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 <shogun/lib/common.h>
00015 #include <shogun/io/SGIO.h>
00016 #include <shogun/features/DotFeatures.h>
00017 #include <shogun/features/StringFeatures.h>
00018 
00019 namespace shogun
00020 {
00021 template <class ST> class CStringFeatures;
00022 
00027 class CExplicitSpecFeatures : public CDotFeatures
00028 {
00029     public:
00031         CExplicitSpecFeatures(void);
00032 
00038         CExplicitSpecFeatures(CStringFeatures<uint16_t>* str, bool normalize=true);
00039 
00041         CExplicitSpecFeatures(const CExplicitSpecFeatures & orig);
00042 
00044         virtual ~CExplicitSpecFeatures();
00045 
00050         virtual CFeatures* duplicate() const;
00051 
00059         inline virtual int32_t get_dim_feature_space() const
00060         {
00061             return spec_size;
00062         }
00063 
00071         virtual float64_t dot(int32_t vec_idx1, CDotFeatures* df, int32_t vec_idx2);
00072 
00079         virtual float64_t dense_dot(int32_t vec_idx1, const float64_t* vec2, int32_t vec2_len);
00080 
00089         virtual void add_to_dense_vec(float64_t alpha, int32_t vec_idx1, float64_t* vec2, int32_t vec2_len, bool abs_val=false);
00090 
00091         #ifndef DOXYGEN_SHOULD_SKIP_THIS
00092 
00093         struct explicit_spec_feature_iterator
00094         {
00096             uint16_t* vec;
00098             int32_t vidx;
00100             int32_t vlen;
00102             bool vfree;
00103 
00105             int32_t index;
00106 
00107         };
00108         #endif
00109 
00119         virtual void* get_feature_iterator(int32_t vector_index)
00120         {
00121             SG_NOTIMPLEMENTED;
00122             return NULL;
00123         }
00124 
00135         virtual bool get_next_feature(int32_t& index, float64_t& value, void* iterator)
00136         {
00137             SG_NOTIMPLEMENTED;
00138             return NULL;
00139         }
00140 
00146         virtual void free_feature_iterator(void* iterator)
00147         {
00148             SG_NOTIMPLEMENTED;
00149         }
00150 
00156         virtual inline int32_t get_nnz_features_for_vector(int32_t num)
00157         {
00158             SG_NOTIMPLEMENTED;
00159             return 0;
00160         }
00161 
00166         inline virtual EFeatureType get_feature_type()
00167         {
00168             return F_UNKNOWN;
00169         }
00170 
00175         inline virtual EFeatureClass get_feature_class()
00176         {
00177             return C_SPEC;
00178         }
00179 
00184         inline virtual int32_t get_num_vectors() const
00185         {
00186             return num_strings;
00187         }
00188 
00193         inline virtual int32_t get_size()
00194         {
00195             return sizeof(float64_t);
00196         }
00197 
00199         inline virtual const char* get_name() const { return "ExplicitSpecFeatures"; }
00200 
00201     protected:
00206         void obtain_kmer_spectrum(CStringFeatures<uint16_t>* str);
00207 
00209         void delete_kmer_spectrum();
00210 
00211     protected:
00213         bool use_normalization;
00215         int32_t num_strings;
00217         int32_t alphabet_size;
00218 
00220         int32_t spec_size;
00222         float64_t** k_spectrum;
00223 };
00224 }
00225 #endif // _EXPLICITSPECFEATURES_H___
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