X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryxE.java;h=fb37c4f0d962e81d86fe3fa7952bb34e7818d7fb;hb=fa7be237a552a2f3d413d6e3e81a51d22097743a;hp=57a0532a31ecbd8eb6683e8a7a6eae0ac1563aad;hpb=da91573ed6cc107d27b2a18ec31c88a1447a4e80;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index 57a0532..fb37c4f 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -96,11 +96,14 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { private JMenuItem _phyloxml_ref_item; private JMenuItem _aptx_ref_item; private JMenuItem _remove_branch_color_item; + private JMenuItem _remove_visual_styles_item; private JCheckBoxMenuItem _show_domain_labels; + private JCheckBoxMenuItem _show_annotation_ref_source; private JCheckBoxMenuItem _color_labels_same_as_parent_branch; private JCheckBoxMenuItem _abbreviate_scientific_names; private JCheckBoxMenuItem _screen_antialias_cbmi; private JCheckBoxMenuItem _background_gradient_cbmi; + private JCheckBoxMenuItem _color_by_taxonomic_group_cbmi; private JRadioButtonMenuItem _non_lined_up_cladograms_rbmi; private JRadioButtonMenuItem _uniform_cladograms_rbmi; private JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi; @@ -123,13 +126,14 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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 JMenu _analysis_menu; private JMenuItem _gsdi_item; private JMenuItem _gsdir_item; private Phylogeny _species_tree; + private JCheckBoxMenuItem _right_line_up_domains_cbmi; + private JCheckBoxMenuItem _line_up_renderable_data_cbmi; @Override public void actionPerformed( final ActionEvent e ) { @@ -163,6 +167,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { else if ( o == _remove_branch_color_item ) { removeBranchColors(); } + else if ( o == _remove_visual_styles_item ) { + removeVisualStyles(); + } else if ( o == _switch_colors_mi ) { switchColors(); } @@ -240,15 +247,18 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } else if ( o == _search_case_senstive_cbmi ) { updateOptions( getOptions() ); - getMainPanel().getControlPanel().search(); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); } else if ( o == _search_whole_words_only_cbmi ) { updateOptions( getOptions() ); - getMainPanel().getControlPanel().search(); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); } else if ( o == _inverse_search_result_cbmi ) { updateOptions( getOptions() ); - getMainPanel().getControlPanel().search(); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); } else if ( o == _show_scale_cbmi ) { updateOptions( getOptions() ); @@ -262,6 +272,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { else if ( o == _label_direction_cbmi ) { updateOptions( getOptions() ); } + else if ( o == _abbreviate_scientific_names ) { + updateOptions( getOptions() ); + } else if ( o == _show_overview_cbmi ) { updateOptions( getOptions() ); if ( getCurrentTreePanel() != null ) { @@ -292,14 +305,16 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { else if ( o == _show_default_node_shapes_external_cbmi ) { updateOptions( getOptions() ); } - else if ( o == _taxonomy_colorize_node_shapes_cbmi ) { - updateOptions( getOptions() ); - } else if ( o == _about_item ) { MainFrame.about(); } else if ( o == _help_item ) { - help(); + try { + AptxUtil.openWebsite( Constants.APTX_DOC_SITE, true, this ); + } + catch ( final IOException e1 ) { + ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); + } } else if ( o == _website_item ) { try { @@ -333,6 +348,21 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); } } + else if ( o == _color_by_taxonomic_group_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _line_up_renderable_data_cbmi ) { + if ( !_line_up_renderable_data_cbmi.isSelected() ) { + _right_line_up_domains_cbmi.setSelected( false ); + } + updateOptions( getOptions() ); + } + else if ( o == _right_line_up_domains_cbmi ) { + if ( _right_line_up_domains_cbmi.isSelected() ) { + _line_up_renderable_data_cbmi.setSelected( true ); + } + updateOptions( getOptions() ); + } repaint(); } @@ -439,45 +469,65 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { setConfiguration( configuration ); setOptions( Options.createInstance( configuration ) ); setupUI(); - URL phys_url = null; - Phylogeny[] phys = null; final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD ); + if ( ForesterUtil.isEmpty( tree_url_str ) ) { + ForesterUtil.printErrorMessage( NAME, "could not get tree URL from " + + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD ); + JOptionPane.showMessageDialog( this, NAME + ": could not get tree URL from " + + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE ); + return; + } AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str ); // Get URL to tree file - if ( tree_url_str != null ) { - try { - phys_url = new URL( tree_url_str ); - } - catch ( final Exception e ) { - ForesterUtil.printErrorMessage( NAME, "error: " + e ); - e.printStackTrace(); - JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str - + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE ); - } + URL phys_url = null; + try { + phys_url = new URL( tree_url_str ); + } + catch ( final Exception e ) { + ForesterUtil.printErrorMessage( NAME, "error: " + e ); + e.printStackTrace(); + JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str + + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE ); + } + if ( phys_url == null ) { + ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from " + + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD ); + JOptionPane.showMessageDialog( this, + NAME + ": Could not create URL from: \"" + tree_url_str, + "Failed to create URL", + JOptionPane.ERROR_MESSAGE ); + return; } // Load the tree from URL - if ( phys_url != null ) { - try { - phys = AptxUtil.readPhylogeniesFromUrl( phys_url, - getConfiguration().isValidatePhyloXmlAgainstSchema(), - getConfiguration().isReplaceUnderscoresInNhParsing(), - getConfiguration().isInternalNumberAreConfidenceForNhParsing(), - getConfiguration().getTaxonomyExtraction(), - getConfiguration().isMidpointReroot() ); - } - 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 ); - } + Phylogeny[] phys = null; + try { + phys = AptxUtil.readPhylogeniesFromUrl( phys_url, + getConfiguration().isValidatePhyloXmlAgainstSchema(), + getConfiguration().isReplaceUnderscoresInNhParsing(), + getConfiguration().isInternalNumberAreConfidenceForNhParsing(), + getConfiguration().getTaxonomyExtraction(), + getConfiguration().isMidpointReroot() ); + } + 