From: cmzmasek@gmail.com Date: Thu, 6 Dec 2012 01:54:57 +0000 (+0000) Subject: work on taxonomy extraction for applets for aLeaves MAFFT suite X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f4f236fff9a5f19dc9cf5dfb960f4a6d13ddb2fb;p=jalview.git work on taxonomy extraction for applets for aLeaves MAFFT suite --- diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index 896bea9..29a378b 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -317,70 +317,12 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { repaint(); } - void help( final Map 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(); } } @@ -458,6 +400,146 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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" ) ); @@ -656,40 +738,18 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _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. } } } @@ -715,24 +775,13 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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 ); } } @@ -748,136 +797,66 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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 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 ) { @@ -915,22 +894,26 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } - 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 ) { @@ -1001,43 +984,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } - 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 ); @@ -1144,16 +1090,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { ( ( 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"; @@ -1198,34 +1134,98 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } - 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 treepanels, final boolean antialias ) {