MolecularFormulaChecker.java

/* $Revision$ $Author$ $Date$
 *
 *  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.
 *  All we ask is that proper credit is given for our work, which includes
 *  - but is not limited to - adding the above copyright notice to the beginning
 *  of your source code files, and to any copyright notice that you may distribute
 *  with programs based on this work.
 *
 *  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;

import java.util.Iterator;
import java.util.List;
import java.util.Map;

import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.formula.rules.IRule;
import org.openscience.cdk.interfaces.IMolecularFormula;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;

/**
 * <p> Validate a molecular formula given in IMolecularformula object. The
 * validation is based according different rules that you have to introduce before
 * see IRule.
 * 
 * @cdk.module  formula
 * @author      miguelrojasch
 * @cdk.created 2007-11-20
 * @cdk.keyword molecule, molecular formula
 * @see         IRule
 */
@TestClass("org.openscience.cdk.formula.MolecularFormulaCheckerTest")
public class MolecularFormulaChecker {

	private ILoggingTool logger =
        LoggingToolFactory.createLoggingTool(MolecularFormulaChecker.class);
	

	/** List of IRules to be applied in the validation.*/
	private List<IRule> rules;
	/**
	 * Construct an instance of MolecularFormulaChecker. It must be initialized
	 * with the rules to applied. 
	 * 
	 * @param rules  A List with IRule to be applied
	 */
	public MolecularFormulaChecker(List<IRule> rules) {
		this.rules = rules;
	}	

	/**
	 * Get the IRules to be applied to validate the IMolecularFormula.
	 * 
	 * @return A List with IRule
	 */
	@TestMethod("testGetRules")
	public List<IRule> getRules(){
		return rules;
	}
	/**
	 * Validate if a IMolecularFormula is valid. The result more close to 1 means
	 * maximal probability to be valid. Opposite more close to 0 means minimal
	 * probability to be valid. To know the result in each IRule use 
	 * {@link #isValid(IMolecularFormula)} 
	 * 
	 * @param  formula      The IMolecularFormula value
	 * @return              The percent of the validity
	 * @see                 #isValid(IMolecularFormula)
	 */
	@TestMethod("testIsValidSum_IMolecularFormula")
	public Double isValidSum(IMolecularFormula formula){
		double result = 1.0;
		
		IMolecularFormula formulaWith = isValid(formula);
		Map<Object, Object> properties = formulaWith.getProperties();
		
		Iterator<IRule> iterRules = rules.iterator();
		while(iterRules.hasNext()){
			result *= (Double)properties.get(iterRules.next().getClass());
		}
		return result;
	}
	/**
	 * Validate if a IMolecularFormula is valid. The results of each IRule which
	 * has to be applied is put into IMolecularFormula as properties. To extract
	 * the result final as the product of rule's result use 
	 * {@link #isValidSum(IMolecularFormula)}.
	 * 
	 * @param  formula      The IMolecularFormula value
	 * @return formulaWith  The IMolecularFormula with the results for each
	 *                      IRule into properties
	 * @see                 #isValidSum(IMolecularFormula)
	 */
	@TestMethod("testIsValid_IMolecularFormula")
	public IMolecularFormula isValid(IMolecularFormula formula){
		logger.info("Generating the validity of the molecular formula");
		
		if(formula.getIsotopeCount() == 0){
			logger.error("Proposed molecular formula has not elements");
			return formula;
		}
		
		Iterator<IRule> iterRules = rules.iterator();
		try {
			while(iterRules.hasNext()){
				IRule rule = iterRules.next();
				double result = rule.validate(formula);
				formula.setProperty(rule.getClass(), result);
				
			}
		} catch (CDKException e) {
			e.printStackTrace();
		}
		
		return formula;
	}
}