X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryxE.java;h=d517e42c67e462b19ec265c71bc8e5f53c91d803;hb=b6366fd2ac865514d2ceacb63432dac532147a85;hp=7f2250164ba39b0f35ff69010e8c3e59d234e76d;hpb=bdf2d2a11d720d6457f52866af7ff909afe98db4;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index 7f22501..d517e42 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -115,6 +115,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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; @@ -122,6 +123,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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; @@ -227,10 +229,10 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() ); } else if ( o == _cycle_node_fill_mi ) { - MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() ); + MainFrame.cycleNodeFill( getOptions() ); } else if ( o == _cycle_node_shape_mi ) { - MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() ); + MainFrame.cycleNodeShape( getOptions() ); } else if ( o == _non_lined_up_cladograms_rbmi ) { updateOptions( getOptions() ); @@ -250,6 +252,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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().search0(); getMainPanel().getControlPanel().search1(); @@ -259,6 +264,17 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { getMainPanel().getControlPanel().search0(); getMainPanel().getControlPanel().search1(); } + 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_scale_cbmi ) { updateOptions( getOptions() ); } @@ -376,7 +392,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { * 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() { @@ -393,7 +409,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { /** * 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 @@ -420,10 +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 @@ -566,66 +582,64 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } // - 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(), - getOptions() - .isAllowFontSizeChange() ); + 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 ); } - } ); - 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(); + 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" ); + 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() ); } - AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() ); - } - try { validate(); setName( NAME ); getMainPanel().getControlPanel().showWholeAll(); @@ -755,18 +769,19 @@ 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_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 ) ); + _options_jmenu + .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( _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( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) ); } - _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 @@ -786,13 +801,14 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _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() ) ); _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 ); @@ -811,6 +827,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { .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 ); @@ -824,6 +842,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi, getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP ); 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() ); @@ -936,7 +955,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } void displayBasicInformation() { - if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { + 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() + "\""; @@ -1312,6 +1332,8 @@ 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.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 ); } @@ -1339,6 +1361,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { && _show_confidence_stddev_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() ) { @@ -1465,7 +1488,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } - private MainPanel getMainPanel() { + MainPanel getMainPanel() { return _mainpanel; }