X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryxE.java;h=68671ef7b2ac1ccbd7dd3695212c8ff1e1db3162;hb=10297bd8b8a4b4ab198a17a42fc6ff24ae2ed49b;hp=d190da0cb8a23adfd7443d4df0634224a00a376a;hpb=89d7b6ec1ddc3a3c1e953cf389c24ba7aae7fbfe;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index d190da0..68671ef 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -11,7 +11,9 @@ 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.NoSuchElementException; import javax.swing.ButtonGroup; import javax.swing.JApplet; @@ -31,8 +33,14 @@ import org.forester.archaeopteryx.AptxUtil.GraphicsExportType; import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE; import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION; import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE; +import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; import org.forester.phylogeny.Phylogeny; +import org.forester.phylogeny.PhylogenyMethods; +import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY; import org.forester.phylogeny.data.SequenceRelation; +import org.forester.sdi.GSDI; +import org.forester.sdi.GSDIR; +import org.forester.sdi.SDIException; import org.forester.util.ForesterConstants; import org.forester.util.ForesterUtil; @@ -50,74 +58,83 @@ 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 JCheckBoxMenuItem _show_confidence_stddev_cbmi; + private final static String NAME = "ArchaeopteryxE"; + private static final long serialVersionUID = -1220055577935759443L; + private Configuration _configuration; + private MainPanelApplets _mainpanel; + 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_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 _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; + 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 _search_with_regex_cbmi; + private JCheckBoxMenuItem _show_overview_cbmi; + private JMenuItem _choose_minimal_confidence_mi; + private JMenuItem _collapse_species_specific_subtrees; + private JMenuItem _overview_placment_mi; + private ButtonGroup _radio_group_1; + private JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi; + private JCheckBoxMenuItem _show_default_node_shapes_external_cbmi; + private JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi; + private JMenuItem _cycle_node_shape_mi; + private JMenuItem _cycle_node_fill_mi; + private JMenuItem _choose_node_size_mi; + 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 ) { @@ -125,17 +142,24 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { if ( o == _midpoint_root_item ) { getMainPanel().getCurrentTreePanel().midpointRoot(); } + else if ( o == _gsdi_item ) { + if ( isSubtreeDisplayed() ) { + return; + } + executeGSDI(); + } + else if ( o == _gsdir_item ) { + if ( isSubtreeDisplayed() ) { + return; + } + executeGSDIR(); + } else if ( o == _taxcolor_item ) { getMainPanel().getCurrentTreePanel().taxColor(); } 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(); @@ -144,15 +168,18 @@ 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(); } + else if ( o == _display_basic_information_item ) { + displayBasicInformation(); + } else if ( o == _view_as_NH_item ) { viewAsNH(); } - else if ( o == _view_as_NHX_item ) { - viewAsNHX(); - } else if ( o == _view_as_XML_item ) { viewAsXML(); } @@ -209,32 +236,46 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } else if ( o == _non_lined_up_cladograms_rbmi ) { updateOptions( getOptions() ); - _main_panel.getControlPanel().showWhole(); + _mainpanel.getControlPanel().showWhole(); } else if ( o == _uniform_cladograms_rbmi ) { updateOptions( getOptions() ); - _main_panel.getControlPanel().showWhole(); + _mainpanel.getControlPanel().showWhole(); } else if ( o == _ext_node_dependent_cladogram_rbmi ) { updateOptions( getOptions() ); - _main_panel.getControlPanel().showWhole(); + _mainpanel.getControlPanel().showWhole(); } 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 ) { + if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) { + _search_with_regex_cbmi.setSelected( false ); + } 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 ) { + else if ( o == _search_with_regex_cbmi ) { + if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) { + _search_whole_words_only_cbmi.setSelected( false ); + } + if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) { + _search_case_senstive_cbmi.setSelected( true ); + } updateOptions( getOptions() ); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); } - else if ( o == _show_branch_length_values_cbmi ) { + else if ( o == _show_scale_cbmi ) { updateOptions( getOptions() ); } else if ( o == _show_confidence_stddev_cbmi ) { @@ -243,6 +284,9 @@ 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 ) { @@ -267,17 +311,22 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { else if ( o == _color_labels_same_as_parent_branch ) { updateOptions( getOptions() ); } - else if ( o == _show_default_node_shapes_cbmi ) { + else if ( o == _show_default_node_shapes_internal_cbmi ) { updateOptions( getOptions() ); } - else if ( o == _taxonomy_colorize_node_shapes_cbmi ) { + else if ( o == _show_default_node_shapes_external_cbmi ) { updateOptions( getOptions() ); } else if ( o == _about_item ) { MainFrame.about(); } else if ( o == _help_item ) { - MainFrame.help( getConfiguration().getWebLinks() ); + 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 { @@ -311,18 +360,62 @@ 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(); } + @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 - * + * * @param format must be NH, NHX, NEXUS or PHYLOXML * @return the phylogeny string * @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(); @@ -343,10 +436,10 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } /** - * This method returns a view of the current phylogeny in a chosen + * This method returns a view of the current phylogeny in a chosen * graphics format, base64-encoded in a string so that in can be used * from javascript. - * + * * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp) * @return the phylogeny string * @author Herve Menager @@ -355,8 +448,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { final ByteArrayOutputStream baos = new ByteArrayOutputStream(); try { AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos, - _main_panel.getWidth(), - _main_panel.getHeight(), + _mainpanel.getWidth(), + _mainpanel.getHeight(), getCurrentTreePanel(), getCurrentTreePanel().getControlPanel(), GraphicsExportType.valueOf( format ), @@ -376,6 +469,235 @@ 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(); + 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 + 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 + 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; + } + else if ( phys.length < 1 ) { + ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are empty" ); + JOptionPane.showMessageDialog( this, + NAME + ": phylogenies from [" + phys_url + "] are empty", + "Failed to read phylogenies", + JOptionPane.ERROR_MESSAGE ); + return; + } + else { + AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url ); + } + // + final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD ); + if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) { + AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" ); + Phylogeny[] species_trees = null; + try { + final URL species_tree_url = new URL( species_tree_url_str ); + species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url, + configuration.isValidatePhyloXmlAgainstSchema(), + configuration.isReplaceUnderscoresInNhParsing(), + false, + TAXONOMY_EXTRACTION.NO, + false ); + } + catch ( final IOException e ) { + ForesterUtil.printErrorMessage( NAME, "could not read species tree from [" + species_tree_url_str + + "]" ); + JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from [" + + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE ); + } + if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) { + AptxUtil.printAppletMessage( NAME, "successfully read species tree" ); + if ( species_trees[ 0 ].isEmpty() ) { + ForesterUtil.printErrorMessage( NAME, "species tree is empty" ); + } + else if ( !species_trees[ 0 ].isRooted() ) { + ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" ); + } + else { + setSpeciesTree( species_trees[ 0 ] ); + AptxUtil.printAppletMessage( NAME, "species tree OK" ); + } + } + } + // + try { + setVisible( false ); + setMainPanel( new MainPanelApplets( getConfiguration(), this ) ); + _jmenubar = new JMenuBar(); + if ( !getConfiguration().isHideControlPanelAndMenubar() ) { + if ( !getConfiguration().isUseNativeUI() ) { + _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); + } + if ( getSpeciesTree() != null ) { + buildAnalysisMenu(); + } + 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().calcParametersForPainting( getMainPanel() + .getCurrentTreePanel() + .getWidth(), + getMainPanel() + .getCurrentTreePanel() + .getHeight() ); + } + } + } ); + if ( getConfiguration().isUseTabbedDisplay() ) { + 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" ); + if ( getSpeciesTree() != null ) { + AptxUtil.printAppletMessage( NAME, + "Warning: gsdi (gene duplication inference) only available tabbed display" ); + } + AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() ); + } + 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 ) { + 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 buildAnalysisMenu() { + _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() ); + _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) ); + _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) ); + customizeJMenuItem( _gsdi_item ); + customizeJMenuItem( _gsdir_item ); + // _analysis_menu.addSeparator(); + // _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) ); + // customizeJMenuItem( _lineage_inference ); + // _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" ); + _jmenubar.add( _analysis_menu ); + } + 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" ) ); @@ -393,7 +715,8 @@ 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" ) ); @@ -423,16 +746,16 @@ 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 ), @@ -449,26 +772,31 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _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 ) ); + .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) ); _options_jmenu - .add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL ) ); + .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) ); _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( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) ); + _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) ); + if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { + _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) ); + _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) ); + } + _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( _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( "" ) ); @@ -479,20 +807,28 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _options_jmenu .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) ); _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) ); + _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) ); + _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP ); _options_jmenu .