uk.ac.ebi.mdk.ui.component.MetaboliteMatchIndication.java Source code

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Here is the source code for uk.ac.ebi.mdk.ui.component.MetaboliteMatchIndication.java

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/*
 * Copyright (c) 2013. EMBL, European Bioinformatics Institute
 *
 * 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 3 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, see <http://www.gnu.org/licenses/>.
 */
package uk.ac.ebi.mdk.ui.component;

import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.openscience.cdk.Element;
import org.openscience.cdk.Isotope;
import org.openscience.cdk.interfaces.IMolecularFormula;
import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator;
import uk.ac.ebi.caf.utility.TextUtility;
import uk.ac.ebi.mdk.domain.annotation.MolecularFormula;
import uk.ac.ebi.mdk.domain.entity.Metabolite;

import javax.swing.*;
import java.util.ArrayList;
import java.util.List;

/**
 * MetaboliteMatchIndication 2012.02.02
 *
 * @author johnmay
 * @author $Author$ (this version)
 *         <p/>
 *         Class description
 * @version $Rev$ : Last Changed $Date$
 */
public class MetaboliteMatchIndication {

    private static final Logger LOGGER = Logger.getLogger(MetaboliteMatchIndication.class);

    private JComponent component;

    private Metabolite query;

    private Metabolite subject;

    private MatchIndication name = new MatchIndication(300, 300);

    private MatchIndication formula = new MatchIndication(300, 300);

    private MatchIndication charge = new MatchIndication(300, 300);

    public MetaboliteMatchIndication() {
        component = Box.createVerticalBox();
        component.add(name.getComponent());
        component.add(formula.getComponent());
        component.add(charge.getComponent());
    }

    public JComponent getComponent() {
        return component;
    }

    public void setQueryName(String string) {
        name.setLeft(string);
    }

    public void setQuery(Metabolite query) {
        this.query = query;
        name.setLeft(query.getName());
        charge.setLeft(query.getCharge() == null ? "N/A" : query.getCharge().toString());
    }

    public void setSubject(Metabolite subject) {
        this.subject = subject;

        name.setRight(subject.getName());

        Integer nameDiff = StringUtils.getLevenshteinDistance(name.getLeft().toLowerCase(),
                subject.getName().toLowerCase());
        name.setDifference(nameDiff.toString());
        name.setQuality(nameDiff <= 2 ? MatchIndication.Quality.Good
                : nameDiff <= 5 ? MatchIndication.Quality.Okay : MatchIndication.Quality.Bad);

        double queryCharge = query.getCharge();
        double subjectCharge = subject.getCharge();

        charge.setRight(Double.toString(subjectCharge));

        double chargeDiff = Math.abs(queryCharge - subjectCharge);

        charge.setQuality(chargeDiff < 1 ? MatchIndication.Quality.Good
                : chargeDiff < 2 ? MatchIndication.Quality.Okay : MatchIndication.Quality.Bad);

        setFormulaQuality();

    }

    public void setFormulaQuality() {

        formula.setQuality(MatchIndication.Quality.Bad);

        List<MolecularFormula> queryMfs = new ArrayList(query.getAnnotationsExtending(MolecularFormula.class));
        List<MolecularFormula> subjectMfs = new ArrayList(subject.getAnnotationsExtending(MolecularFormula.class));

        formula.setLeft("N/A");
        formula.setRight("N/A");

        if (!queryMfs.isEmpty()) {
            formula.setLeft(TextUtility.html(queryMfs.get(0).toHTML()));
        }
        if (!subjectMfs.isEmpty()) {
            formula.setRight(TextUtility.html(subjectMfs.get(0).toHTML()));
        }

        Isotope hydrogen = new Isotope(new Element("H"));
        for (MolecularFormula queryMf : queryMfs) {
            for (MolecularFormula subjectMf : subjectMfs) {

                if (MolecularFormulaManipulator.compare(queryMf.getFormula(), subjectMf.getFormula())) {
                    formula.setQuality(MatchIndication.Quality.Good);
                    formula.setLeft(TextUtility.html(queryMf.toHTML()));
                    formula.setRight(TextUtility.html(subjectMf.toHTML()));
                    return;
                } else {
                    IMolecularFormula mf1 = queryMf.getFormula();
                    IMolecularFormula mf2 = subjectMf.getFormula();

                    int mf1hc = MolecularFormulaManipulator.getElementCount(mf1, hydrogen);
                    int mf2hc = MolecularFormulaManipulator.getElementCount(mf2, hydrogen);

                    mf1 = MolecularFormulaManipulator.removeElement(mf1, hydrogen);
                    mf2 = MolecularFormulaManipulator.removeElement(mf2, hydrogen);

                    if (MolecularFormulaManipulator.compare(mf1, mf2)) {
                        formula.setQuality(MatchIndication.Quality.Okay);
                        formula.setLeft(TextUtility.html(queryMf.toHTML()));
                        formula.setRight(TextUtility.html(subjectMf.toHTML()));
                    }

                    mf1.addIsotope(hydrogen, mf1hc);
                    mf2.addIsotope(hydrogen, mf2hc);

                }
            }
        }

    }
}