X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrame.java;h=ac08d253a4a02ab0467d92e07e84153ad48b3f3f;hb=65a8c5b4114a280f1ec4977c89e2f5373fd68104;hp=4ade5da273dc6a90db247b2b045f217344103981;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index 4ade5da..ac08d25 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -24,6 +24,8 @@ package org.forester.archaeopteryx; +import java.awt.Color; +import java.awt.Component; import java.awt.Container; import java.awt.Font; import java.awt.event.ActionEvent; @@ -41,54 +43,68 @@ import javax.swing.JMenuBar; import javax.swing.JMenuItem; import javax.swing.JOptionPane; import javax.swing.JRadioButtonMenuItem; +import javax.swing.SwingUtilities; 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.archaeopteryx.tools.InferenceManager; +import org.forester.archaeopteryx.tools.ProcessPool; +import org.forester.archaeopteryx.tools.ProcessRunning; import org.forester.phylogeny.Phylogeny; +import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE; +import org.forester.phylogeny.data.NodeVisualization.NodeFill; +import org.forester.phylogeny.data.NodeVisualization.NodeShape; import org.forester.util.ForesterConstants; import org.forester.util.ForesterUtil; public abstract class MainFrame extends JFrame implements ActionListener { - static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]"; - static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME - static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE; - private static final long serialVersionUID = 3655000897845508358L; - final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(), - Font.PLAIN, - 10 ); - static final String TYPE_MENU_HEADER = "Type"; - static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular"; - static final String EURO_TYPE_CBMI_LABEL = "Euro Type"; - static final String CURVED_TYPE_CBMI_LABEL = "Curved"; - static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular"; - static final String CONVEX_TYPE_CBMI_LABEL = "Convex"; - static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded"; - static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO - static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO - static final String OPTIONS_HEADER = "Options"; - static final String SEARCH_SUBHEADER = "Search:"; - static final String DISPLAY_SUBHEADER = "Display:"; - static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only"; - static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive"; - static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result"; - static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Display Branch Length Values"; - static final String DISPLAY_SCALE_LABEL = "Display Scale"; - static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms"; - static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms"; - static final String LABEL_DIRECTION_LABEL = "Radial Labels"; - static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types"; - static final String SCREEN_ANTIALIAS_LABEL = "Antialias"; - static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch"; - static final String BG_GRAD_LABEL = "Background Color Gradient"; - static final String DISPLAY_NODE_BOXES_LABEL = "Display Node Boxes"; - static final String SHOW_OVERVIEW_LABEL = "Show Overview"; - static final String FONT_SIZE_MENU_LABEL = "Font Size"; - static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms"; - static final String SHOW_DOMAIN_LABELS_LABEL = "Show Domain Labels"; - static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent"; - static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names"; + static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]"; + static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME + static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE; + private static final long serialVersionUID = 3655000897845508358L; + final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(), + Font.PLAIN, + 10 ); + static final String TYPE_MENU_HEADER = "Type"; + static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular"; + static final String EURO_TYPE_CBMI_LABEL = "Euro Type"; + static final String CURVED_TYPE_CBMI_LABEL = "Curved"; + static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular"; + static final String CONVEX_TYPE_CBMI_LABEL = "Convex"; + static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded"; + static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO + static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO + static final String OPTIONS_HEADER = "Options"; + static final String SEARCH_SUBHEADER = "Search:"; + static final String DISPLAY_SUBHEADER = "Display:"; + static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only"; + static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive"; + static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result"; + static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Display Branch Length Values"; + static final String DISPLAY_SCALE_LABEL = "Display Scale"; + static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms"; + static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms"; + static final String LABEL_DIRECTION_LABEL = "Radial Labels"; + static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types"; + static