GUIKernel.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) 1999-2008 Soeren Sonnenburg
 * Written (W) 1999-2008 Gunnar Raetsch
 * Copyright (C) 1999-2008 Fraunhofer Institute FIRST and Max-Planck-Society
 */

#ifndef __GUIKERNEL__H
#define __GUIKERNEL__H

#include <shogun/lib/config.h>
#include <shogun/base/SGObject.h>
#include <shogun/kernel/Kernel.h>

namespace shogun
{
class CSGInterface;

class CGUIKernel : public CSGObject
{
 public:
    CGUIKernel() { };
    CGUIKernel(CSGInterface* interface);

    ~CGUIKernel();

    CKernel* get_kernel();
    bool set_normalization(char* normalization, float64_t c=0.0, float64_t r=0.0);
    bool set_kernel(CKernel* kern);
    bool add_kernel(CKernel* kern, float64_t weight=1);
    bool del_last_kernel();

    bool init_kernel(const char* target);
    bool init_kernel_optimization();
    bool delete_kernel_optimization();
    bool save_kernel(char* filename);
    bool clean_kernel();
#ifdef USE_SVMLIGHT

    bool resize_kernel_cache(int32_t size);
#endif //USE_SVMLIGHT

    bool set_optimization_type(char* opt_type);
    bool precompute_subkernels();

    bool is_initialized() { return initialized; }

    CKernel* create_oligo(int32_t size, int32_t k, float64_t width);
    CKernel* create_diag(int32_t size=10, float64_t diag=1);
    CKernel* create_const(int32_t size=10, float64_t c=1);
    CKernel* create_custom(float64_t* kmatrix, int32_t num_feat, int32_t num_vec,
        bool source_is_diag, bool dest_is_diag);
    CKernel* create_gaussianshift(
        int32_t size=10, float64_t width=1, int32_t max_shift=0,
        int32_t shift_step=1);
    CKernel* create_sparsegaussian(int32_t size=10, float64_t width=1);
    CKernel* create_gaussian(int32_t size=10, float64_t width=1);
    CKernel* create_sigmoid(
        int32_t size=10, float64_t gamma=0.01, float64_t coef0=0);
    CKernel* create_tppk(
        int32_t size, float64_t* km, int32_t rows, int32_t cols);
    CKernel* create_sparsepoly(
        int32_t size=10, int32_t degree=2, bool inhomogene=false,
        bool normalize=true);
    CKernel* create_poly(
        int32_t size=10, int32_t degree=2, bool inhomogene=false,
        bool normalize=true);
    CKernel* create_wavelet(
        int32_t size=10, float64_t Wdilation=5.0, float64_t Wtranslation=2.0);
    CKernel* create_localityimprovedstring(
        int32_t size=10, int32_t length=3, int32_t inner_degree=3,
        int32_t outer_degree=1, EKernelType ktype=K_LOCALITYIMPROVED);
    CKernel* create_weighteddegreestring(
        int32_t size=10, int32_t order=3, int32_t max_mismatch=1,
        bool use_normalization=true, int32_t mkl_stepsize=1,
        bool block_computation=true, int32_t single_degree=-1);
    CKernel* create_weighteddegreepositionstring(
        int32_t size=10, int32_t order=3, int32_t max_mismatch=1,
        int32_t length=0, int32_t center=0, float64_t step=1);
    CKernel* create_weighteddegreepositionstring3(
        int32_t size=10, int32_t order=3, int32_t max_mismatch=1,
        int32_t* shifts=NULL, int32_t length=0, int32_t mkl_stepsize=1,
        float64_t* position_weights=NULL);
    CKernel* create_weighteddegreepositionstring2(
        int32_t size=10, int32_t order=3, int32_t max_mismatch=1,
        int32_t* shifts=NULL, int32_t length=0, bool use_normalization=true);
    CKernel* create_weighteddegreerbf(int32_t size=10, int32_t degree=1, int32_t nof_properties=1, float64_t width=1);
    CKernel* create_spectrummismatchrbf(int32_t size=10, float64_t* AA_matrix = NULL, int32_t nr=128, int32_t nc=128, int32_t max_mismatch=1, int32_t degree=1, float64_t width=1);
    CKernel* create_localalignmentstring(int32_t size=10);
    CKernel* create_fixeddegreestring(int32_t size=10, int32_t d=3);
    CKernel* create_chi2(int32_t size=10, float64_t width=1);
    CKernel* create_commstring(
        int32_t size=10, bool use_sign=false, char* norm_str=NULL,
        EKernelType ktype=K_WEIGHTEDCOMMWORDSTRING);
    CKernel* create_matchwordstring(
        int32_t size=10, int32_t d=3, bool normalize=true);
    CKernel* create_polymatchstring(
        int32_t size=10, int32_t degree=2, bool inhomogene=false,
        bool normalize=true);
    CKernel* create_polymatchwordstring(
        int32_t size=10, int32_t degree=2, bool inhomogene=false,
        bool normalize=true);
    CKernel* create_salzbergword(int32_t size=10);
    CKernel* create_histogramword(int32_t size=10);
    CKernel* create_linearbyte(int32_t size=10, float64_t scale=-1);
    CKernel* create_linearword(int32_t size=10, float64_t scale=-1);
    CKernel* create_linearstring(int32_t size=10, float64_t scale=-1);
    CKernel* create_linear(int32_t size=10, float64_t scale=-1);
    CKernel* create_sparselinear(int32_t size=10, float64_t scale=-1);
    CKernel* create_distance(int32_t size=10, float64_t width=1);
    CKernel* create_combined(
        int32_t size=10, bool append_subkernel_weights=false);

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

 protected:
    CKernel* kernel;
    CSGInterface* ui;
    bool initialized;

 private:
    float64_t* get_weights(int32_t order, int32_t max_mismatch);
};
}
#endif