repaint();
}
- void help( final Map<String, WebLink> weblinks ) {
- final StringBuilder sb = new StringBuilder();
- sb.append( "Display options\n" );
- sb.append( "-------------------\n" );
- sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
- sb.append( "Clickable tree nodes\n" );
- sb.append( "--------------------\n" );
- sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
- sb.append( "or by right clicking:\n" );
- sb.append( "o Display Node Data -- display information for a node\n" );
- sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
- sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
- sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
- sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
- sb.append( "o Colorize Subtree -- color a subtree\n" );
- sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
- sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
- sb.append( "- there may be additional choices depending on this particular setup\n\n" );
- sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
- sb.append( "Zooming\n" );
- sb.append( "---------\n" );
- sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
- sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
- sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
- sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
- sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
- sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
- sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
- sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
- sb.append( "Quick tree manipulation:\n" );
- sb.append( "------------------------\n" );
- sb.append( "Order Subtrees -- order the tree by branch length\n" );
- sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
- sb.append( "Memory problems (Java heap space error)\n" );
- sb.append( "---------------------------------------\n" );
- sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
- sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
- sb.append( "the '-Xmx' Java command line option. For example:\n" );
- sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
- if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
- sb.append( "Active web links\n" );
- sb.append( "--------------------\n" );
- for( final String key : weblinks.keySet() ) {
- sb.append( " " + weblinks.get( key ).toString() + "\n" );
- }
- }
- sb.append( "\n" );
- sb.append( "phyloXML\n" );
- sb.append( "-------------------\n" );
- sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
- sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
- sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
- sb.append( "\n" );
- sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
- sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
- TextFrame.instantiate( sb.toString(), "Help", _textframes );
- }
-
- void setCurrentExternalNodesDataBuffer( final String s ) {
- if ( !ForesterUtil.isEmpty( s ) ) {
- _ext_node_data_buffer = s.trim();
- }
- else {
- _ext_node_data_buffer = "";
+ @Override
+ public void destroy() {
+ AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
+ removeAllTextFrames();
+ if ( getMainPanel() != null ) {
+ getMainPanel().terminate();
}
}
return dataImg;
}
+ public Options getOptions() {
+ return _options;
+ }
+
+ @Override
+ public void init() {
+ final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
+ AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
+ final Configuration configuration = new Configuration( config_filename, true, true, true );
+ setConfiguration( configuration );
+ setOptions( Options.createInstance( configuration ) );
+ setupUI();
+ URL phys_url = null;
+ Phylogeny[] phys = null;
+ final String phys_url_string = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+ AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + phys_url_string );
+ // Get URL to tree file
+ if ( phys_url_string != null ) {
+ try {
+ phys_url = new URL( phys_url_string );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.printErrorMessage( NAME, "error: " + e );
+ e.printStackTrace();
+ JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + phys_url_string
+ + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
+ }
+ }
+ // Load the tree from URL
+ if ( phys_url != null ) {
+ try {
+ phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
+ getConfiguration().isValidatePhyloXmlAgainstSchema(),
+ getConfiguration().isReplaceUnderscoresInNhParsing(),
+ getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
+ getConfiguration().getTaxonomyExtraction() );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.printErrorMessage( NAME, e.toString() );
+ e.printStackTrace();
+ JOptionPane.showMessageDialog( this,
+ NAME + ": Failed to read phylogenies: " + "\nException: " + e,
+ "Failed to read phylogenies",
+ JOptionPane.ERROR_MESSAGE );
+ }
+ }
+ if ( ( phys == null ) || ( phys.length < 1 ) ) {
+ ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null or empty" );
+ JOptionPane.showMessageDialog( this,
+ NAME + ": phylogenies from [" + phys_url + "] are null or empty",
+ "Failed to read phylogenies",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ else {
+ AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
+ }
+ setVisible( false );
+ setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
+ _jmenubar = new JMenuBar();
+ if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
+ if ( !getConfiguration().isUseNativeUI() ) {
+ _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
+ }
+ buildToolsMenu();
+ buildViewMenu();
+ buildFontSizeMenu();
+ buildOptionsMenu();
+ buildTypeMenu();
+ buildHelpMenu();
+ setJMenuBar( _jmenubar );
