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: https://sites.google.com/site/cmzmasek/home/software/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 _tree_url_str = "";
51 private String _species_tree_url_str = "";
52 private String _message_1 = "";
53 private String _message_2 = "";
54 public final static String NAME = "ArchaeopteryxA";
57 public void destroy() {
58 AptxUtil.printAppletMessage( NAME, "going to be destroyed" );
59 if ( getMainFrameApplet() != null ) {
60 getMainFrameApplet().close();
65 * This method returns the current external node data which
66 * has been selected by the user by clicking the "Return ..."
67 * menu item. This method is expected to be called from Javascript or
70 * @return current external node data as String
72 public String getCurrentExternalNodesDataBuffer() {
73 return getMainFrameApplet().getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
76 public int getCurrentExternalNodesDataBufferChangeCounter() {
77 return getMainFrameApplet().getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
80 public int getCurrentExternalNodesDataBufferLength() {
81 return getMainFrameApplet().getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
84 public String getSpeciesTreeUrlStr() {
85 return _species_tree_url_str;
88 public String getTreeUrlStr() {
94 boolean has_exception = false;
96 setTreeUrlStr( getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD ) );
97 setSpeciesTreeUrlStr( getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD ) );
98 if ( !ForesterUtil.isEmpty( getTreeUrlStr() ) ) {
99 AptxUtil.printAppletMessage( NAME, "URL of tree(s) to load: " + getTreeUrlStr() );
102 ForesterUtil.printErrorMessage( NAME, "no URL for tree(s) to load!" );
103 setBackground( ex_background_color );
104 setForeground( ex_font_color );
105 has_exception = true;
106 setMessage1( "no URL for tree(s) to load" );
109 if ( !ForesterUtil.isEmpty( getSpeciesTreeUrlStr() ) ) {
110 AptxUtil.printAppletMessage( NAME, "URL of species tree to load: " + getSpeciesTreeUrlStr() );
112 setBackground( background_color );
113 setForeground( font_color );
118 s = System.getProperty( "java.version" );
120 catch ( final Exception e ) {
121 ForesterUtil.printWarningMessage( NAME, "minor error: " + e.getLocalizedMessage() );
123 if ( ( s != null ) && ( s.length() > 0 ) ) {
124 setMessage2( "[Your Java version: " + s + "]" );
127 final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
128 AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
129 final Configuration configuration = new Configuration( config_filename, true, true, true );
131 if ( configuration.isUseNativeUI() ) {
132 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
135 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
138 _mainframe_applet = new MainFrameApplet( this, configuration, getSpeciesTreeUrlStr() );
139 final URL tree_url = new URL( getTreeUrlStr() );
140 final Phylogeny[] phys = AptxUtil.readPhylogeniesFromUrl( tree_url, configuration
141 .isValidatePhyloXmlAgainstSchema(), configuration.isReplaceUnderscoresInNhParsing(), configuration
142 .isInternalNumberAreConfidenceForNhParsing(), configuration.getTaxonomyExtraction(), configuration
143 .isMidpointReroot() );
144 if ( phys == null ) {
145 ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + tree_url + "] are null" );
147 else if ( phys.length < 1 ) {
148 ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + tree_url + "] are empty" );
151 AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + tree_url );
153 AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "loaded " + phys.length + " phylogenies from: "
155 AptxUtil.addPhylogeniesToTabs( phys,
156 new File( tree_url.getFile() ).getName(),
158 getMainFrameApplet().getConfiguration(),
159 getMainFrameApplet().getMainPanel() );
160 getMainFrameApplet().getMainPanel().getControlPanel().showWholeAll();
161 getMainFrameApplet().getMainPanel().getControlPanel().showWhole();
164 catch ( final Exception e ) {
165 ForesterUtil.printErrorMessage( NAME, e.toString() );
166 setBackground( ex_background_color );
167 setForeground( ex_font_color );
168 has_exception = true;
169 setMessage1( "Exception: " + e );
173 if ( !has_exception ) {
174 setMessage1( NAME + " is now ready!" );
176 AptxUtil.printAppletMessage( NAME, "successfully initialized" );
178 KeyboardFocusManager.getCurrentKeyboardFocusManager().clearGlobalFocusOwner();
179 getMainFrameApplet().requestFocus();
180 getMainFrameApplet().requestFocusInWindow();
181 getMainFrameApplet().requestFocus();
183 final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
184 if ( default_relation != null ) {
185 getMainFrameApplet().getMainPanel().getControlPanel().getSequenceRelationTypeBox()
186 .setSelectedItem( default_relation );
188 final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
189 if ( default_sequence != null ) {
190 getMainFrameApplet().getMainPanel().getControlPanel().getSequenceRelationBox()
191 .setSelectedItem( default_sequence );
197 * Prints message when initialization is finished. Called automatically.
203 public void paint( final Graphics g ) {
204 g.setColor( background_color );
205 g.fillRect( 0, 0, 300, 60 );
206 g.setColor( font_color );
207 g.drawString( getMessage2(), 10, 20 );
208 g.drawString( getMessage1(), 10, 40 );
212 public void start() {
213 getMainFrameApplet().getMainPanel().validate();
214 getMainFrameApplet().requestFocus();
215 getMainFrameApplet().requestFocusInWindow();
216 getMainFrameApplet().requestFocus();
217 AptxUtil.printAppletMessage( NAME, "started" );
220 private MainFrameApplet getMainFrameApplet() {
221 return _mainframe_applet;
224 private String getMessage1() {
228 private String getMessage2() {
232 private void setMessage1( final String message_1 ) {
233 _message_1 = message_1;
236 private void setMessage2( final String message_2 ) {
237 _message_2 = message_2;
240 private void setSpeciesTreeUrlStr( final String url_string ) {
241 _species_tree_url_str = url_string;
244 private void setTreeUrlStr( final String url_string ) {
245 _tree_url_str = url_string;