X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryxE.java;h=d186d16d176b295ff39f185e29dde1b58c2cb073;hb=10f90f7787d4b1287a910d4e6ae895da14866929;hp=a24176cb0159847e7ced78800139e6fe7302b7dd;hpb=5958d8c92c06f76da04a466ef7636e93a640b6a3;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index a24176c..d186d16 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -11,7 +11,10 @@ import java.io.ByteArrayOutputStream; import java.io.File; import java.io.IOException; import java.net.URL; +import java.util.LinkedList; import java.util.List; +import java.util.Map; +import java.util.NoSuchElementException; import javax.swing.ButtonGroup; import javax.swing.JApplet; @@ -50,74 +53,78 @@ import org.forester.util.ForesterUtil; // public class ArchaeopteryxE extends JApplet implements ActionListener { - private final static String NAME = "ArchaeopteryxE"; - private static final long serialVersionUID = -1220055577935759443L; - private Configuration _configuration; - private MainPanelApplets _main_panel; - private JMenuBar _jmenubar; - private JMenu _options_jmenu; - private JMenu _font_size_menu; - private JMenuItem _super_tiny_fonts_mi; - private JMenuItem _tiny_fonts_mi; - private JMenuItem _small_fonts_mi; - private JMenuItem _medium_fonts_mi; - private JMenuItem _large_fonts_mi; - private TextFrame _textframe; - private JMenu _tools_menu; - private JMenuItem _taxcolor_item; - private JMenuItem _confcolor_item; - private JMenuItem _midpoint_root_item; - private JMenu _view_jmenu; - private JMenuItem _view_as_XML_item; - private JMenuItem _view_as_NH_item; - private JMenuItem _view_as_NHX_item; - private JMenuItem _view_as_nexus_item; - private JMenu _type_menu; - private JCheckBoxMenuItem _rectangular_type_cbmi; - private JCheckBoxMenuItem _triangular_type_cbmi; - private JCheckBoxMenuItem _curved_type_cbmi; - private JCheckBoxMenuItem _convex_type_cbmi; - private JCheckBoxMenuItem _euro_type_cbmi; - private JCheckBoxMenuItem _rounded_type_cbmi; - private JCheckBoxMenuItem _unrooted_type_cbmi; - private JCheckBoxMenuItem _circular_type_cbmi; - private JMenuItem _help_item; - private JMenuItem _about_item; - private JMenu _help_jmenu; - private JMenuItem _website_item; - private JMenuItem _phyloxml_website_item; - private JMenuItem _phyloxml_ref_item; - private JMenuItem _aptx_ref_item; - private JMenuItem _remove_branch_color_item; - private JMenuItem _infer_common_sn_names_item; - private JCheckBoxMenuItem _show_domain_labels; - private JCheckBoxMenuItem _color_labels_same_as_parent_branch; - private JCheckBoxMenuItem _abbreviate_scientific_names; - private JCheckBoxMenuItem _screen_antialias_cbmi; - private JCheckBoxMenuItem _background_gradient_cbmi; - private JRadioButtonMenuItem _non_lined_up_cladograms_rbmi; - private JRadioButtonMenuItem _uniform_cladograms_rbmi; - private JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi; - private Options _options; - private JMenuItem _choose_font_mi; - private JMenuItem _switch_colors_mi; - JCheckBoxMenuItem _label_direction_cbmi; - private JCheckBoxMenuItem _show_scale_cbmi; - private JCheckBoxMenuItem _search_case_senstive_cbmi; - private JCheckBoxMenuItem _search_whole_words_only_cbmi; - private JCheckBoxMenuItem _inverse_search_result_cbmi; - private JCheckBoxMenuItem _show_overview_cbmi; - private JMenuItem _choose_minimal_confidence_mi; - private JCheckBoxMenuItem _show_branch_length_values_cbmi; - private JMenuItem _collapse_species_specific_subtrees; - private JMenuItem _overview_placment_mi; - private ButtonGroup _radio_group_1; - private JCheckBoxMenuItem _show_default_node_shapes_cbmi; - private JMenuItem _cycle_node_shape_mi; - private JMenuItem _cycle_node_fill_mi; - private JMenuItem _choose_node_size_mi; - private JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi; + private final static String NAME = "ArchaeopteryxE"; + private static final long serialVersionUID = -1220055577935759443L; + private Configuration _configuration; + private MainPanelApplets _main_panel; + private JMenuBar _jmenubar; + private JMenu _options_jmenu; + private JMenu _font_size_menu; + private JMenuItem _super_tiny_fonts_mi; + private JMenuItem _tiny_fonts_mi; + private JMenuItem _small_fonts_mi; + private JMenuItem _medium_fonts_mi; + private JMenuItem _large_fonts_mi; + private JMenu _tools_menu; + private JMenuItem _taxcolor_item; + private JMenuItem _confcolor_item; + private JMenuItem _midpoint_root_item; + private JMenu _view_jmenu; + private JMenuItem _view_as_XML_item; + private JMenuItem _view_as_NH_item; + private JMenuItem _view_as_NHX_item; + private JMenuItem _view_as_nexus_item; + private JMenuItem _display_basic_information_item; + private JMenu _type_menu; + private JCheckBoxMenuItem _rectangular_type_cbmi; + private JCheckBoxMenuItem _triangular_type_cbmi; + private JCheckBoxMenuItem _curved_type_cbmi; + private JCheckBoxMenuItem _convex_type_cbmi; + private JCheckBoxMenuItem _euro_type_cbmi; + private JCheckBoxMenuItem _rounded_type_cbmi; + private JCheckBoxMenuItem _unrooted_type_cbmi; + private JCheckBoxMenuItem _circular_type_cbmi; + private JMenuItem _help_item; + private JMenuItem _about_item; + private JMenu _help_jmenu; + private JMenuItem _website_item; + private JMenuItem _phyloxml_website_item; + private JMenuItem _phyloxml_ref_item; + private JMenuItem _aptx_ref_item; + private JMenuItem _remove_branch_color_item; + private JMenuItem _infer_common_sn_names_item; + private JCheckBoxMenuItem _show_domain_labels; + private