SNPFeatures.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 <shogun/features/SNPFeatures.h>
#include <shogun/io/SGIO.h>
#include <shogun/features/Alphabet.h>

using namespace shogun;

CSNPFeatures::CSNPFeatures()
{
    SG_UNSTABLE("CSNPFeatures::CSNPFeatures()", "\n");

    strings = NULL;

    string_length = 0;
    num_strings = 0;
    w_dim = 0;

    normalization_const = 0.0;

    m_str_min = NULL;
    m_str_maj = NULL;
}

CSNPFeatures::CSNPFeatures(CStringFeatures<uint8_t>* str) : CDotFeatures(),
    m_str_min(NULL), m_str_maj(NULL)
{
    ASSERT(str);
    ASSERT(str->have_same_length());
    SG_REF(str);

    strings=str;
    string_length=str->get_max_vector_length();
    ASSERT((string_length & 1) == 0); // length divisible by 2
    w_dim=3*string_length/2;
    num_strings=str->get_num_vectors();
    CAlphabet* alpha=str->get_alphabet();
    ASSERT(alpha->get_alphabet()==SNP);
    SG_UNREF(alpha);

    obtain_base_strings();
    set_normalization_const();

}

CSNPFeatures::CSNPFeatures(const CSNPFeatures& orig)
    : CDotFeatures(orig), strings(orig.strings),
    normalization_const(orig.normalization_const),
    m_str_min(NULL), m_str_maj(NULL)
{
    SG_REF(strings);
    string_length=strings->get_max_vector_length();
    ASSERT((string_length & 1) == 0); // length divisible by 2
    w_dim=3*string_length;
    num_strings=strings->get_num_vectors();
    CAlphabet* alpha=strings->get_alphabet();
    SG_UNREF(alpha);

    obtain_base_strings();
}

CSNPFeatures::~CSNPFeatures()
{
    SG_UNREF(strings);
}

int32_t CSNPFeatures::get_dim_feature_space() const
{
    return w_dim;
}

int32_t CSNPFeatures::get_nnz_features_for_vector(int32_t num)
{
    return w_dim/3;
}

EFeatureType CSNPFeatures::get_feature_type() const
{
    return F_UNKNOWN;
}

EFeatureClass CSNPFeatures::get_feature_class() const
{
    return C_WD;
}

int32_t CSNPFeatures::get_num_vectors() const
{
    return num_strings;
}

int32_t CSNPFeatures::get_size() const
{
    return sizeof(float64_t);
}

float64_t CSNPFeatures::get_normalization_const()
{
    return normalization_const;
}

void CSNPFeatures::set_minor_base_string(const char* str)
{
    m_str_min=(uint8_t*) strdup(str);
}

void CSNPFeatures::set_major_base_string(const char* str)
{
    m_str_maj=(uint8_t*) strdup(str);
}

char* CSNPFeatures::get_minor_base_string()
{
    return (char*) m_str_min;
}

char* CSNPFeatures::get_major_base_string()
{
    return (char*) m_str_maj;
}

float64_t CSNPFeatures::dot(int32_t idx_a, CDotFeatures* df, int32_t idx_b)
{
    ASSERT(df);
    ASSERT(df->get_feature_type() == get_feature_type());
    ASSERT(df->get_feature_class() == get_feature_class());
    CSNPFeatures* sf=(CSNPFeatures*) df;

    int32_t alen, blen;
    bool free_avec, free_bvec;

    uint8_t* avec = strings->get_feature_vector(idx_a, alen, free_avec);
    uint8_t* bvec = sf->strings->get_feature_vector(idx_b, blen, free_bvec);

