uicomponents.GeneralMSInfoPanel.java Source code

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Here is the source code for uicomponents.GeneralMSInfoPanel.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 java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import uicomponents.Styles;

import com.vaadin.data.Property.ValueChangeEvent;
import com.vaadin.data.Property.ValueChangeListener;
import com.vaadin.shared.ui.combobox.FilteringMode;

import com.vaadin.ui.ComboBox;
import com.vaadin.ui.OptionGroup;
import com.vaadin.ui.TextArea;
import com.vaadin.ui.VerticalLayout;

public class GeneralMSInfoPanel extends VerticalLayout {

    /**
     * 
     */
    private static final long serialVersionUID = -2282545855402710972L;

    private ComboBox lcmsMethodBox;
    private TextArea lcmsSpecial;
    private ComboBox chromType;
    private ComboBox deviceBox;
    private DBVocabularies vocabs;

    OptionGroup conditionsSet;

    public GeneralMSInfoPanel(DBVocabularies vocabs, String name) {
        this.setCaption(name);
        this.vocabs = vocabs;

        List<String> chromTypes = new ArrayList<String>(vocabs.getChromTypesMap().keySet());
        Collections.sort(chromTypes);

        deviceBox = new ComboBox("MS Device");
        deviceBox.setFilteringMode(FilteringMode.CONTAINS);
        deviceBox.setStyleName(Styles.boxTheme);
        deviceBox.setWidth("300px");
        chromType = new ComboBox("MS Chromatography Type", chromTypes);
        chromType.setFilteringMode(FilteringMode.CONTAINS);
        chromType.setStyleName(Styles.boxTheme);
        lcmsMethodBox = new ComboBox("MS LCMS Method");
        lcmsMethodBox.setFilteringMode(FilteringMode.CONTAINS);
        lcmsMethodBox.setStyleName(Styles.boxTheme);
        lcmsMethodBox.setWidth("350px");

        lcmsSpecial = new TextArea("LCMS Method Name");
        lcmsSpecial.setStyleName(Styles.areaTheme);
        lcmsSpecial.setVisible(false);
        addComponent(Styles.questionize(deviceBox, "The MS device that is used to conduct the experiment.",
                "MS Device"));
        addComponent(Styles.questionize(chromType,
                "Specifies the kind of chromatography that is coupled to the mass spectrometer.",
                "Chromatography Type"));
        addComponent(Styles.questionize(lcmsMethodBox, "Labratory specific parameters for LCMS measurements.",
                "LCMS Method"));
        addComponent(lcmsSpecial);

        lcmsMethodBox.addValueChangeListener(new ValueChangeListener() {

            @Override
            public void valueChange(ValueChangeEvent event) {
                String val = (String) lcmsMethodBox.getValue();
                boolean special = val.equals("SPECIAL_METHOD");
                lcmsSpecial.setVisible(special);
                if (!special)
                    lcmsSpecial.setValue("");
            }
        });

        setSpacing(true);
    }

    public Map<String, Object> getExperimentalProperties() {
        Map<String, Object> res = new HashMap<String, Object>();

        if (deviceBox.getValue() != null)
            res.put("Q_MS_DEVICE", vocabs.getDeviceMap().get(deviceBox.getValue()));
        if (lcmsMethodBox.getValue() != null)
            res.put("Q_MS_LCMS_METHOD", lcmsMethodBox.getValue());
        if (chromType.getValue() != null)
            res.put("Q_CHROMATOGRAPHY_TYPE", vocabs.getChromTypesMap().get(chromType.getValue()));
        if (!lcmsSpecial.getValue().isEmpty())
            res.put("Q_MS_LCMS_METHOD_INFO", lcmsSpecial.getValue());

        // res.put("Q_MS_DEVICE", vocabs.getDeviceMap().get(deviceBox.getValue()));
        // res.put("Q_MS_LCMS_METHOD", lcmsMethodBox.getValue());
        // res.put("Q_CHROMATOGRAPHY_TYPE", chromType.getValue());
        // res.put("Q_MS_LCMS_METHOD_INFO", lcmsSpecial.getValue());
        List<String> remove = new ArrayList<String>();
        for (String key : res.keySet()) {
            String val = (String) res.get(key);
            if (val == null || val.isEmpty())
                remove.add(key);
        }
        for (String key : remove)
            res.remove(key);
        return res;
    }

    public boolean isValid() {
        // TODO restrictions?
        // Set<String> uniques = new HashSet<String>();
        // boolean nonEmpty = false;
        // for (EnzymeChooser c : choosers) {
        // uniques.add(c.getEnzyme());
        // nonEmpty |= (!(c.getEnzyme() == null) && !c.getEnzyme().isEmpty());
        // }
        // if (uniques.size() < choosers.size() || !nonEmpty) {
        // Functions.notification("Wrong input", "Please input at least one enzyme and the same enzyme
        // only once.", NotificationType.ERROR);
        // return false;
        // } else
        return true;
    }

    public void filterDictionariesByPrefix(String prefix, List<String> dontFilter) {
        List<String> devices = new ArrayList<String>();
        List<String> lcmsMethods = new ArrayList<String>();
        if (prefix.isEmpty()) {
            devices.addAll(vocabs.getDeviceMap().keySet());
        } else {
            for (String device : vocabs.getDeviceMap().keySet()) {
                if (device.contains("(" + prefix + ")") || dontFilter.contains(device))
                    devices.add(device);
            }
        }
        for (String lcmsMethod : vocabs.getLcmsMethods()) {
            if (lcmsMethod.startsWith(prefix) || dontFilter.contains(lcmsMethod))
                lcmsMethods.add(lcmsMethod);
        }
        Collections.sort(devices);
        Collections.sort(lcmsMethods);
        deviceBox.removeAllItems();
        deviceBox.addItems(devices);
        lcmsMethodBox.removeAllItems();
        lcmsMethodBox.addItems(lcmsMethods);
    }

}