001/*
002 * Copyright (c) 2004-2010 The Regents of the University of California.
003 * All rights reserved.
004 *
005 * '$Author: crawl $'
006 * '$Date: 2015-08-24 22:48:48 +0000 (Mon, 24 Aug 2015) $' 
007 * '$Revision: 33634 $'
008 * 
009 * Permission is hereby granted, without written agreement and without
010 * license or royalty fees, to use, copy, modify, and distribute this
011 * software and its documentation for any purpose, provided that the above
012 * copyright notice and the following two paragraphs appear in all copies
013 * of this software.
014 *
015 * IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY
016 * FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES
017 * ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF
018 * THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF
019 * SUCH DAMAGE.
020 *
021 * THE UNIVERSITY OF CALIFORNIA SPECIFICALLY DISCLAIMS ANY WARRANTIES,
022 * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
023 * MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE
024 * PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF
025 * CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES,
026 * ENHANCEMENTS, OR MODIFICATIONS.
027 *
028 */
029
030package org.cipres.kepler;
031
032import forester.atv.ATVjframe;
033// Ptolemy packages
034import ptolemy.actor.TypedAtomicActor;
035import ptolemy.actor.TypedIOPort;
036import ptolemy.data.StringToken;
037import ptolemy.data.type.BaseType;
038import ptolemy.kernel.CompositeEntity;
039import ptolemy.kernel.util.IllegalActionException;
040import ptolemy.kernel.util.NameDuplicationException;
041
042//////////////////////////////////////////////////////////////////////////
043//// TreeVizForester
044/**
045 * Given a tree expression (in newick format), the TreeVizForester actor
046 * displays the phylogenetic tree in the Forester tree view window.
047 * 
048 * @author Zhijie Guan
049 * @version $Id: TreeVizForester.java 33634 2015-08-24 22:48:48Z crawl $
050 */
051
052public class TreeVizForester extends TypedAtomicActor {
053
054        /**
055         * Construct a TreeVizForester actor with the given container and name.
056         * 
057         * @param container
058         *            The container.
059         * @param name
060         *            The name of this actor.
061         * @exception IllegalActionException
062         *                If the entity cannot be contained by the proposed
063         *                container.
064         * @exception NameDuplicationException
065         *                If the container already has an actor with this name.
066         */
067
068        public TreeVizForester(CompositeEntity container, String name)
069                        throws NameDuplicationException, IllegalActionException {
070                super(container, name);
071
072                // construct the input port inputTreeString
073                inputTreeString = new TypedIOPort(this, "inputTreeString", true, false);
074                inputTreeString.setDisplayName("Tree Expression (Newick)");
075                // inputTreeString.setDisplayName("Tree Expression (Newick)");
076                inputTreeString.setTypeEquals(BaseType.GENERAL);
077
078                _attachText("_iconDescription", "<svg>\n" + "<rect x=\"0\" y=\"0\" "
079                                + "width=\"60\" height=\"20\" " + "style=\"fill:white\"/>\n"
080                                + "</svg>\n");
081
082        }
083
084        // /////////////////////////////////////////////////////////////////
085        // // ports and parameters ////
086
087        /**
088         * Tree expression to pass to the Forester tree display package. This port
089         * is an input port of type GENERAL.
090         */
091        public TypedIOPort inputTreeString = null;
092
093        // /////////////////////////////////////////////////////////////////
094        // // functional variables ////
095
096        // /////////////////////////////////////////////////////////////////
097        // // public methods ////
098
099        /**
100         * Display the phylogenetic tree ported in from the input port with the
101         * Forester package.
102         * 
103         * @exception IllegalActionException
104         *                if it is thrown by the super.fire() method.
105         */
106        public void fire() throws IllegalActionException {
107                super.fire();
108
109                if (inputTreeString.hasToken(0)) {
110                        // get the tree expression
111                        String treeDescription = ((StringToken) inputTreeString.get(0))
112                                        .stringValue();
113                        try {
114                                // create the tree in Forester
115                                forester.tree.Tree displayedTree = new forester.tree.Tree(
116                                                treeDescription);
117                                // create the Forester tree view window
118                                ATVjframe atvframe = new ATVjframe(displayedTree);
119                                // atvframe.setTitle(treeDescription);
120                                // display the tree
121                                atvframe.showWhole();
122                        } catch (Exception e) {
123                                e.printStackTrace();
124                        }
125                }
126
127        }
128}