SparseSpatialSampleStringKernel.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) 2010 Soeren Sonnenburg
 * Copyright (C) 2010 Berlin Institute of Technology
 */

#ifndef _SPARSESPATIALSAMPLESTRINGKERNEL_H___
#define _SPARSESPATIALSAMPLESTRINGKERNEL_H___

#include <shogun/lib/common.h>
#include <shogun/kernel/StringKernel.h>

namespace shogun
{
    struct SSKFeatures
    {
        int *features;
        int *group;
        int n; 
    };

class CSparseSpatialSampleStringKernel: public CStringKernel<char>
{
    public:
        CSparseSpatialSampleStringKernel();

        CSparseSpatialSampleStringKernel(CStringFeatures<char>* l, CStringFeatures<char>* r);

        virtual ~CSparseSpatialSampleStringKernel();

        virtual bool init(CFeatures* l, CFeatures* r);

        virtual void cleanup();

        virtual EKernelType get_kernel_type()
        {
            return K_SPARSESPATIALSAMPLE;
        }

        void set_d(int32_t max_distance)
        {
            ASSERT(d>0);
            d=max_distance;
        }

        int32_t get_d()
        {
            return d;
        }

        void set_t(int32_t sequence_length)
        {
            ASSERT(t==2 || t==3);
            t=sequence_length;
        }

        int32_t get_t()
        {
            return t;
        }

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

    protected:
        virtual float64_t compute(int32_t idx_a, int32_t idx_b);

        SSKFeatures *extractTriple(int **S, int *len, int nStr, int d1, int d2);
        SSKFeatures *extractDouble(int **S, int *len, int nStr, int d1);
        void compute_double(int32_t idx_a, int32_t idx_b);
        void compute_triple(int32_t idx_a, int32_t idx_b);
        int* cntsrtna(int *sx, int k, int r, int na);
        void countAndUpdate(int *outK, int *sx, int *g, int k, int r, int nStr);

    protected:
        int32_t t;

        int32_t d;

        bool isVerbose;
};
}
#endif /* _SPARSESPATIALSAMPLESTRINGKERNEL_H___ */