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 ) { + ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null" ); + JOptionPane.showMessageDialog( this, + NAME + ": phylogenies from [" + phys_url + "] are null", + "Failed to read phylogenies", + JOptionPane.ERROR_MESSAGE ); + return; } - if ( ( phys == null ) || ( phys.length < 1 ) ) { - ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null or empty" ); + else if ( phys.length < 1 ) { + ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are empty" ); JOptionPane.showMessageDialog( this, - NAME + ": phylogenies from [" + phys_url + "] are null or empty", + NAME + ": phylogenies from [" + phys_url + "] are empty", "Failed to read phylogenies", JOptionPane.ERROR_MESSAGE ); return; @@ -558,12 +608,18 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } ); if ( getConfiguration().isUseTabbedDisplay() ) { - AptxUtil.printAppletMessage( NAME, "using tabbed display" ); - AptxUtil.addPhylogeniesToTabs( phys, - new File( phys_url.getFile() ).getName(), - phys_url.toString(), - getConfiguration(), - getMainPanel() ); + try { + AptxUtil.printAppletMessage( NAME, "using tabbed display" ); + AptxUtil.addPhylogeniesToTabs( phys, + new File( phys_url.getFile() ).getName(), + phys_url.toString(), + getConfiguration(), + getMainPanel() ); + } + catch ( final Exception e ) { + ForesterUtil.printErrorMessage( NAME, e.toString() ); + e.printStackTrace(); + } } else { AptxUtil.printAppletMessage( NAME, "not using tabbed display" ); @@ -573,28 +629,34 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } 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 ); + try { + validate(); + setName( NAME ); + getMainPanel().getControlPanel().showWholeAll(); + getMainPanel().getControlPanel().showWhole(); + /* 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 */ + System.gc(); + AptxUtil.printAppletMessage( NAME, "successfully initialized" ); + setVisible( true ); + } + catch ( final Exception e ) { + ForesterUtil.printErrorMessage( NAME, e.toString() ); + e.printStackTrace(); + } } public void showTextFrame( final String s, final String title ) { @@ -643,7 +705,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { void buildHelpMenu() { _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() ); - _help_jmenu.add( _help_item = new JMenuItem( "Help" ) ); + _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) ); + _help_jmenu.addSeparator(); _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) ); _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) ); @@ -673,16 +736,16 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() ); MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) ); - MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(), - _show_scale_cbmi, - _show_branch_length_values_cbmi, - _non_lined_up_cladograms_rbmi, - _uniform_cladograms_rbmi, - _ext_node_dependent_cladogram_rbmi, - _label_direction_cbmi ); MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() ); MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() ); MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() ); + try { + getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB(); + getMainPanel().getControlPanel().setVisibilityOfX(); + } + catch ( final Exception ignore ) { + // do nothing, not important. + } } } ); _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ), @@ -696,35 +759,40 @@ 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_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) ); _options_jmenu .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) ); + if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { + _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) ); + _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) ); + } + _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) ); + _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) ); + _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) ); _options_jmenu - .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) ); - _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( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) ); + .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) ); _options_jmenu .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) ); _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP ); _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) ); + _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) ); _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP ); _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) ); _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) ); - if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { - _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) ); - } + _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( _choose_minimal_confidence_mi = new JMenuItem( "" ) ); _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) ); _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) ); _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) ); + ///// _options_jmenu.addSeparator(); _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ), getConfiguration() ) ); @@ -737,17 +805,18 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { customizeJMenuItem( _choose_minimal_confidence_mi ); customizeJMenuItem( _switch_colors_mi ); customizeJMenuItem( _overview_placment_mi ); + customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() ); customizeCheckBoxMenuItem( _label_direction_cbmi, getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL ); customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() ); customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() ); customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() ); + customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() ); customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() ); customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions() .isShowDefaultNodeShapesExternal() ); customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions() .isShowDefaultNodeShapesInternal() ); - customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() ); customizeJMenuItem( _cycle_node_shape_mi ); customizeJMenuItem( _cycle_node_fill_mi ); customizeJMenuItem( _choose_node_size_mi ); @@ -765,6 +834,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() ); customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() ); customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() ); + customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() ); + customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() ); _jmenubar.add( _options_jmenu ); } @@ -774,8 +845,13 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { customizeJMenuItem( _confcolor_item ); _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) ); customizeJMenuItem( _taxcolor_item ); - _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) ); - _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." ); + _tools_menu.addSeparator(); + _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) ); + _remove_visual_styles_item + .