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();
63 private MainFrameApplet getMainFrameApplet() {
64 return _mainframe_applet;
67 private String getMessage1() {
71 private String getMessage2() {
75 public String getUrlString() {
81 boolean has_exception = false;
83 setUrlString( getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD ) );
84 AptxUtil.printAppletMessage( NAME, "URL of phylogenies to load: \"" + getUrlString() + "\"" );
85 setBackground( background_color );
86 setForeground( font_color );
91 s = System.getProperty( "java.version" );
93 catch ( final Exception e ) {
94 ForesterUtil.printWarningMessage( NAME, "minor error: " + e.getLocalizedMessage() );
96 if ( ( s != null ) && ( s.length() > 0 ) ) {
97 setMessage2( "[Your Java version: " + s + "]" );
100 final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
101 AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
102 final Configuration configuration = new Configuration( config_filename, true, true, true );
104 if ( configuration.isUseNativeUI() ) {
105 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
108 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
111 _mainframe_applet = new MainFrameApplet( this, configuration );
113 url = new URL( getUrlString() );
114 final Phylogeny[] phys = AptxUtil.readPhylogeniesFromUrl( url,
115 configuration.isValidatePhyloXmlAgainstSchema() );
116 AptxUtil.addPhylogeniesToTabs( phys,
117 new File( url.getFile() ).getName(),
119 getMainFrameApplet().getConfiguration(),
120 getMainFrameApplet().getMainPanel() );
121 getMainFrameApplet().getMainPanel().getControlPanel().showWholeAll();
122 getMainFrameApplet().getMainPanel().getControlPanel().showWhole();
125 catch ( final Exception e ) {
126 ForesterUtil.printErrorMessage( NAME, e.toString() );
127 setBackground( ex_background_color );
128 setForeground( ex_font_color );
129 has_exception = true;
130 setMessage1( "Exception: " + e );
134 if ( !has_exception ) {
135 setMessage1( NAME + " is now ready!" );
137 AptxUtil.printAppletMessage( NAME, "successfully initialized" );
139 KeyboardFocusManager.getCurrentKeyboardFocusManager().clearGlobalFocusOwner();
140 getMainFrameApplet().requestFocus();
141 getMainFrameApplet().requestFocusInWindow();
142 getMainFrameApplet().requestFocus();
144 final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
145 if ( default_relation != null ) {
146 getMainFrameApplet().getMainPanel().getControlPanel().getSequenceRelationTypeBox()
147 .setSelectedItem( default_relation );
149 final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
150 if ( default_sequence != null ) {
151 getMainFrameApplet().getMainPanel().getControlPanel().getSequenceRelationBox()
152 .setSelectedItem( default_sequence );
158 * Prints message when initialization is finished. Called automatically.
164 public void paint( final Graphics g ) {
165 g.setColor( background_color );
166 g.fillRect( 0, 0, 300, 60 );
167 g.setColor( font_color );
168 g.drawString( getMessage2(), 10, 20 );
169 g.drawString( getMessage1(), 10, 40 );
172 private void setMessage1( final String message_1 ) {
173 _message_1 = message_1;
176 private void setMessage2( final String message_2 ) {
177 _message_2 = message_2;
180 private void setUrlString( final String url_string ) {
181 _url_string = url_string;
185 public void start() {
186 getMainFrameApplet().getMainPanel().validate();
187 getMainFrameApplet().requestFocus();
188 getMainFrameApplet().requestFocusInWindow();
189 getMainFrameApplet().requestFocus();
190 AptxUtil.printAppletMessage( NAME, "started" );