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=37bec4557adb317499358db28b838378a39c2196;hpb=9e1353590a88991e7593d38c8e307f713a0f3d5b;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index 37bec45..68671ef 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -115,14 +115,15 @@ 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 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_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; @@ -132,10 +133,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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; - + private JCheckBoxMenuItem _right_line_up_domains_cbmi; + private JCheckBoxMenuItem _line_up_renderable_data_cbmi; @Override public void actionPerformed( final ActionEvent e ) { @@ -253,6 +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(); @@ -262,10 +264,18 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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 ) { @@ -353,14 +363,18 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { else if ( o == _color_by_taxonomic_group_cbmi ) { updateOptions( getOptions() ); } - else if ( o == _right_line_up_domains_cbmi ) { + 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 == _line_up_renderable_data_cbmi ) { + 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(); } @@ -378,7 +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() { @@ -395,7 +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 @@ -422,10 +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 @@ -568,81 +582,91 @@ 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() ); + 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 ( getSpeciesTree() != null ) { - buildAnalysisMenu(); + 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(); + } } - 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() ); + 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() ); } - } ); - 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" ); - if ( getSpeciesTree() != null ) { - AptxUtil.printAppletMessage( NAME, - "Warning: gsdi (gene duplication inference) only available tabbed display" ); + 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 ); } - 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 ); + /* 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 ) { @@ -722,16 +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 ), @@ -745,20 +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_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_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 @@ -778,13 +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 ); @@ -803,6 +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 ); @@ -815,11 +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 ); } @@ -927,7 +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() + "\""; @@ -1094,8 +1123,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { return _options; } - - void initializeTypeMenu( final Options options ) { setTypeMenuToAllUnselected(); try { @@ -1305,6 +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 ); } @@ -1330,11 +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() ) { @@ -1364,17 +1391,12 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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 ) { @@ -1466,7 +1488,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } - private MainPanel getMainPanel() { + MainPanel getMainPanel() { return _mainpanel; }