ExplicitSpecFeatures.cpp

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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
 */

#include "features/ExplicitSpecFeatures.h"
#include "lib/io.h"

using namespace shogun;

CExplicitSpecFeatures::CExplicitSpecFeatures(CStringFeatures<uint16_t>* str, bool normalize) : CDotFeatures()
{
    ASSERT(str);

    use_normalization=normalize;
    num_strings = str->get_num_vectors();
    spec_size = str->get_num_symbols();

    obtain_kmer_spectrum(str);

    SG_DEBUG("SPEC size=%d, num_str=%d\n", spec_size, num_strings);
}

CExplicitSpecFeatures::CExplicitSpecFeatures(const CExplicitSpecFeatures& orig) : CDotFeatures(orig), 
    num_strings(orig.num_strings), alphabet_size(orig.alphabet_size), spec_size(orig.spec_size)
{
    k_spectrum= new float64_t*[num_strings];
    for (int32_t i=0; i<num_strings; i++)
        k_spectrum[i]=CMath::clone_vector(k_spectrum[i], spec_size);
}

CExplicitSpecFeatures::~CExplicitSpecFeatures()
{
    delete_kmer_spectrum();
}

float64_t CExplicitSpecFeatures::dot(int32_t vec_idx1, int32_t vec_idx2)
{
    ASSERT(vec_idx1 < num_strings);
    ASSERT(vec_idx2 < num_strings);
    float64_t* vec1=k_spectrum[vec_idx1];
    float64_t* vec2=k_spectrum[vec_idx2];

    return CMath::dot(vec1, vec2, spec_size);
}

float64_t CExplicitSpecFeatures::dense_dot(int32_t vec_idx1, float64_t* vec2, int32_t vec2_len)
{
    ASSERT(vec2_len == spec_size);
    ASSERT(vec_idx1 < num_strings);
    float64_t* vec1=k_spectrum[vec_idx1];
    float64_t result=0;
    
    for (int32_t i=0; i<spec_size; i++)
        result+=vec1[i]*vec2[i];

    return result;
}

void CExplicitSpecFeatures::add_to_dense_vec(float64_t alpha, int32_t vec_idx1, float64_t* vec2, int32_t vec2_len, bool abs_val)
{
    ASSERT(vec2_len == spec_size);
    ASSERT(vec_idx1 < num_strings);
    float64_t* vec1=k_spectrum[vec_idx1];

    if (abs_val)
    {
        for (int32_t i=0; i<spec_size; i++)
            vec2[i]+=alpha*CMath::abs(vec1[i]);
    }
    else
    {
        for (int32_t i=0; i<spec_size; i++)
            vec2[i]+=alpha*vec1[i];
    }
}

void CExplicitSpecFeatures::obtain_kmer_spectrum(CStringFeatures<uint16_t>* str)
{
    k_spectrum= new float64_t*[num_strings];

    for (int32_t i=0; i<num_strings; i++)
    {
        k_spectrum[i]=new float64_t[spec_size];
        memset(k_spectrum[i], 0, sizeof(float64_t)*spec_size);

        int32_t len=0;
        bool free_fv;
        uint16_t* fv=str->get_feature_vector(i, len, free_fv);

        for (int32_t j=0; j<len; j++)
            k_spectrum[i][fv[j]]++;

        str->free_feature_vector(fv, i, free_fv);

        if (use_normalization)
        {
            float64_t n=0;
            for (int32_t j=0; j<spec_size; j++)
                n+=CMath::sq(k_spectrum[i][j]);

            n=CMath::sqrt(n);

            for (int32_t j=0; j<spec_size; j++)
                k_spectrum[i][j]/=n;
        }
    }
}

void CExplicitSpecFeatures::delete_kmer_spectrum()
{
    for (int32_t i=0; i<num_strings; i++)
        delete[] k_spectrum[i];

    delete[] k_spectrum;
    k_spectrum=NULL;
}

CFeatures* CExplicitSpecFeatures::duplicate() const
{
    return new CExplicitSpecFeatures(*this);
}