QSAR/kernel.h

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/* kernel.h
 * 
 * Copyright (C) 2009 Marcel Schumann
 * 
 * This file is part of QuEasy -- A Toolbox for Automated QSAR Model
 * Construction and Validation.
 * QuEasy 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.
 * 
 * QuEasy is distributed in the hope that it will be useful, but
 * WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, see <http://www.gnu.org/licenses/>.
 */

  // -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
//

#ifndef KERNEL
#define KERNEL

#ifndef LMODEL
#include <BALL/QSAR/linearModel.h>
#endif

#ifndef MODEL
#include <BALL/QSAR/Model.h>
#endif

#ifndef QSAR_EXCEPTION
#include <BALL/QSAR/exception.h>
#endif

#ifndef REGRESSION
#include <BALL/QSAR/regressionModel.h>
#endif

#include <cmath>
#include <sstream>


namespace BALL
{
  namespace QSAR
  {
    class BALL_EXPORT Kernel
    { 
      
    
      public:
        Kernel(Model* m, int k_type, double p1, double p2=-1);
        
        Kernel(Model* m, String f, String g);
            
        Kernel(Model* m, Vector<double>& w);
        
        Kernel(Model* m, const LinearModel& lm, int column);

        ~Kernel();
        
        
        void calculateKernelMatrix(Matrix<double>& input, Matrix<double>& output);
        
        void calculateKernelMatrix(Matrix<double>& K, Matrix<double>& m1, Matrix<double>& m2, Matrix<double>& output);
        
        
        void calculateKernelVector(Matrix<double>& K,Vector<double>& m1, Matrix<double>& m2, Vector<double>& output);
        
        void gridSearch(double step_width, int steps, int recursions, int k, bool opt=0);
        
        
        int type;
        
        double par1, par2;
        
        String equation1;
        
        String equation2;
        
        
      protected:

        void gridSearch(double step_width, int steps, bool first_rec, int k, double par1_start, double par2_start, bool opt);

        void calculateWeightedKernelMatrix(Matrix<double>& input, Matrix<double>& output);
        
        
        void calculateWeightedKernelMatrix(Matrix<double>& m1, Matrix<double>& m2, Matrix<double>& output);
        
        
        void calculateKernelMatrix1(Matrix<double>& input, Matrix<double>& output);
        
        void calculateKernelMatrix2(Matrix<double>& input, Matrix<double>& output);
        
        void calculateKernelMatrix3(Matrix<double>& input, Matrix<double>& output);
        
        void calculateKernelMatrix4(Matrix<double>& input, Matrix<double>& output);
        
        
        void calculateKernelMatrix1(Matrix<double>& m1, Matrix<double>& m2, Matrix<double>& output);
        
        void calculateKernelMatrix2(Matrix<double>& m1, Matrix<double>& m2, Matrix<double>& output);
        
        void calculateKernelMatrix3(Matrix<double>& m1, Matrix<double>& m2, Matrix<double>& output);
        
        void calculateKernelMatrix4(Matrix<double>& m1, Matrix<double>& m2, Matrix<double>& output);
        
        
        Model* model_;
        
        Vector<double> weights_;
        
        
        friend class FeatureSelection;
      
    };
  }
}

#endif // KERNEL