root/trunk/plugins/examples/org/pathvisio/example/ExExporter.java

// 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.example;

import java.io.File;
import java.io.FileWriter;
import java.io.IOException;

import org.pathvisio.biopax.reflect.BiopaxElement;
import org.pathvisio.biopax.reflect.PublicationXref;
import org.pathvisio.gui.swing.PvDesktop;
import org.pathvisio.model.ConverterException;
import org.pathvisio.model.Pathway;
import org.pathvisio.model.PathwayExporter;
import org.pathvisio.plugin.Plugin;

/**
 * Shows how to implement a new file format,
 * and how to register it with PathVisio.
 * <p>
 * In this case we'll create an exporter to
 * export only the literature references of
 * a Pathway.
 */
public class ExExporter implements Plugin
{
        private PvDesktop desktop;

        public void init(PvDesktop desktop)
        {
                this.desktop = desktop;
                // here we register an instance of our exporter
                desktop.getSwingEngine().getEngine().addPathwayExporter(new BibliographyExporter());
        }

        /**
         * Export all literature references of a pathway
         * as a simple plain-text format.
         * This is not any standard format, it's just an example
         * of what an exporter can do.BibliographyExporter
         */
        private static class BibliographyExporter implements PathwayExporter
        {
                /**  Called after the user has selected a file to export */
                public void doExport(File file, Pathway pathway)
                                throws ConverterException {

                        try {
                                // open the file for writing
                                FileWriter fos = new FileWriter(file);
                                int i = 0;
                                // loop over all embedded Biopax elements of the Pathway
                                for (BiopaxElement be : pathway.getBiopaxElementManager().getElements())
                                {
                                        fos.write ("BIBLIOGRAPHY\n");
                                        fos.write ("============\n");
                                        // check if this is a publication reference
                                        if (be instanceof PublicationXref)
                                        {
                                                // print some information in a very simple text format
                                                PublicationXref pxref = (PublicationXref)be;
                                                fos.write ("\n");
                                                i++;
                                                fos.write ("#" + i + ":\n");
                                                fos.write("Authors: " + pxref.getAuthors() + "\n");
                                                fos.write("Title: " + pxref.getTitle() + "\n");
                                                fos.write("Source: " + pxref.getSource() + "\n");
                                                fos.write("Year: " + pxref.getYear() + "\n");
                                                fos.write("PMID: " + pxref.getPubmedId() + "\n");
                                        }
                                }
                                // if i remains at zero, there were no references
                                if (i == 0)
                                {
                                        fos.write ("\nNo publication references found\n");
                                }
                                fos.close();
                        }
                        catch (IOException e)
                        {
                                throw new ConverterException (e);
                        }

                }

                private static final String[] EXTENSIONS = new String[] { "txt" };

                /**
                 * Valid extensions for this file type. The first
                 * of these will be automatically appended to the File passed to doExport.
                 */
                public String[] getExtensions()
                {
                        return EXTENSIONS;
                }

                /**
                 * A suitable name to display in the JFileChooser dialog.
                 */
                public String getName()
                {
                        return "Text Bibliography Exporter";
                }
        }

        public void done() {}
}