MolecularFormulaRangeManipulator.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.
 * 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.tools.manipulator;

import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.formula.MolecularFormulaRange;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IIsotope;
import org.openscience.cdk.interfaces.IMolecularFormula;
import org.openscience.cdk.interfaces.IMolecularFormulaSet;

/**
 * Class with convenience methods that provide methods to manipulate
 * MolecularFormulaRange's. 
 *
 * @cdk.module  formula
 * @author      miguelrojasch
 * @cdk.created 2007-11-20
 */
@TestClass("org.openscience.cdk.formula.MolecularFormulaRangeManipulatorTest")
public class MolecularFormulaRangeManipulator {
	
	/**
	 * Extract from a set of MolecularFormula the range of each each element found and
	 * put the element and occurrence in a new MolecularFormulaRange.
	 * 
	 * @param mfSet    The set of molecularFormules to inspect
	 * @return         A MolecularFormulaRange containing range occurrence of the elements
	 */
    @TestMethod("testGetRange_IMolecularFormulaSet")
	public static MolecularFormulaRange getRange(IMolecularFormulaSet mfSet){
		MolecularFormulaRange mfRange = new MolecularFormulaRange();
		
		for(IMolecularFormula mf: mfSet.molecularFormulas()){
            for (IIsotope isotope : mf.isotopes()) {
                int occur_new = mf.getIsotopeCount(isotope);
                if (!mfRange.contains(isotope)) {
                    mfRange.addIsotope(isotope, occur_new, occur_new);
                } else {
                    int occur_old_Max = mfRange.getIsotopeCountMax(isotope);
                    int occur_old_Min = mfRange.getIsotopeCountMin(isotope);
                    if (occur_new > occur_old_Max) {
                        mfRange.removeIsotope(isotope);
                        mfRange.addIsotope(isotope, occur_old_Min, occur_new);
                    } else if (occur_new < occur_old_Min) {
                        mfRange.removeIsotope(isotope);
                        mfRange.addIsotope(isotope, occur_new, occur_old_Max);
                    }
                }
            }
		}
		// looking for those Isotopes which are not contained which then should be 0.
		for(IMolecularFormula mf: mfSet.molecularFormulas()){
			if(mf.getIsotopeCount() != mfRange.getIsotopeCount()){
                for (IIsotope isotope : mfRange.isotopes()) {
                    if (!mf.contains(isotope)) {
                        int occurMax = mfRange.getIsotopeCountMax(isotope);
                        mfRange.addIsotope(isotope, 0, occurMax);
                    }
                }
			}
		}
		return mfRange;
	}
	/**
	 * Returns the maximal occurrence of the IIsotope into IMolecularFormula 
	 * from this MolelecularFormulaRange.
	 * 
	 * @param   mfRange The MolecularFormulaRange to analyze
	 * @return  A IMolecularFormula containing the maximal occurrence of each isotope 
	 */
    @TestMethod("testGetMaximalFormula_MolecularFormulaRange_IChemObjectBuilder")
	public static IMolecularFormula getMaximalFormula(MolecularFormulaRange mfRange, IChemObjectBuilder builder){
		IMolecularFormula formula = builder.newMolecularFormula();

        for (IIsotope isotope : mfRange.isotopes()) {
            formula.addIsotope(isotope, mfRange.getIsotopeCountMax(isotope));
        }
		
		return formula;
	}

	/**
	 * Returns the minimal occurrence of the IIsotope into IMolecularFormula 
	 * from this MolelecularFormulaRange.
	 * 
	 * @param   mfRange The MolecularFormulaRange to analyze
	 * @return  A IMolecularFormula containing the minimal occurrence of each isotope 
	 */
    @TestMethod("testGetMinimalFormula_MolecularFormulaRange_IChemObjectBuilder")
	public static IMolecularFormula getMinimalFormula(MolecularFormulaRange mfRange, IChemObjectBuilder builder){
		IMolecularFormula formula = builder.newMolecularFormula();

        for (IIsotope isotope : mfRange.isotopes()) {
            formula.addIsotope(isotope, mfRange.getIsotopeCountMin(isotope));
        }
		
		return formula;
	}

}