ExplicitSpecFeatures.h

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/*
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 3 of the License, or
 * (at your option) any later version.
 *
 * Written (W) 2009 Soeren Sonnenburg
 * Copyright (C) 2009 Fraunhofer Institute FIRST and Max-Planck-Society
 */

#ifndef _EXPLICITSPECFEATURES_H___
#define _EXPLICITSPECFEATURES_H___

#include <shogun/lib/common.h>
#include <shogun/features/DotFeatures.h>
#include <shogun/features/StringFeatures.h>

namespace shogun
{
template <class ST> class CStringFeatures;

class CExplicitSpecFeatures : public CDotFeatures
{
    public:
        CExplicitSpecFeatures();

        CExplicitSpecFeatures(CStringFeatures<uint16_t>* str, bool normalize=true);

        CExplicitSpecFeatures(const CExplicitSpecFeatures & orig);

        virtual ~CExplicitSpecFeatures();

        virtual CFeatures* duplicate() const;

        virtual int32_t get_dim_feature_space() const;

        virtual float64_t dot(int32_t vec_idx1, CDotFeatures* df, int32_t vec_idx2);

        virtual float64_t dense_dot(int32_t vec_idx1, const float64_t* vec2, int32_t vec2_len);

        virtual void add_to_dense_vec(float64_t alpha, int32_t vec_idx1,
                float64_t* vec2, int32_t vec2_len, bool abs_val=false);

        #ifndef DOXYGEN_SHOULD_SKIP_THIS

        struct explicit_spec_feature_iterator
        {
            uint16_t* vec;
            int32_t vidx;
            int32_t vlen;
            bool vfree;

            int32_t index;

        };
        #endif

        virtual void* get_feature_iterator(int32_t vector_index);

        virtual bool get_next_feature(int32_t& index, float64_t& value, void* iterator);

        virtual void free_feature_iterator(void* iterator);

        virtual int32_t get_nnz_features_for_vector(int32_t num);

        virtual EFeatureType get_feature_type();

        virtual EFeatureClass get_feature_class();

        virtual int32_t get_num_vectors() const;

        virtual int32_t get_size();

        inline virtual const char* get_name() const { return "ExplicitSpecFeatures"; }

    protected:
        void obtain_kmer_spectrum(CStringFeatures<uint16_t>* str);

        void delete_kmer_spectrum();

    protected:
        bool use_normalization;
        int32_t num_strings;
        int32_t alphabet_size;

        int32_t spec_size;
        float64_t** k_spectrum;
};
}
#endif // _EXPLICITSPECFEATURES_H___