root/trunk/plugins/GexPlugin/src/org/pathvisio/plugins/gex/GexPlugin.java @ 3128

// PathVisio,
// a tool for data visualization and analysis using Biological Pathways
// Copyright 2006-2009 BiGCaT Bioinformatics
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
package org.pathvisio.plugins.gex;

import java.awt.event.ActionEvent;

import javax.swing.AbstractAction;
import javax.swing.JOptionPane;

import org.bridgedb.rdb.construct.DBConnector;
import org.pathvisio.data.DBConnectorSwing;
import org.pathvisio.debug.Logger;
import org.pathvisio.gui.swing.PvDesktop;
import org.pathvisio.plugin.Plugin;

/**
 * This plugin enables Gex functionality. Currently only adds menu items
 * to import or load a Gex
 * @author thomas
 */
public class GexPlugin implements Plugin {

        public void init(PvDesktop desktop)
        {
                ImportGexDataAction importAction = new ImportGexDataAction(desktop);
                SelectGexAction selectAction = new SelectGexAction(desktop);

                desktop.registerMenuAction ("Data", importAction);
                desktop.registerMenuAction ("Data", selectAction);
        }

        public void done() {};

        /**
         * Import gex data and create a new gex database from it
         */
        public static class ImportGexDataAction extends AbstractAction
        {
                private static final long serialVersionUID = 1L;

                private final PvDesktop sae;

                public ImportGexDataAction(PvDesktop sae)
                {
                        super();
                        this.sae = sae;
                        putValue (NAME, "Import expression data");
                        putValue (SHORT_DESCRIPTION, "Import data from a tab delimited text file, for example experimental data from a high-throughput experiment");
                }

                public void actionPerformed (ActionEvent e)
                {
                        GexImportWizard wizard = new GexImportWizard(sae);
                        wizard.showModalDialog(sae.getSwingEngine().getFrame());
                }
        }

        /**
         * Let the user open an expression dataset
         * @author thomas
         */
        public static class SelectGexAction extends AbstractAction
        {
                private static final long serialVersionUID = 1L;
                private final PvDesktop se;

                public SelectGexAction(PvDesktop standaloneEngine) {
                        se = standaloneEngine;
                        putValue(NAME, "Select expression dataset");
                        putValue(SHORT_DESCRIPTION, "Select expression dataset");
                }

                public void actionPerformed(ActionEvent e) {
                        try
                        {
                                /**
                                 * Get the preferred database connector to connect to Gex databases,
                                 * and try to cast it to swingDbConnector.
                                 * throws an exception if that fails
                                 */
                                DBConnectorSwing dbcon;
                                DBConnector dbc = se.getGexManager().getDBConnector();
                                if(dbc instanceof DBConnectorSwing)
                                {
                                        dbcon = (DBConnectorSwing)dbc;
                                }
                                else
                                {
                                        //TODO: better handling of error
                                        throw new IllegalArgumentException("Not a Swing database connector");
                                }
                                String dbName = dbcon.openChooseDbDialog(null);

                                if(dbName == null) return;

                                se.getGexManager().setCurrentGex(dbName, false);
                                se.loadGexCache();
                        }
                        catch(Exception ex)
                        {
                                String msg = "Failed to open expression dataset; " + ex.getMessage();
                                JOptionPane.showMessageDialog(null,
                                                "Error: " + msg + "\n\n" + "See the error log for details.",
                                                "Error",
                                                JOptionPane.ERROR_MESSAGE);
                                Logger.log.error(msg, ex);
                        }
                }
        }
}