root/trunk/plugins/examples/org/pathvisio/example/ExImporter.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.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;

import org.pathvisio.gui.swing.PvDesktop;
import org.pathvisio.model.ConverterException;
import org.pathvisio.model.ObjectType;
import org.pathvisio.model.Pathway;
import org.pathvisio.model.PathwayElement;
import org.pathvisio.model.PathwayImporter;
import org.pathvisio.plugin.Plugin;

/**
 * Example of how to create and register a Pathway importer.
 * <p>
 * Here we convert a text file to a pathway, by making a separate
 * label out of each line.
 */
public class ExImporter implements Plugin
{
        private PvDesktop desktop;

        public void init(PvDesktop desktop)
        {
                this.desktop = desktop;

                // instantiate TextLinesImporter, our own importer, and register it
                desktop.getSwingEngine().getEngine().addPathwayImporter(new TextLinesImporter());
        }

        public void done() {}

        private static class TextLinesImporter implements PathwayImporter
        {
                /**
                 * Called after the user selected a file and picked this importer from the
                 * File types dropdown.
                 * <p>
                 * Our job is to create a new Pathway object, fill its contents
                 * and return it.
                 */
                public Pathway doImport(File file)
                                throws ConverterException
                {
                        Pathway pathway = new Pathway();
                        try
                        {
                                // some constants: this is the size of each label
                                double xpos = 300;
                                double ypos = 300;
                                double height = 300;
                                double width = 1500;

                                // open file for reading
                                BufferedReader reader = null;
                                reader = new BufferedReader(new FileReader (file));
                                String line;
                                // go over each line
                                while ((line = reader.readLine()) != null)
                                {
                                        line = line.trim();
                                        // skip empty lines
                                        if (line.equals ("")) { continue; }

                                        // construct a new label object, set the properties
                                        PathwayElement elt = PathwayElement.createPathwayElement(ObjectType.LABEL);
                                        elt.setMWidth(width);
                                        elt.setMHeight(height);
                                        elt.setMTop(ypos);
                                        elt.setMLeft(xpos);
                                        elt.setTextLabel(line);
                                        // add the object to the pathway
                                        pathway.add(elt);
                                        ypos += height; // move to next line
                                }
                                // set the pathway title
                                pathway.getMappInfo().setMapInfoName(file.getName());
                                reader.close();
                        }
                        catch (IOException ex)
                        {
                                throw new ConverterException (ex);
                        }
                        return pathway;
                }

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

                public String[] getExtensions()
                {
                        return EXTENSIONS;
                }

                public String getName()
                {
                        return "Lines from text file";
                }
        }
}