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) ); customizeJMenuItem( _choose_font_mi ); 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_cbmi, getOptions().isShowDefaultNodeShapes() ); - customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() ); + customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions() + .isShowDefaultNodeShapesExternal() ); + customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions() + .isShowDefaultNodeShapesInternal() ); + customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions() + .isShowDefaultNodeShapesForMarkedNodes() ); customizeJMenuItem( _cycle_node_shape_mi ); customizeJMenuItem( _cycle_node_fill_mi ); customizeJMenuItem( _choose_node_size_mi ); @@ -505,11 +841,13 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP ); customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi, getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP ); - customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() ); customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() ); + customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() ); 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 ); } @@ -519,16 +857,18 @@ 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" ) ); customizeJMenuItem( _midpoint_root_item ); _tools_menu.addSeparator(); - _tools_menu - .add( _infer_common_sn_names_item = new JMenuItem( "Infer Common Parts of Internal Scientific Names" ) ); - customizeJMenuItem( _infer_common_sn_names_item ); _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) ); customizeJMenuItem( _collapse_species_specific_subtrees ); _jmenubar.add( _tools_menu ); @@ -559,56 +899,40 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } void buildViewMenu() { - _view_jmenu = MainFrame.createMenu( "View as Text", getConfiguration() ); - _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" ) ); + _view_jmenu = MainFrame.createMenu( "View", getConfiguration() ); + _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( "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_NHX_item ); customizeJMenuItem( _view_as_XML_item ); customizeJMenuItem( _view_as_nexus_item ); _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 ); @@ -630,24 +954,156 @@ 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() != null ) && ( getMainPanel().getCurrentPhylogeny() != null ) + && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { + String title = "Basic Information"; + if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { + title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\""; } - item.setSelected( is_selected ); - item.addActionListener( this ); + showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title ); } } - @Override - public void destroy() { - AptxUtil.printAppletMessage( NAME, "going to be destroyed " ); - removeTextFrame(); - if ( getMainPanel() != null ) { - getMainPanel().terminate(); + void executeGSDI() { + if ( !isOKforSDI( false, true ) ) { + return; + } + if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) { + JOptionPane.showMessageDialog( this, + "Gene tree is not rooted.", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return; + } + final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy(); + gene_tree.setAllNodesToNotCollapse(); + gene_tree.recalculateNumberOfExternalDescendants( false ); + GSDI gsdi = null; + final Phylogeny species_tree = _species_tree.copy(); + try { + gsdi = new GSDI( gene_tree, species_tree, false, true, true, true ); + } + catch ( final SDIException e ) { + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Error during GSDI", + JOptionPane.ERROR_MESSAGE ); + return; + } + catch ( final Exception e ) { + AptxUtil.unexpectedException( e ); + return; + } + gene_tree.setRerootable( false ); + gene_tree.clearHashIdToNodeMap(); + gene_tree.recalculateNumberOfExternalDescendants( true ); + _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null ); + getMainPanel().getControlPanel().setShowEvents( true ); + showWhole(); + final int selected = _mainpanel.getTabbedPane().getSelectedIndex(); + _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null ); + showWhole(); + _mainpanel.getTabbedPane().setSelectedIndex( selected ); + showWhole(); + _mainpanel.getCurrentTreePanel().setEdited( true ); + final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree ); + if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) { + JOptionPane.showMessageDialog( this, + "Duplications: " + gsdi.getDuplicationsSum() + "\n" + + "Potential duplications: " + + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + + "Speciations: " + gsdi.getSpeciationsSum() + "\n" + + "Stripped gene tree nodes: " + + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n" + + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n" + + "Number of polytomies in species tree used: " + poly + "\n", + "GSDI successfully completed", + JOptionPane.WARNING_MESSAGE ); + } + else { + JOptionPane.showMessageDialog( this, + "Duplications: " + gsdi.getDuplicationsSum() + "\n" + + "Potential duplications: " + + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + + "Speciations: " + gsdi.getSpeciationsSum() + "\n" + + "Stripped gene tree nodes: " + + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n" + + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n" + + "Number of polytomies in species tree used: " + poly + "\n", + "GSDI successfully completed", + JOptionPane.INFORMATION_MESSAGE ); + } + } + + void executeGSDIR() { + if ( !isOKforSDI( false, false ) ) { + return; + } + final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() ); + if ( ( p > 0 ) + && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) { + JOptionPane.showMessageDialog( this, + "Gene tree is not completely binary", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return; + } + final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy(); + gene_tree.setAllNodesToNotCollapse(); + gene_tree.recalculateNumberOfExternalDescendants( false ); + GSDIR gsdir = null; + final Phylogeny species_tree = _species_tree.copy(); + try { + gsdir = new GSDIR( gene_tree, species_tree, true, true, true ); + } + catch ( final SDIException e ) { + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Error during GSDIR", + JOptionPane.ERROR_MESSAGE ); + return; + } + catch ( final Exception e ) { + AptxUtil.unexpectedException( e ); + return; + } + final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree(); + result_gene_tree.setRerootable( false ); + result_gene_tree.clearHashIdToNodeMap(); + result_gene_tree.recalculateNumberOfExternalDescendants( true ); + PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME ); + _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null ); + getMainPanel().getControlPanel().setShowEvents( true ); + showWhole(); + final int selected = _mainpanel.getTabbedPane().getSelectedIndex(); + _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null ); + showWhole(); + _mainpanel.getTabbedPane().setSelectedIndex( selected ); + showWhole(); + _mainpanel.getCurrentTreePanel().setEdited( true ); + final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree ); + if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) { + JOptionPane.showMessageDialog( this, + "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n" + + "Speciations: " + gsdir.getSpeciationsSum() + "\n" + + "Stripped gene tree nodes: " + + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n" + + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n" + + "Number of polytomies in species tree used: " + poly + "\n", + "GSDIR successfully completed", + JOptionPane.WARNING_MESSAGE ); + } + else { + JOptionPane.showMessageDialog( this, + "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n" + + "Speciations: " + gsdir.getSpeciationsSum() + "\n" + + "Stripped gene tree nodes: " + + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n" + + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n" + + "Number of polytomies in species tree used: " + poly + "\n", + "GSDIR successfully completed", + JOptionPane.INFORMATION_MESSAGE ); } } @@ -663,134 +1119,10 @@ 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 ); - } - } - } ); - 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 ); - } - void initializeTypeMenu( final Options options ) { setTypeMenuToAllUnselected(); try { @@ -826,31 +1158,63 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } - private boolean isScreenAntialias() { - return true; + boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) { + if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) { + return false; + } + else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) { + JOptionPane.showMessageDialog( this, + "No species tree loaded", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return false; + } + else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) { + JOptionPane.showMessageDialog( this, + "Species tree is not completely binary", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return false; + } + else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) { + JOptionPane.showMessageDialog( this, + "Gene tree is not completely binary", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return false; + } + else { + return true; + } } - private void removeBranchColors() { - if ( getMainPanel().getCurrentPhylogeny() != null ) { - AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() ); + boolean isSubtreeDisplayed() { + if ( getCurrentTreePanel() != null ) { + if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) { + JOptionPane + .showMessageDialog( this, + "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.", + "Operation can not be exectuted on a sub-tree", + JOptionPane.WARNING_MESSAGE ); + return true; + } } + return false; } - 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; } @@ -919,41 +1283,8 @@ 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 showWhole() { + _mainpanel.getControlPanel().showWhole(); } void switchColors() { @@ -991,14 +1322,18 @@ 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 ) && _color_labels_same_as_parent_branch.isSelected() ); - options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null ) - && _show_default_node_shapes_cbmi.isSelected() ); - options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null ) - && _taxonomy_colorize_node_shapes_cbmi.isSelected() ); + options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null ) + && _show_default_node_shapes_internal_cbmi.isSelected() ); + options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null ) + && _show_default_node_shapes_external_cbmi.isSelected() ); + options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null ) + && _show_default_node_shapes_for_marked_cbmi.isSelected() ); if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) { options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP ); } @@ -1024,11 +1359,9 @@ 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() ); - } options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ); + options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() ); options.setInverseSearchResult( ( _inverse_search_result_cbmi != null ) && _inverse_search_result_cbmi.isSelected() ); if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) { @@ -1055,6 +1388,15 @@ 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 ) { @@ -1063,39 +1405,145 @@ 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() + "\" in " + 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() + "\" in " + title; + } + showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( 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; + void viewAsXML() { + if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { + String title = "phyloXML"; + if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; + } + showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title ); } - _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNewHampshireX() ); } - void viewAsXML() { - removeTextFrame(); - if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty() - || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) { - return; + 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 ); + } + } + + MainPanel getMainPanel() { + return _mainpanel; + } + + private Phylogeny getSpeciesTree() { + return _species_tree; + } + + private boolean isScreenAntialias() { + return true; + } + + private void removeBranchColors() { + if ( getMainPanel().getCurrentPhylogeny() != null ) { + AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() ); + } + } + + private void removeVisualStyles() { + if ( getMainPanel().getCurrentPhylogeny() != null ) { + AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() ); + } + } + + private void setMainPanel( final MainPanelApplets main_panel ) { + _mainpanel = main_panel; + } + + private void setSpeciesTree( final Phylogeny species_tree ) { + _species_tree = species_tree; + } + + 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 ) {