JCheckBoxMenuItem _color_labels_same_as_parent_branch; + private JCheckBoxMenuItem _abbreviate_scientific_names; + private JCheckBoxMenuItem _screen_antialias_cbmi; + private JCheckBoxMenuItem _background_gradient_cbmi; + private JRadioButtonMenuItem _non_lined_up_cladograms_rbmi; + private JRadioButtonMenuItem _uniform_cladograms_rbmi; + private JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi; + private Options _options; + private JMenuItem _choose_font_mi; + private JMenuItem _switch_colors_mi; + JCheckBoxMenuItem _label_direction_cbmi; + private JCheckBoxMenuItem _show_scale_cbmi; + private JCheckBoxMenuItem _search_case_senstive_cbmi; + private JCheckBoxMenuItem _search_whole_words_only_cbmi; + private JCheckBoxMenuItem _inverse_search_result_cbmi; + private JCheckBoxMenuItem _show_overview_cbmi; + private JMenuItem _choose_minimal_confidence_mi; + private JCheckBoxMenuItem _show_branch_length_values_cbmi; + private JMenuItem _collapse_species_specific_subtrees; + private JMenuItem _overview_placment_mi; + private ButtonGroup _radio_group_1; + private JCheckBoxMenuItem _show_default_node_shapes_cbmi; + private JMenuItem _cycle_node_shape_mi; + private JMenuItem _cycle_node_fill_mi; + private JMenuItem _choose_node_size_mi; + private JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi; + private JCheckBoxMenuItem _show_confidence_stddev_cbmi; + private final LinkedList _textframes = new LinkedList(); + // private String _ext_node_data_buffer = ""; + // private int _ext_node_data_buffer_change_counter = 0; @Override public void actionPerformed( final ActionEvent e ) { final Object o = e.getSource(); @@ -130,11 +137,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { else if ( o == _confcolor_item ) { getMainPanel().getCurrentTreePanel().confColor(); } - else if ( o == _infer_common_sn_names_item ) { - if ( getCurrentTreePanel() != null ) { - getCurrentTreePanel().inferCommonPartOfScientificNames(); - } - } else if ( o == _collapse_species_specific_subtrees ) { if ( getCurrentTreePanel() != null ) { getCurrentTreePanel().collapseSpeciesSpecificSubtrees(); @@ -146,6 +148,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { else if ( o == _switch_colors_mi ) { switchColors(); } + else if ( o == _display_basic_information_item ) { + displayBasicInformation(); + } else if ( o == _view_as_NH_item ) { viewAsNH(); } @@ -236,6 +241,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { else if ( o == _show_branch_length_values_cbmi ) { updateOptions( getOptions() ); } + else if ( o == _show_confidence_stddev_cbmi ) { + updateOptions( getOptions() ); + } else if ( o == _label_direction_cbmi ) { updateOptions( getOptions() ); } @@ -273,7 +281,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { MainFrame.about(); } else if ( o == _help_item ) { - MainFrame.help( getConfiguration().getWebLinks() ); + help( getConfiguration().getWebLinks() ); } else if ( o == _website_item ) { try { @@ -310,6 +318,35 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { repaint(); } + @Override + public void destroy() { + AptxUtil.printAppletMessage( NAME, "going to be destroyed " ); + removeAllTextFrames(); + if ( getMainPanel() != null ) { + getMainPanel().terminate(); + } + } + + /** + * This method returns the current external node data which + * has been selected by the user by clicking the "Return ..." + * menu item. This method is expected to be called from Javascript or + * something like it. + * + * @return current external node data as String + */ + public String getCurrentExternalNodesDataBuffer() { + return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString(); + } + + public int getCurrentExternalNodesDataBufferChangeCounter() { + return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter(); + } + + public int getCurrentExternalNodesDataBufferLength() { + return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length(); + } + /** * This method returns the current phylogeny as a string in the chosen format * @@ -318,7 +355,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { * @author Herve Menager */ public String getCurrentPhylogeny( final String format ) { - removeTextFrame(); + removeAllTextFrames(); if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty() || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) { return new String(); @@ -372,6 +409,146 @@ 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" ) ); @@ -442,7 +619,11 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _radio_group_1.add( _ext_node_dependent_cladogram_rbmi ); _radio_group_1.add( _uniform_cladograms_rbmi ); _radio_group_1.add( _non_lined_up_cladograms_rbmi ); - // + _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) ); + _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) ); + _options_jmenu + .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) ); + _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) ); _options_jmenu .add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL ) ); _options_jmenu @@ -450,11 +631,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) ); _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) ); _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) ); - // - _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) ); - _options_jmenu - .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) ); - _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) ); _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) ); _options_jmenu .