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." ); + customizeJMenuItem( _remove_visual_styles_item ); + _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) ); + _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." ); customizeJMenuItem( _remove_branch_color_item ); _tools_menu.addSeparator(); _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) ); @@ -812,11 +888,12 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { void buildViewMenu() { _view_jmenu = MainFrame.createMenu( "View", getConfiguration() ); - _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) ); + _view_jmenu + .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) ); _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_nexus_item = new JMenuItem( "View as Nexus" ) ); + _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) ); + _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) ); + _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) ); customizeJMenuItem( _display_basic_information_item ); customizeJMenuItem( _view_as_NH_item ); customizeJMenuItem( _view_as_XML_item ); @@ -869,9 +946,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { String title = "Basic Information"; if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { - title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\""; } - showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title ); + showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title ); } } @@ -892,7 +969,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { GSDI gsdi = null; final Phylogeny species_tree = _species_tree.copy(); try { - gsdi = new GSDI( gene_tree, species_tree, false, true, true ); + gsdi = new GSDI( gene_tree, species_tree, false, true, true, true ); } catch ( final SDIException e ) { JOptionPane.showMessageDialog( this, @@ -965,7 +1042,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { GSDIR gsdir = null; final Phylogeny species_tree = _species_tree.copy(); try { - gsdir = new GSDIR( gene_tree, species_tree, true, true ); + gsdir = new GSDIR( gene_tree, species_tree, true, true, true ); } catch ( final SDIException e ) { JOptionPane.showMessageDialog( this, @@ -1033,50 +1110,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { return _options; } - void help() { - 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( "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 ) { setTypeMenuToAllUnselected(); try { @@ -1276,6 +1309,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { options.setBackgroundColorGradient( ( _background_gradient_cbmi != null ) && _background_gradient_cbmi.isSelected() ); options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() ); + options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null ) + && _show_annotation_ref_source.isSelected() ); options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null ) && _abbreviate_scientific_names.isSelected() ); options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null ) @@ -1284,8 +1319,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { && _show_default_node_shapes_internal_cbmi.isSelected() ); options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null ) && _show_default_node_shapes_external_cbmi.isSelected() ); - options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null ) - && _taxonomy_colorize_node_shapes_cbmi.isSelected() ); if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) { options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP ); } @@ -1342,6 +1375,15 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) { options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ); } + if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) { + options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() ); + } + if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) { + options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() ); + } + if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) { + options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() ); + } } void updateTypeCheckboxes( final Options options, final Object o ) { @@ -1353,7 +1395,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { String title = "Nexus"; if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { - title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions() .getNhConversionSupportValueStyle() ), @@ -1365,10 +1407,10 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { String title = "New Hampshire"; if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { - title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } - showTextFrame( getMainPanel().getCurrentPhylogeny() - .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ), + showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions() + .getNhConversionSupportValueStyle() ), title ); } } @@ -1377,7 +1419,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { String title = "phyloXML"; if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { - title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title ); } @@ -1451,6 +1493,12 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } + private void removeVisualStyles() { + if ( getMainPanel().getCurrentPhylogeny() != null ) { + AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() ); + } + } + private void setMainPanel( final MainPanelApplets main_panel ) { _mainpanel = main_panel; }