ExplicitSpecFeatures.h

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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) 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 namespace shogun
00020 {
00021 template <class ST> class CStringFeatures;
00022 
00027 class CExplicitSpecFeatures : public CDotFeatures
00028 {
00029     public:
00030 
00036         CExplicitSpecFeatures(CStringFeatures<uint16_t>* str, bool normalize=true);
00037 
00039         CExplicitSpecFeatures(const CExplicitSpecFeatures & orig);
00040 
00042         virtual ~CExplicitSpecFeatures();
00043 
00048         virtual CFeatures* duplicate() const;
00049 
00057         inline virtual int32_t get_dim_feature_space()
00058         {
00059             return spec_size;
00060         }
00061 
00068         virtual float64_t dot(int32_t vec_idx1, int32_t vec_idx2);
00069 
00076         virtual float64_t dense_dot(int32_t vec_idx1, const float64_t* vec2, int32_t vec2_len);
00077 
00086         virtual void add_to_dense_vec(float64_t alpha, int32_t vec_idx1, float64_t* vec2, int32_t vec2_len, bool abs_val=false);
00087 
00093         virtual inline int32_t get_nnz_features_for_vector(int32_t num)
00094         {
00095             SG_NOTIMPLEMENTED;
00096             return 0;
00097         }
00098 
00103         inline virtual EFeatureType get_feature_type()
00104         {
00105             return F_UNKNOWN;
00106         }
00107 
00112         inline virtual EFeatureClass get_feature_class()
00113         {
00114             return C_SPEC;
00115         }
00116 
00121         inline virtual int32_t get_num_vectors()
00122         {
00123             return num_strings;
00124         }
00125 
00130         inline virtual int32_t get_size()
00131         {
00132             return sizeof(float64_t);
00133         }
00134 
00136         inline virtual const char* get_name() const { return "ExplicitSpecFeatures"; }
00137 
00138     protected:
00143         void obtain_kmer_spectrum(CStringFeatures<uint16_t>* str);
00144 
00146         void delete_kmer_spectrum();
00147 
00148     protected:
00150         bool use_normalization;
00152         int32_t num_strings;
00154         int32_t alphabet_size;
00155 
00157         int32_t spec_size;
00159         float64_t** k_spectrum;
00160 };
00161 }
00162 #endif // _EXPLICITSPECFEATURES_H___

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