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) ); @@ -506,6 +682,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() ); customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() ); customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() ); + customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() ); _jmenubar.add( _options_jmenu ); } @@ -555,11 +732,14 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } void buildViewMenu() { - _view_jmenu = MainFrame.createMenu( "View as Text", getConfiguration() ); + _view_jmenu = MainFrame.createMenu( "View", getConfiguration() ); + _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) ); + _view_jmenu.addSeparator(); _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) ); _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) ); _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) ); _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) ); + customizeJMenuItem( _display_basic_information_item ); customizeJMenuItem( _view_as_NH_item ); customizeJMenuItem( _view_as_NHX_item ); customizeJMenuItem( _view_as_XML_item ); @@ -567,44 +747,26 @@ 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. } } } + void clearCurrentExternalNodesDataBuffer() { + getCurrentTreePanel().clearCurrentExternalNodesDataBuffer(); + } + void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) { if ( item != null ) { item.setFont( MainFrame.menu_font ); @@ -626,24 +788,13 @@ 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 " ); - removeTextFrame(); - if ( getMainPanel() != null ) { - getMainPanel().terminate(); + showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title ); } } @@ -659,132 +810,66 @@ 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() ); - } - 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 ) { @@ -822,31 +907,19 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } - private boolean isScreenAntialias() { - return true; - } - - private void removeBranchColors() { - if ( getMainPanel().getCurrentPhylogeny() != null ) { - AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() ); - } - } - - void removeTextFrame() { - if ( _textframe != null ) { - _textframe.close(); - _textframe = null; + 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 setOptions( final Options options ) { _options = options; } @@ -915,43 +988,6 @@ 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 ); @@ -1018,6 +1054,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() ); + options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null ) + && _show_confidence_stddev_cbmi.isSelected() ); if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) { options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() ); } @@ -1057,39 +1095,141 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } void viewAsNexus() { - removeTextFrame(); - if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty() - || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) { - return; + if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { + String title = "Nexus"; + if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { + title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + } + showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions() + .getNhConversionSupportValueStyle() ), + title ); } - _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNexus() ); } void viewAsNH() { - removeTextFrame(); - if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty() - || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) { - return; + if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { + String title = "New Hampshire"; + if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { + title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + } + showTextFrame( getMainPanel().getCurrentPhylogeny() + .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ), + title ); } - _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNewHampshire( false ) ); } void viewAsNHX() { - removeTextFrame(); - if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty() - || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) { - return; + if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { + String title = "NHX"; + if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { + title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + } + showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshireX(), title ); } - _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNewHampshireX() ); } void viewAsXML() { - removeTextFrame(); - if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty() - || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) { - return; + if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { + String title = "phyloXML"; + if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { + title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + } + showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title ); + } + } + + 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 ); + } + catch ( final Exception ex ) { + success = false; + } + } + else { + success = false; + } + if ( success && ( m >= 0.0 ) ) { + getOptions().setMinConfidenceValue( m ); + } + } + } + + 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() ); + } + } + 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() ); } - _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ) ); } static void setupScreenTextAntialias( final List treepanels, final boolean antialias ) {