+ }
+ final Container contentpane = getContentPane();
+ contentpane.setLayout( new BorderLayout() );
+ contentpane.add( getMainPanel(), BorderLayout.CENTER );
+ addComponentListener( new ComponentAdapter() {
+
+ @Override
+ public void componentResized( final ComponentEvent e ) {
+ if ( getMainPanel().getCurrentTreePanel() != null ) {
+ getMainPanel().getCurrentTreePanel().setParametersForPainting( getMainPanel().getCurrentTreePanel()
+ .getWidth(),
+ getMainPanel().getCurrentTreePanel()
+ .getHeight(),
+ false );
+ }
+ }
+ } );
+ if ( getConfiguration().isUseTabbedDisplay() ) {
+ AptxUtil.printAppletMessage( NAME, "using tabbed display" );
+ AptxUtil.addPhylogeniesToTabs( phys,
+ new File( phys_url.getFile() ).getName(),
+ phys_url.toString(),
+ getConfiguration(),
+ getMainPanel() );
+ }
+ else {
+ AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
+ AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
+ }
+ validate();
+ setName( NAME );
+ getMainPanel().getControlPanel().showWholeAll();
+ getMainPanel().getControlPanel().showWhole();
+ System.gc();
+ AptxUtil.printAppletMessage( NAME, "successfully initialized" );
+ /* GUILHEM_BEG */
+ getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
+ for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
+ .getRelevantSequenceRelationTypes() ) {
+ getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
+ }
+ final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
+ if ( default_relation != null ) {
+ getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
+ }
+ final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
+ if ( default_sequence != null ) {
+ getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
+ /* GUILHEM_END */
+ }
+ setVisible( true );
+ }
+
+ public void showTextFrame( final String s, final String title ) {
+ checkTextFrames();
+ _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
+ }
+
+ @Override
+ public void start() {
+ if ( getMainPanel() != null ) {
+ getMainPanel().validate();
+ }
+ requestFocus();
+ requestFocusInWindow();
+ requestFocus();
+ AptxUtil.printAppletMessage( NAME, "started" );
+ }
+
void buildFontSizeMenu() {
_font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
_font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
_jmenubar.add( _view_jmenu );
}
- private void chooseFont() {
- final FontChooser fc = new FontChooser();
- fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
- fc.showDialog( this, "Select the Base Font" );
- getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
- }
-
- private void chooseMinimalConfidence() {
- final String s = ( String ) JOptionPane
- .showInputDialog( this,
- "Please the minimum for confidence values to be displayed.\n" + "[current value: "
- + getOptions().getMinConfidenceValue() + "]\n",
- "Minimal Confidence Value",
- JOptionPane.QUESTION_MESSAGE,
- null,
- null,
- getOptions().getMinConfidenceValue() );
- if ( !ForesterUtil.isEmpty( s ) ) {
- boolean success = true;
- double m = 0.0;
- final String m_str = s.trim();
- if ( !ForesterUtil.isEmpty( m_str ) ) {
- try {
- m = Double.parseDouble( m_str );
+ void checkTextFrames() {
+ if ( _textframes.size() > 5 ) {
+ try {
+ if ( _textframes.getFirst() != null ) {
+ _textframes.getFirst().removeMe();
}
- catch ( final Exception ex ) {
- success = false;
+ else {
+ _textframes.removeFirst();
}
}
- else {
- success = false;
- }
- if ( success && ( m >= 0.0 ) ) {
- getOptions().setMinConfidenceValue( m );
+ catch ( final NoSuchElementException e ) {
+ // Ignore.
}
}
}
jmi.addActionListener( this );
}
- private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
- if ( item != null ) {
- item.setFont( MainFrame.menu_font );
- if ( !getConfiguration().isUseNativeUI() ) {
- item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
- item.setForeground( getConfiguration().getGuiMenuTextColor() );
+ void displayBasicInformation() {
+ if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
+ String title = "Basic Information";
+ if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
+ title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
}
- item.setSelected( is_selected );
- item.addActionListener( this );
- }
- }
-
- @Override
- public void destroy() {
- AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
- removeAllTextFrames();
- if ( getMainPanel() != null ) {
- getMainPanel().terminate();
+ showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title );
}
}
return _label_direction_cbmi;
}
- private MainPanel getMainPanel() {
- return _main_panel;
- }
-
- public Options getOptions() {
- return _options;
- }
-
Options getOtions() {
return _options;
}
- @Override
- public void init() {
- final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
- AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
- final Configuration configuration = new Configuration( config_filename, true, true, true );
- setConfiguration( configuration );
- setOptions( Options.createInstance( configuration ) );
- setupUI();
- URL phys_url = null;
- Phylogeny[] phys = null;
- final String phys_url_string = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
- AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + phys_url_string );
- // Get URL to tree file
- if ( phys_url_string != null ) {
- try {
- phys_url = new URL( phys_url_string );
- }
- catch ( final Exception e ) {
- ForesterUtil.printErrorMessage( NAME, "error: " + e );
- e.printStackTrace();
- JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + phys_url_string
- + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
- }
- }
- // Load the tree from URL
- if ( phys_url != null ) {
- try {
- phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
- getConfiguration().isValidatePhyloXmlAgainstSchema(),
- getConfiguration().isReplaceUnderscoresInNhParsing(),
- getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
- getConfiguration().getTaxonomyExtraction() );
- }
- catch ( final Exception e ) {
- ForesterUtil.printErrorMessage( NAME, e.toString() );
- e.printStackTrace();
- JOptionPane.showMessageDialog( this,
- NAME + ": Failed to read phylogenies: " + "\nException: " + e,
- "Failed to read phylogenies",
- JOptionPane.ERROR_MESSAGE );
- }
- }
- if ( ( phys == null ) || ( phys.length < 1 ) ) {
- ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null or empty" );
- JOptionPane.showMessageDialog( this,
- NAME + ": phylogenies from [" + phys_url + "] are null or empty",
- "Failed to read phylogenies",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- else {
- AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
- }
- setVisible( false );
- setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
- _jmenubar = new JMenuBar();
- if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
- if ( !getConfiguration().isUseNativeUI() ) {
- _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
- }
- buildToolsMenu();
- buildViewMenu();
- buildFontSizeMenu();
- buildOptionsMenu();
- buildTypeMenu();
- buildHelpMenu();
- setJMenuBar( _jmenubar );
- }
- final Container contentpane = getContentPane();
- contentpane.setLayout( new BorderLayout() );
- contentpane.add( getMainPanel(), BorderLayout.CENTER );
- addComponentListener( new ComponentAdapter() {
-
- @Override
- public void componentResized( final ComponentEvent e ) {
- if ( getMainPanel().getCurrentTreePanel() != null ) {
- getMainPanel().getCurrentTreePanel().setParametersForPainting( getMainPanel().getCurrentTreePanel()
- .getWidth(),
- getMainPanel().getCurrentTreePanel()
- .getHeight(),
- false );
- }
+ void help( final Map<String, WebLink> weblinks ) {
+ final StringBuilder sb = new StringBuilder();
+ sb.append( "Display options\n" );
+ sb.append( "-------------------\n" );
+ sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
+ sb.append( "Clickable tree nodes\n" );
+ sb.append( "--------------------\n" );
+ sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
+ sb.append( "or by right clicking:\n" );
+ sb.append( "o Display Node Data -- display information for a node\n" );
+ sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
+ sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
+ sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
+ sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
+ sb.append( "o Colorize Subtree -- color a subtree\n" );
+ sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
+ sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
+ sb.append( "- there may be additional choices depending on this particular setup\n\n" );
+ sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
+ sb.append( "Zooming\n" );
+ sb.append( "---------\n" );
+ sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
+ sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
+ sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
+ sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
+ sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
+ sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
+ sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
+ sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
+ sb.append( "Quick tree manipulation:\n" );
+ sb.append( "------------------------\n" );
+ sb.append( "Order Subtrees -- order the tree by branch length\n" );
+ sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
+ sb.append( "Memory problems (Java heap space error)\n" );
+ sb.append( "---------------------------------------\n" );
+ sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
+ sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
+ sb.append( "the '-Xmx' Java command line option. For example:\n" );
+ sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
+ if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
+ sb.append( "Active web links\n" );
+ sb.append( "--------------------\n" );
+ for( final String key : weblinks.keySet() ) {
+ sb.append( " " + weblinks.get( key ).toString() + "\n" );
}
- } );
- if ( getConfiguration().isUseTabbedDisplay() ) {
- AptxUtil.printAppletMessage( NAME, "using tabbed display" );
- AptxUtil.addPhylogeniesToTabs( phys,
- new File( phys_url.getFile() ).getName(),
- phys_url.toString(),
- getConfiguration(),
- getMainPanel() );
- }
- else {
- AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
- AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
- }
- validate();
- setName( NAME );
- getMainPanel().getControlPanel().showWholeAll();
- getMainPanel().getControlPanel().showWhole();
- System.gc();
- AptxUtil.printAppletMessage( NAME, "successfully initialized" );
- /* GUILHEM_BEG */
- getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
- for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
- .getRelevantSequenceRelationTypes() ) {
- getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
- }
- final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
- if ( default_relation != null ) {
- getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
- }
- final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
- if ( default_sequence != null ) {
- getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
- /* GUILHEM_END */
}
- setVisible( true );
+ sb.append( "\n" );
+ sb.append( "phyloXML\n" );
+ sb.append( "-------------------\n" );
+ sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
+ sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
+ sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
+ sb.append( "\n" );
+ sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
+ sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
+ TextFrame.instantiate( sb.toString(), "Help", _textframes );
}
void initializeTypeMenu( final Options options ) {
}
}
- private boolean isScreenAntialias() {
- return true;
- }
-
- private void removeBranchColors() {
- if ( getMainPanel().getCurrentPhylogeny() != null ) {
- AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
+ void removeAllTextFrames() {
+ for( final TextFrame tf : _textframes ) {
+ if ( tf != null ) {
+ tf.close();
+ }
}
+ _textframes.clear();
}
void setConfiguration( final Configuration configuration ) {
_configuration = configuration;
}
- private void setMainPanel( final MainPanelApplets main_panel ) {
- _main_panel = main_panel;
+ void setCurrentExternalNodesDataBuffer( final String s ) {
+ if ( !ForesterUtil.isEmpty( s ) ) {
+ _ext_node_data_buffer = s.trim();
+ }
+ else {
+ _ext_node_data_buffer = "";
+ }
}
void setOptions( final Options options ) {
}
}
- private void setupUI() {
- try {
- if ( getConfiguration().isUseNativeUI() ) {
- UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
- }
- else {
- UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
- }
- }
- catch ( final UnsupportedLookAndFeelException e ) {
- AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
- }
- catch ( final ClassNotFoundException e ) {
- AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
- }
- catch ( final InstantiationException e ) {
- AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
- }
- catch ( final IllegalAccessException e ) {
- AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
- }
- catch ( final Exception e ) {
- AptxUtil.dieWithSystemError( e.toString() );
- }
- }
-
- @Override
- public void start() {
- if ( getMainPanel() != null ) {
- getMainPanel().validate();
- }
- requestFocus();
- requestFocusInWindow();
- requestFocus();
- AptxUtil.printAppletMessage( NAME, "started" );
- }
-
void switchColors() {
final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
( ( JCheckBoxMenuItem ) o ).setSelected( true );
}
- void displayBasicInformation() {
- if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
- String title = "Basic Information";
- if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
- title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
- }
- showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title );
- }
- }
-
void viewAsNexus() {
if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
String title = "Nexus";
}
}
- public void showTextFrame( final String s, final String title ) {
- checkTextFrames();
- _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
+ private void chooseFont() {
+ final FontChooser fc = new FontChooser();
+ fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
+ fc.showDialog( this, "Select the Base Font" );
+ getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
}
- void checkTextFrames() {
- if ( _textframes.size() > 5 ) {
- try {
- if ( _textframes.getFirst() != null ) {
- _textframes.getFirst().removeMe();
+ private void chooseMinimalConfidence() {
+ final String s = ( String ) JOptionPane
+ .showInputDialog( this,
+ "Please the minimum for confidence values to be displayed.\n" + "[current value: "
+ + getOptions().getMinConfidenceValue() + "]\n",
+ "Minimal Confidence Value",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ getOptions().getMinConfidenceValue() );
+ if ( !ForesterUtil.isEmpty( s ) ) {
+ boolean success = true;
+ double m = 0.0;
+ final String m_str = s.trim();
+ if ( !ForesterUtil.isEmpty( m_str ) ) {
+ try {
+ m = Double.parseDouble( m_str );
}
- else {
- _textframes.removeFirst();
+ catch ( final Exception ex ) {
+ success = false;
}
}
- catch ( final NoSuchElementException e ) {
- // Ignore.
+ else {
+ success = false;
+ }
+ if ( success && ( m >= 0.0 ) ) {
+ getOptions().setMinConfidenceValue( m );
}
}
}
- void removeAllTextFrames() {
- for( final TextFrame tf : _textframes ) {
- if ( tf != null ) {
- tf.close();
+ private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
+ if ( item != null ) {
+ item.setFont( MainFrame.menu_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
+ item.setForeground( getConfiguration().getGuiMenuTextColor() );
+ }
+ item.setSelected( is_selected );
+ item.addActionListener( this );
+ }
+ }
+
+ private MainPanel getMainPanel() {
+ return _main_panel;
+ }
+
+ private boolean isScreenAntialias() {
+ return true;
+ }
+
+ private void removeBranchColors() {
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {
+ AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
+ }
+ }
+
+ private void setMainPanel( final MainPanelApplets main_panel ) {
+ _main_panel = main_panel;
+ }
+
+ private void setupUI() {
+ try {
+ if ( getConfiguration().isUseNativeUI() ) {
+ UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
+ }
+ else {
+ UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
}
}
- _textframes.clear();
+ catch ( final UnsupportedLookAndFeelException e ) {
+ AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
+ }
+ catch ( final ClassNotFoundException e ) {
+ AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
+ }
+ catch ( final InstantiationException e ) {
+ AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
+ }
+ catch ( final IllegalAccessException e ) {
+ AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
+ }
+ catch ( final Exception e ) {
+ AptxUtil.dieWithSystemError( e.toString() );
+ }
}
static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
git://source.jalview.org / jalview.git / commitdiff