FuncEquivFilter.h

/**************************************************************************
 * Copyright (c) 2007 Clifford Conley Owens III                           *
 *                                                                        *
 * This file is part of Biorithm.                                         *
 *                                                                        *
 * Biorithm 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.                                    *
 *                                                                        *
 * Biorithm 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 Biorithm.  If not, see <http://www.gnu.org/licenses/>.      *
 *                                                                        *
 **************************************************************************/

#ifndef FUNCEQUIVFILTER_H
#define FUNCEQUIVFILTER_H

// ---------------------------- Internal Headers ---------------------------- //

#include "Filter.h"

// ---------------------------- External Headers ---------------------------- //

#include "annotations.h"
#include "GO.h"

class FuncEquivFilter: public Filter
{
    protected:
        // The gene ontology file
        string obofile;

        // The functional annotations file
        string fafile;

        // Whether or not we have set the data
        bool setdata;

        // Whether or not there was a problem with the data
        bool problem;

        // The gene ontology
        GeneOntology go;

        // The functional annotations
        MyAnnotations fa;

        // Helper methods
        bool setupData();

  // the name of the file to print row set stats to.
  string rowSetFileName;
  ofstream rsstr;
  // the name of the file to print FE results to. 
  string feFileName;
  // and the corresponding output stream.
  ofstream festr;
  
  
    public:
  FuncEquivFilter(const string& obofile, const string& fafile);
        FuncEquivFilter(const FuncEquivFilter& src);
        virtual ~FuncEquivFilter();
        virtual FuncEquivFilter& operator =(const FuncEquivFilter& rhs);
        virtual bool filter(const ItemSet& is, TruthMatrix& tm, string& msg);
};

#endif