PositionalPWM.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) 2011 Soeren Sonnenburg
 * Copyright (C) 2011 Berlin Institute of Technology and Max-Planck-Society
 */

#ifndef _POSITIONAL_PWM_H__
#define _POSITIONAL_PWM_H__

#include <shogun/distributions/Distribution.h>
#include <shogun/features/StringFeatures.h>
#include <shogun/lib/common.h>
#include <shogun/mathematics/Math.h>

namespace shogun
{
class CPositionalPWM : public CDistribution
{
    public:
        CPositionalPWM();

        virtual ~CPositionalPWM();

        virtual bool train(CFeatures* data=NULL);

        virtual int32_t get_num_model_parameters();

        virtual float64_t get_log_model_parameter(int32_t num_param);

        virtual float64_t get_log_derivative(
            int32_t num_param, int32_t num_example);

        virtual float64_t get_log_likelihood_example(int32_t num_example);

        float64_t get_log_likelihood_window(uint8_t* window, int32_t len, float64_t pos);

        virtual inline float64_t get_sigma()
        {
            return m_sigma;
        }

        virtual inline void set_sigma(float64_t sigma)
        {
            m_sigma=sigma;
        }

        virtual inline float64_t get_mean()
        {
            return m_mean;
        }

        virtual inline void set_mean(float64_t mean)
        {
            m_mean=mean;
        }

        virtual inline void set_pwm(SGMatrix<float64_t> pwm)
        {
            m_pwm=pwm.matrix;
            m_pwm_rows=pwm.num_rows;
            m_pwm_cols=pwm.num_cols;
        }

        virtual inline SGMatrix<float64_t> get_pwm()
        {
            return SGMatrix<float64_t>(m_pwm,m_pwm_rows,m_pwm_cols);
        }

        virtual inline SGMatrix<float64_t> get_w()
        {
            return SGMatrix<float64_t>(m_w,m_w_rows,m_w_cols);
        }

        virtual SGMatrix<float64_t> get_scoring(int32_t d);

        void compute_w(int32_t num_pos);

        void compute_scoring(int32_t max_degree);

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

    private:
        void register_params();

    protected:

        int32_t m_pwm_rows;

        int32_t m_pwm_cols;

        float64_t* m_pwm;

        float64_t m_sigma;

        float64_t m_mean;

        int32_t m_w_rows;

        int32_t m_w_cols;

        float64_t* m_w;

        int32_t m_poim_len;

        float64_t* m_poim;

};
}
#endif //_POSITIONAL_PWM_H__