    ASSERT(alen==blen);
    if (alen!=string_length)
        SG_ERROR("alen (%d) !=string_length (%d)\n", alen, string_length);
    ASSERT(m_str_min);
    ASSERT(m_str_maj);

    float64_t total=0;

    for (int32_t i = 0; i<alen-1; i+=2)
    {
        int32_t sumaa=0;
        int32_t sumbb=0;
        int32_t sumab=0;

        uint8_t a1=avec[i];
        uint8_t a2=avec[i+1];
        uint8_t b1=bvec[i];
        uint8_t b2=bvec[i+1];

        if ((a1!=a2 || a1=='0' || a1=='0') && (b1!=b2 || b1=='0' || b2=='0'))
            sumab++;
        else if (a1==a2 && b1==b2)
        {
            if (a1!=b1)
                continue;

            if (a1==m_str_min[i])
                sumaa++;
            else if (a1==m_str_maj[i])
                sumbb++;
            else
            {
                SG_ERROR("The impossible happened i=%d a1=%c "
                        "a2=%c b1=%c b2=%c min=%c maj=%c\n", i, a1,a2, b1,b2, m_str_min[i], m_str_maj[i]);
            }

        }
        total+=sumaa+sumbb+sumab;
    }

    strings->free_feature_vector(avec, idx_a, free_avec);
    sf->strings->free_feature_vector(bvec, idx_b, free_bvec);
    return total;
}

float64_t CSNPFeatures::dense_dot(int32_t vec_idx1, const float64_t* vec2, int32_t vec2_len)
{
    if (vec2_len != w_dim)
        SG_ERROR("Dimensions don't match, vec2_dim=%d, w_dim=%d\n", vec2_len, w_dim);

    float64_t sum=0;
    int32_t len;
    bool free_vec1;
    uint8_t* vec = strings->get_feature_vector(vec_idx1, len, free_vec1);
    int32_t offs=0;

    for (int32_t i=0; i<len; i+=2)
    {
        int32_t dim=0;

        char a1=vec[i];
        char a2=vec[i+1];

        if (a1==a2 && a1!='0' && a2!='0')
        {
            if (a1==m_str_min[i])
                dim=1;
            else if (a1==m_str_maj[i])
                dim=2;
            else
            {
                SG_ERROR("The impossible happened i=%d a1=%c a2=%c min=%c maj=%c\n",
                        i, a1,a2, m_str_min[i], m_str_maj[i]);
            }
        }

        sum+=vec2[offs+dim];
        offs+=3;
    }
    strings->free_feature_vector(vec, vec_idx1, free_vec1);

    return sum/normalization_const;
}

void CSNPFeatures::add_to_dense_vec(float64_t alpha, int32_t vec_idx1, float64_t* vec2, int32_t vec2_len, bool abs_val)
{
    if (vec2_len != w_dim)
        SG_ERROR("Dimensions don't match, vec2_dim=%d, w_dim=%d\n", vec2_len, w_dim);

    int32_t len;
    bool free_vec1;
    uint8_t* vec = strings->get_feature_vector(vec_idx1, len, free_vec1);
    int32_t offs=0;

    if (abs_val)
        alpha=CMath::abs(alpha);

    for (int32_t i=0; i<len; i+=2)
    {
        int32_t dim=0;

        char a1=vec[i];
        char a2=vec[i+1];

        if (a1==a2 && a1!='0' && a2!='0')
        {
            if (a1==m_str_min[i])
                dim=1;
            else if (a1==m_str_maj[i])
                dim=2;
            else
            {
                SG_ERROR("The impossible happened i=%d a1=%c a2=%c min=%c maj=%c\n",
                        i, a1,a2, m_str_min[i], m_str_maj[i]);
            }
        }

        vec2[offs+dim]+=alpha;
        offs+=3;
    }
    strings->free_feature_vector(vec, vec_idx1, free_vec1);
}

void CSNPFeatures::find_minor_major_strings(uint8_t* minor, uint8_t* major)
{
    for (int32_t i=0; i<num_strings; i++)
    {
        int32_t len;
        bool free_vec;
        uint8_t* vec = ((CStringFeatures<uint8_t>*) strings)->get_feature_vector(i, len, free_vec);
        ASSERT(string_length==len);

        for (int32_t j=0; j<len; j++)
        {
            // skip sequencing errors
            if (vec[j]=='0')
                continue;

            if (minor[j]==0)
                minor[j]=vec[j];
            else if (major[j]==0 && vec[j]!=minor[j])
                major[j]=vec[j];
        }

