2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.archaeopteryx;
28 import java.awt.Color;
30 import java.awt.Graphics;
31 import java.awt.KeyboardFocusManager;
35 import javax.swing.JApplet;
36 import javax.swing.UIManager;
38 import org.forester.phylogeny.Phylogeny;
39 import org.forester.util.ForesterUtil;
41 public class ArchaeopteryxA extends JApplet {
43 private static final long serialVersionUID = 2314899014580484146L;
44 private final static Color background_color = new Color( 0, 0, 0 );
45 private final static Color font_color = new Color( 0, 255, 0 );
46 private final static Color ex_background_color = new Color( 0, 0, 0 );
47 private final static Color ex_font_color = new Color( 255, 0, 0 );
48 private final static Font font = new Font( Configuration.getDefaultFontFamilyName(), Font.BOLD, 9 );
49 private MainFrameApplet _mainframe_applet;
50 private String _url_string = "";
51 private String _message_1 = "";
52 private String _message_2 = "";
53 public final static String NAME = "ArchaeopteryxA";
56 public void destroy() {
57 AptxUtil.printAppletMessage( NAME, "going to be destroyed" );
58 if ( getMainFrameApplet() != null ) {
59 getMainFrameApplet().close();
64 * This method returns the current external node data which
65 * has been selected by the user by clicking the "Return ..."
66 * menu item. This method is expected to be called from Javascript or
69 * @return current external node data as String
71 public String getCurrentExternalNodesDataBuffer() {
72 return getMainFrameApplet().getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
75 public int getCurrentExternalNodesDataBufferChangeCounter() {
76 return getMainFrameApplet().getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
79 public int getCurrentExternalNodesDataBufferLength() {
80 return getMainFrameApplet().getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
83 public String getUrlString() {
89 boolean has_exception = false;
91 setUrlString( getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD ) );
92 AptxUtil.printAppletMessage( NAME, "URL of phylogenies to load: \"" + getUrlString() + "\"" );
93 setBackground( background_color );
94 setForeground( font_color );
99 s = System.getProperty( "java.version" );
101 catch ( final Exception e ) {
102 ForesterUtil.printWarningMessage( NAME, "minor error: " + e.getLocalizedMessage() );
104 if ( ( s != null ) && ( s.length() > 0 ) ) {
105 setMessage2( "[Your Java version: " + s + "]" );
108 final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
109 AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
110 final Configuration configuration = new Configuration( config_filename, true, true, true );
112 if ( configuration.isUseNativeUI() ) {
113 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
116 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
119 _mainframe_applet = new MainFrameApplet( this, configuration );
121 url = new URL( getUrlString() );
122 final Phylogeny[] phys = AptxUtil.readPhylogeniesFromUrl( url, configuration
123 .isValidatePhyloXmlAgainstSchema(), configuration.isReplaceUnderscoresInNhParsing(), configuration
124 .isInternalNumberAreConfidenceForNhParsing(), configuration.getTaxonomyExtraction() );
125 AptxUtil.addPhylogeniesToTabs( phys,
126 new File( url.getFile() ).getName(),
128 getMainFrameApplet().getConfiguration(),
129 getMainFrameApplet().getMainPanel() );
130 getMainFrameApplet().getMainPanel().getControlPanel().showWholeAll();
131 getMainFrameApplet().getMainPanel().getControlPanel().showWhole();
134 catch ( final Exception e ) {
135 ForesterUtil.printErrorMessage( NAME, e.toString() );
136 setBackground( ex_background_color );
137 setForeground( ex_font_color );
138 has_exception = true;
139 setMessage1( "Exception: " + e );
143 if ( !has_exception ) {
144 setMessage1( NAME + " is now ready!" );
146 AptxUtil.printAppletMessage( NAME, "successfully initialized" );
148 KeyboardFocusManager.getCurrentKeyboardFocusManager().clearGlobalFocusOwner();
149 getMainFrameApplet().requestFocus();
150 getMainFrameApplet().requestFocusInWindow();
151 getMainFrameApplet().requestFocus();
153 final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
154 if ( default_relation != null ) {
155 getMainFrameApplet().getMainPanel().getControlPanel().getSequenceRelationTypeBox()
156 .setSelectedItem( default_relation );
158 final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
159 if ( default_sequence != null ) {
160 getMainFrameApplet().getMainPanel().getControlPanel().getSequenceRelationBox()
161 .setSelectedItem( default_sequence );
167 * Prints message when initialization is finished. Called automatically.
173 public void paint( final Graphics g ) {
174 g.setColor( background_color );
175 g.fillRect( 0, 0, 300, 60 );
176 g.setColor( font_color );
177 g.drawString( getMessage2(), 10, 20 );
178 g.drawString( getMessage1(), 10, 40 );
182 public void start() {
183 getMainFrameApplet().getMainPanel().validate();
184 getMainFrameApplet().requestFocus();
185 getMainFrameApplet().requestFocusInWindow();
186 getMainFrameApplet().requestFocus();
187 AptxUtil.printAppletMessage( NAME, "started" );
190 private MainFrameApplet getMainFrameApplet() {
191 return _mainframe_applet;
194 private String getMessage1() {
198 private String getMessage2() {
202 private void setMessage1( final String message_1 ) {
203 _message_1 = message_1;
206 private void setMessage2( final String message_2 ) {
207 _message_2 = message_2;
210 private void setUrlString( final String url_string ) {
211 _url_string = url_string;