SNPStringKernel.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 Berlin Institute of Technology
 */

#include "lib/common.h"
#include "lib/io.h"
#include "kernel/SNPStringKernel.h"
#include "kernel/SqrtDiagKernelNormalizer.h"
#include "features/Features.h"
#include "features/StringFeatures.h"

using namespace shogun;

CSNPStringKernel::CSNPStringKernel(int32_t size,
        int32_t degree, int32_t win_len, bool inhomogene)
: CStringKernel<char>(size),
    m_degree(degree), m_win_len(2*win_len), m_inhomogene(inhomogene)
{
    m_str_min=NULL;
    m_str_maj=NULL;
    set_normalizer(new CSqrtDiagKernelNormalizer());
}

CSNPStringKernel::CSNPStringKernel(
    CStringFeatures<char>* l, CStringFeatures<char>* r,
    int32_t degree, int32_t win_len, bool inhomogene)
: CStringKernel<char>(10), m_degree(degree), m_win_len(2*win_len),
    m_inhomogene(inhomogene)
{
    m_str_min=NULL;
    m_str_maj=NULL;
    set_normalizer(new CSqrtDiagKernelNormalizer());
    if (l==r)
        obtain_base_strings();
    init(l, r);
}

CSNPStringKernel::~CSNPStringKernel()
{
    cleanup();
}

bool CSNPStringKernel::init(CFeatures* l, CFeatures* r)
{
    CStringKernel<char>::init(l, r);
    return init_normalizer();
}

void CSNPStringKernel::cleanup()
{
    CKernel::cleanup();
    free(m_str_min);
    free(m_str_maj);
}

void CSNPStringKernel::obtain_base_strings()
{
    //should only be called on training data
    ASSERT(lhs==rhs);

    m_str_len=0;

    for (int32_t i=0; i<num_lhs; i++)
    {
        int32_t len;
        bool free_vec;
        char* vec = ((CStringFeatures<char>*) lhs)->get_feature_vector(i, len, free_vec);

        if (m_str_len==0)
        {
            m_str_len=len;
            size_t tlen=(len+1)*sizeof(char);
            m_str_min=(char*) malloc(tlen);
            m_str_maj=(char*) malloc(tlen);
            memset(m_str_min, 0, tlen);
            memset(m_str_maj, 0, tlen);
        }
        else
        {
            ASSERT(m_str_len==len);
        }

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

            if (m_str_min[j]==0)
                m_str_min[j]=vec[j];
            else if (m_str_maj[j]==0 && vec[j]!=m_str_min[j])
                m_str_maj[j]=vec[j];
        }

        ((CStringFeatures<char>*) lhs)->free_feature_vector(vec, i, free_vec);
    }

    for (int32_t j=0; j<m_str_len; j++)
    {
        // if only one 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]);
    }
}

float64_t CSNPStringKernel::compute(int32_t idx_a, int32_t idx_b)
{
    int32_t alen, blen;
    bool free_avec, free_bvec;

    char* avec = ((CStringFeatures<char>*) lhs)->get_feature_vector(idx_a, alen, free_avec);
    char* bvec = ((CStringFeatures<char>*) rhs)->get_feature_vector(idx_b, blen, free_bvec);

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

    float64_t total=0;
    int32_t inhomogene= (m_inhomogene) ? 1 : 0;

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

        for (int32_t l=0; l<m_win_len && i+l<alen-1; l+=2)
        {
            char a1=avec[i+l];
            char a2=avec[i+l+1];
            char b1=bvec[i+l];
            char b2=bvec[i+l+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+l])
                    sumaa++;
                else if (a1==m_str_maj[i+l])
                    sumbb++;
                else
                {
                    SG_ERROR("The impossible happened i=%d l=%d a1=%c "
                            "a2=%c b1=%c b2=%c min=%c maj=%c\n", i, l, a1,a2, b1,b2, m_str_min[i+l], m_str_maj[i+l]);
                }
            }

        }
        total+=CMath::pow(float64_t(sumaa+sumbb+sumab+inhomogene),
                (int32_t) m_degree);
    }

    ((CStringFeatures<char>*) lhs)->free_feature_vector(avec, idx_a, free_avec);
    ((CStringFeatures<char>*) rhs)->free_feature_vector(bvec, idx_b, free_bvec);
    return total;
}