        ((CStringFeatures<uint8_t>*) strings)->free_feature_vector(vec, i, free_vec);
    }
}

void CSNPFeatures::obtain_base_strings(CSNPFeatures* snp)
{
    SG_FREE(m_str_min);
    SG_FREE(m_str_maj);
    size_t tlen=(string_length+1)*sizeof(uint8_t);

    m_str_min=SG_CALLOC(uint8_t, tlen);
    m_str_maj=SG_CALLOC(uint8_t, tlen);

    find_minor_major_strings(m_str_min, m_str_maj);

    if (snp)
        snp->find_minor_major_strings(m_str_min, m_str_maj);

    for (int32_t j=0; j<string_length; j++)
    {
        // if only one symbol occurs use 0
        if (m_str_min[j]==0)
            m_str_min[j]='0';
        if (m_str_maj[j]==0)
            m_str_maj[j]='0';

        if (m_str_min[j]>m_str_maj[j])
            CMath::swap(m_str_min[j], m_str_maj[j]);
    }
}

void CSNPFeatures::set_normalization_const(float64_t n)
{
    if (n==0)
    {
        normalization_const=string_length;
        normalization_const=CMath::sqrt(normalization_const);
    }
    else
        normalization_const=n;

    SG_DEBUG("normalization_const:%f\n", normalization_const);
}

void* CSNPFeatures::get_feature_iterator(int32_t vector_index)
{
    return NULL;
}

bool CSNPFeatures::get_next_feature(int32_t& index, float64_t& value, void* iterator)
{
    return false;
}

void CSNPFeatures::free_feature_iterator(void* iterator)
{
}

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

SGMatrix<float64_t> CSNPFeatures::get_histogram(bool normalize)
{
    int32_t nsym=3;
    float64_t* h= SG_CALLOC(float64_t, size_t(nsym)*string_length/2);

    float64_t* h_normalizer=SG_MALLOC(float64_t, string_length/2);
    memset(h_normalizer, 0, string_length/2*sizeof(float64_t));
    int32_t num_str=get_num_vectors();
    for (int32_t i=0; i<num_str; i++)
    {
        int32_t len;
        bool free_vec;
        uint8_t* vec = strings->get_feature_vector(i, len, free_vec);

        for (int32_t j=0; j<len; j+=2)
        {
            int32_t dim=0;

            char a1=vec[j];
            char a2=vec[j+1];

            if (a1==a2 && a1!='0' && a2!='0')
            {
                if (a1==m_str_min[j])
                    dim=1;
                else if (a1==m_str_maj[j])
                    dim=2;
                else
                {
                    SG_ERROR("The impossible happened j=%d a1=%c a2=%c min=%c maj=%c\n",
                            j, a1,a2, m_str_min[j], m_str_maj[j]);
                }
            }

            h[int64_t(j/2)*nsym+dim]++;
            h_normalizer[j/2]++;
        }

        strings->free_feature_vector(vec, i, free_vec);
    }

    if (normalize)
    {
        for (int32_t i=0; i<string_length/2; i++)
        {
            for (int32_t j=0; j<nsym; j++)
            {
                if (h_normalizer && h_normalizer[i])
                    h[int64_t(i)*nsym+j]/=h_normalizer[i];
            }
        }
    }
    SG_FREE(h_normalizer);

    return SGMatrix<float64_t>(h, nsym, string_length/2);
}

SGMatrix<float64_t> CSNPFeatures::get_2x3_table(CSNPFeatures* pos, CSNPFeatures* neg)
{

    ASSERT(pos->strings->get_max_vector_length() == neg->strings->get_max_vector_length());
    int32_t len=pos->strings->get_max_vector_length();

    float64_t* table=SG_MALLOC(float64_t, 3*2*len/2);

    SGMatrix<float64_t> p_hist=pos->get_histogram(false);
    SGMatrix<float64_t> n_hist=neg->get_histogram(false);


    for (int32_t i=0; i<3*len/2; i++)
    {
        table[2*i]=p_hist.matrix[i];
        table[2*i+1]=n_hist.matrix[i];
    }
    return SGMatrix<float64_t>(table, 2,3*len/2);
}