00155 int32_t spec_size; 00157 float64_t** k_spectrum; 00158 }; 00159 #endif // _EXPLICITSPECFEATURES_H___