IsotopePatternRule.java

/*  $RCSfile$
 *  $Author$
 *  $Date$
 *  $Revision$
 *
 *  Copyright (C) 2007  Miguel Rojasch <miguelrojasch@users.sf.net>
 *
 *  Contact: cdk-devel@lists.sourceforge.net
 *
 *  This program is free software; you can redistribute it and/or
 *  modify it under the terms of the GNU Lesser General Public License
 *  as published by the Free Software Foundation; either version 2.1
 *  of the License, or (at your option) any later version.
 *
 *  This program 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 Lesser General Public License for more details.
 *
 *  You should have received a copy of the GNU Lesser General Public License
 *  along with this program; if not, write to the Free Software
 *  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 */
package org.openscience.cdk.formula.rules;

import java.io.IOException;
import java.util.List;

import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.formula.IsotopeContainer;
import org.openscience.cdk.formula.IsotopePattern;
import org.openscience.cdk.formula.IsotopePatternGenerator;
import org.openscience.cdk.formula.IsotopePatternManipulator;
import org.openscience.cdk.formula.IsotopePatternSimilarity;
import org.openscience.cdk.interfaces.IMolecularFormula;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
 * This class validate if the Isotope Pattern from a given IMolecularFormula
 *  correspond with other to compare.
 * 
 *
 * <p>This rule uses these parameters:
 * <table border="1">
 *   <tr>
 *     <td>Name</td>
 *     <td>Default</td>
 *     <td>Description</td>
 *   </tr>
 *   <tr>
 *     <td>isotopePattern</td>
 *     <td>List <Double[]></td>
 *     <td>The Isotope Pattern to compare</td>
 *   </tr>
 * </table>
 * 
 * @cdk.module  formula
 * @author      Miguel Rojas Cherto
 * @cdk.created 2007-11-20
 */
public class IsotopePatternRule implements IRule{


	private static ILoggingTool logger =
	    LoggingToolFactory.createLoggingTool(IsotopePatternRule.class);

	/** Accuracy on the mass measuring isotope pattern*/
	private double toleranceMass = 0.001;

	private IsotopePattern  pattern;

	IsotopePatternGenerator isotopeGe;

	private IsotopePatternSimilarity is;
	
    /**
     *  Constructor for the IsotopePatternRule object.
     *
     *  @throws IOException            If an error occurs when reading atom type information
     *  @throws ClassNotFoundException If an error occurs during tom typing
     */
    public IsotopePatternRule() {
    	isotopeGe = new IsotopePatternGenerator(0.01);
    	is = new IsotopePatternSimilarity();
		is.seTolerance(toleranceMass);
    }

    /**
     * Sets the parameters attribute of the IsotopePatternRule object.
     *
     * @param params          The new parameters value
     * @throws CDKException   Description of the Exception
     * 
     * @see                   #getParameters
     */
    public void setParameters(Object[] params) throws CDKException {
    	 if (params.length != 2) 
             throw new CDKException("IsotopePatternRule expects two parameter");
         
       	 if(!(params[0] instanceof List ))
       		 throw new CDKException("The parameter one must be of type List<Double[]>");
       	 

       	 if(!(params[1] instanceof Double ))
       		 throw new CDKException("The parameter two must be of type Double");
       	
       	 pattern = new IsotopePattern();
       	 for(double[] listISO:(List<double[]>) params[0]){
       		 pattern.addIsotope(new IsotopeContainer(listISO[0],listISO[1]));
       	 }
       	 
         is.seTolerance((Double) params[1]);
    }

    /**
     * Gets the parameters attribute of the IsotopePatternRule object.
     *
     * @return The parameters value
     * @see    #setParameters
     */
    public Object[] getParameters() {
    	// return the parameters as used for the rule validation
        Object[] params = new Object[2];
        params[0] = pattern;
        params[1] = toleranceMass;
        return params;
    }

    
    /**
     * Validate the isotope pattern of this IMolecularFormula. Important, first
     * you have to add with the {@link #setParameters(Object[])} a IMolecularFormulaSet
     * which represents the isotope pattern to compare.
     *
     * @param formula   Parameter is the IMolecularFormula
     * @return          A double value meaning 1.0 True, 0.0 False
     */

    public double validate(IMolecularFormula formula) throws CDKException {
    	logger.info("Start validation of ",formula);
    	
    	
    	IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(0.1);
		IsotopePattern patternIsoPredicted = isotopeGe.getIsotopes(formula);
		IsotopePattern patternIsoNormalize = IsotopePatternManipulator.normalize(patternIsoPredicted);
		
    	return is.compare(pattern, patternIsoNormalize);
    }
    
}