uicomponents.MSOptionComponent.java Source code

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Here is the source code for uicomponents.MSOptionComponent.java

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/*******************************************************************************
 * QBiC Project Wizard enables users to create hierarchical experiments including different study
 * conditions using factorial design. Copyright (C) "2016" Andreas Friedrich
 *
 * This program 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.
 *
 * 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
 * General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License along with this program. If
 * not, see <http://www.gnu.org/licenses/>.
 *******************************************************************************/
package uicomponents;

import io.DBVocabularies;
import logging.Log4j2Logger;
import uicomponents.Styles;

import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Map;

import org.vaadin.teemu.wizards.WizardStep;

import steps.MSAnalyteStep;

import com.vaadin.data.Property.ValueChangeEvent;
import com.vaadin.data.Property.ValueChangeListener;
import com.vaadin.ui.CheckBox;
import com.vaadin.ui.ComboBox;

import control.WizardController.Steps;

import com.vaadin.ui.VerticalLayout;

public class MSOptionComponent extends VerticalLayout {

    /**
     * 
     */
    private static final long serialVersionUID = 6966022066367510739L;

    private CheckBox proteinPooling;
    private CheckBox shortGel;
    private CheckBox purification;
    private CheckBox measurePeptides;
    private ComboBox purificationMethods;

    logging.Logger logger = new Log4j2Logger(MSOptionComponent.class);

    public MSOptionComponent(DBVocabularies vocabs) {
        this.setCaption("MS Experiment Options");
        setSpacing(true);
        proteinPooling = new CheckBox("Pool Before Protein Fractionation/Enrichment");
        measurePeptides = new CheckBox("Measure Peptides");
        shortGel = new CheckBox("Use Short Gel");
        purification = new CheckBox("Protein Purification");

        addComponent(purification);
        purificationMethods = new ComboBox("Purification Method");
        purificationMethods.setNullSelectionAllowed(false);
        purificationMethods.setStyleName(Styles.boxTheme);
        purificationMethods.setVisible(false);
        List<String> methods = new ArrayList<String>(vocabs.getProteinPurificationMethodsMap().values());
        Collections.sort(methods);
        purificationMethods.addItems(methods);
        addComponent(purificationMethods);

        purification.addValueChangeListener(new ValueChangeListener() {

            @Override
            public void valueChange(ValueChangeEvent event) {
                purificationMethods.setVisible(purification.getValue());
            }
        });
        addComponent(shortGel);
        addComponent(proteinPooling);
        addComponent(measurePeptides);
    }

    public List<WizardStep> getNextMSSteps(Map<control.WizardController.Steps, WizardStep> steps) {
        boolean poolProteins = proteinPooling.getValue();
        boolean peps = measurePeptides.getValue();
        List<WizardStep> res = new ArrayList<WizardStep>();
        if (poolProteins) {
            res.add(steps.get(Steps.Test_Sample_Pooling));
        }
        MSAnalyteStep f1 = (MSAnalyteStep) steps.get(Steps.Protein_Fractionation);
        res.add(f1);
        if (peps) {
            MSAnalyteStep f2 = (MSAnalyteStep) steps.get(Steps.Peptide_Fractionation);
            f1.setNeedsDigestion(true);
            res.add(f2);
        } else {
            f1.setNeedsDigestion(false);
        }
        res.add(steps.get(Steps.Registration));
        return res;
    }

    public boolean usesShortGel() {
        return shortGel.getValue();
    }

    public boolean usesPurification() {
        return purification.getValue() && purificationMethods.getValue() != null;
    }

    public String getPurificationMethod() {
        return purificationMethods.getValue().toString();
    }

    public boolean isValid() {
        return true;
    }

    public void addMSListener(ValueChangeListener msExpChangedListener) {
        proteinPooling.addValueChangeListener(msExpChangedListener);
        measurePeptides.addValueChangeListener(msExpChangedListener);
    }

    public boolean hasProteinPoolBeforeFractionation() {
        return proteinPooling.getValue();
    }

    public void selectMeasurePeptides(boolean select) {
        measurePeptides.setValue(select);
    }

    public void selectUseShortGel(boolean select) {
        shortGel.setValue(select);
    }

    public void selectProteinPurification(String option) {
        if (option.isEmpty()) {
            purification.setValue(false);
            purificationMethods.setNullSelectionAllowed(true);
            purificationMethods.setValue(purificationMethods.getNullSelectionItemId());
            purificationMethods.setNullSelectionAllowed(false);
        } else {
            purification.setValue(true);
            purificationMethods.setValue(option);
        }
    }

}