final String SCREEN_ANTIALIAS_LABEL = "Antialias"; + static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch"; + static final String BG_GRAD_LABEL = "Background Color Gradient"; + static final String DISPLAY_NODE_BOXES_LABEL = "Show Node Shapes"; + static final String SHOW_OVERVIEW_LABEL = "Show Overview"; + static final String FONT_SIZE_MENU_LABEL = "Font Size"; + static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms"; + static final String SHOW_DOMAIN_LABELS_LABEL = "Show Domain Labels"; + static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent"; + static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names"; + static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy"; + static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes"; + static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type"; + static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size"; + static final String SHOW_CONF_STDDEV_LABEL = "Show Confidence Standard Deviations"; + static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values"; + static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values"; JMenuBar _jmenubar; JMenu _file_jmenu; JMenu _tools_menu; @@ -109,10 +125,13 @@ public abstract class MainFrame extends JFrame implements ActionListener { JMenuItem _midpoint_root_item; JMenuItem _taxcolor_item; JMenuItem _confcolor_item; + JMenuItem _color_rank_jmi; JMenuItem _infer_common_sn_names_item; JMenuItem _collapse_species_specific_subtrees; - JMenuItem _collapse_below_threshold; //TODO implememt me + JMenuItem _collapse_below_threshold; //TODO implememt me JMenuItem _obtain_detailed_taxonomic_information_jmi; + JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi; + JMenuItem _obtain_uniprot_seq_information_jmi; JMenuItem _move_node_names_to_tax_sn_jmi; JMenuItem _move_node_names_to_seq_names_jmi; JMenuItem _extract_tax_code_from_node_names_jmi; @@ -130,18 +149,23 @@ public abstract class MainFrame extends JFrame implements ActionListener { // _ screen display JCheckBoxMenuItem _screen_antialias_cbmi; JCheckBoxMenuItem _background_gradient_cbmi; - JCheckBoxMenuItem _show_node_boxes_cbmi; JRadioButtonMenuItem _non_lined_up_cladograms_rbmi; JRadioButtonMenuItem _uniform_cladograms_rbmi; JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi; JCheckBoxMenuItem _show_branch_length_values_cbmi; - JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me + JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me JCheckBoxMenuItem _show_overview_cbmi; JCheckBoxMenuItem _show_domain_labels; JCheckBoxMenuItem _abbreviate_scientific_names; JCheckBoxMenuItem _color_labels_same_as_parent_branch; JMenuItem _overview_placment_mi; JMenuItem _choose_minimal_confidence_mi; + JCheckBoxMenuItem _show_default_node_shapes_cbmi; + JMenuItem _cycle_node_shape_mi; + JMenuItem _cycle_node_fill_mi; + JMenuItem _choose_node_size_mi; + JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi; + JCheckBoxMenuItem _show_confidence_stddev_cbmi; // _ print JCheckBoxMenuItem _graphics_export_visible_only_cbmi; JCheckBoxMenuItem _antialias_print_cbmi; @@ -154,6 +178,8 @@ public abstract class MainFrame extends JFrame implements ActionListener { JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi; JCheckBoxMenuItem _extract_pfam_style_tax_codes_cbmi; JCheckBoxMenuItem _replace_underscores_cbmi; + JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi; + JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi; // _ search JCheckBoxMenuItem _search_case_senstive_cbmi; JCheckBoxMenuItem _search_whole_words_only_cbmi; @@ -173,6 +199,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { JMenuItem _view_as_NHX_item; JMenuItem _view_as_XML_item; JMenuItem _view_as_nexus_item; + JMenuItem _display_basic_information_item; // help menu: JMenuItem _about_item; JMenuItem _help_item; @@ -180,6 +207,8 @@ public abstract class MainFrame extends JFrame implements ActionListener { JMenuItem _phyloxml_website_item; JMenuItem _phyloxml_ref_item; JMenuItem _aptx_ref_item; + // process menu: + JMenu _process_menu; // Handy pointers to child components: MainPanel _mainpanel; Container _contentpane; @@ -187,9 +216,15 @@ public abstract class MainFrame extends JFrame implements ActionListener { Configuration _configuration; JMenuItem _remove_branch_color_item; Options _options; + InferenceManager _inference_manager; + final ProcessPool _process_pool; MainFrame() { - // Empty constructor. + _process_pool = ProcessPool.createInstance(); + } + + public ProcessPool getProcessPool() { + return _process_pool; } /** @@ -217,6 +252,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _confcolor_item ) { confColor(); } + else if ( o == _color_rank_jmi ) { + colorRank(); + } else if ( o == _infer_common_sn_names_item ) { if ( isSubtreeDisplayed() ) { return; @@ -248,6 +286,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _switch_colors_mi ) { switchColors(); } + else if ( o == _display_basic_information_item ) { + displayBasicInformation(); + } else if ( o == _view_as_NH_item ) { viewAsNH(); } @@ -296,9 +337,18 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _choose_minimal_confidence_mi ) { chooseMinimalConfidence(); } + else if ( o == _choose_node_size_mi ) { + chooseNodeSize( getOptions(), this ); + } else if ( o == _overview_placment_mi ) { MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() ); } + else if ( o == _cycle_node_fill_mi ) { + MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() ); + } + else if ( o == _cycle_node_shape_mi ) { + MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() ); + } else if ( o == _screen_antialias_cbmi ) { updateOptions( getOptions() ); updateScreenTextAntialias( getMainPanel().getTreePanels() ); @@ -315,7 +365,10 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _color_labels_same_as_parent_branch ) { updateOptions( getOptions() ); } - else if ( o == _show_node_boxes_cbmi ) { + else if ( o == _show_default_node_shapes_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _taxonomy_colorize_node_shapes_cbmi ) { updateOptions( getOptions() ); } else if ( o == _non_lined_up_cladograms_rbmi ) { @@ -348,6 +401,21 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _show_branch_length_values_cbmi ) { updateOptions( getOptions() ); } + else if ( o == _show_confidence_stddev_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) { + if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) { + _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false ); + } + updateOptions( getOptions() ); + } + else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) { + if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) { + _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false ); + } + updateOptions( getOptions() ); + } else if ( o == _label_direction_cbmi ) { updateOptions( getOptions() ); } @@ -370,7 +438,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { } else if ( o == _website_item ) { try { - Util.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet ); + AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet ); } catch ( final IOException e1 ) { ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); @@ -378,7 +446,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { } else if ( o == _phyloxml_website_item ) { try { - Util.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet ); + AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet ); } catch ( final IOException e1 ) { ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); @@ -386,7 +454,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { } else if ( o == _aptx_ref_item ) { try { - Util.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet ); + AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet ); } catch ( final IOException e1 ) { ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); @@ -394,7 +462,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { } else if ( o == _phyloxml_ref_item ) { try { - Util.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet ); + AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet ); } catch ( final IOException e1 ) { ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); @@ -413,13 +481,15 @@ public abstract class MainFrame extends JFrame implements ActionListener { } boolean isSubtreeDisplayed() { - 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; + 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; } @@ -478,6 +548,43 @@ public abstract class MainFrame extends JFrame implements ActionListener { _jmenubar.add( _help_jmenu ); } + public void updateProcessMenu() { + // In general Swing is not thread safe. + // See "Swing's Threading Policy". + SwingUtilities.invokeLater( new Runnable() { + + public void run() { + doUpdateProcessMenu(); + } + } ); + } + + private void doUpdateProcessMenu() { + if ( _process_pool.size() > 0 ) { + if ( _process_menu == null ) { + _process_menu = createMenu( "", getConfiguration() ); + _process_menu.setForeground( Color.RED ); + } + _process_menu.removeAll(); + final String text = "processes running: " + _process_pool.size(); + _process_menu.setText( text ); + _jmenubar.add( _process_menu ); + for( int i = 0; i < _process_pool.size(); ++i ) { + final ProcessRunning p = _process_pool.getProcessByIndex( i ); + _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) ); + } + } + else { + if ( _process_menu != null ) { + _process_menu.removeAll(); + _jmenubar.remove( _process_menu ); + } + } + _jmenubar.validate(); + _jmenubar.repaint(); + repaint(); + } + void buildTypeMenu() { _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() ); _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) ); @@ -503,11 +610,14 @@ public abstract class MainFrame extends JFrame implements ActionListener { } void buildViewMenu() { - _view_jmenu = createMenu( "View as Text", getConfiguration() ); + _view_jmenu = createMenu( "View", getConfiguration() ); + _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) ); + _view_jmenu.addSeparator(); _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) ); _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) ); _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) ); _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) ); + customizeJMenuItem( _display_basic_information_item ); customizeJMenuItem( _view_as_NH_item ); customizeJMenuItem( _view_as_NHX_item ); customizeJMenuItem( _view_as_XML_item ); @@ -553,6 +663,40 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } + static void chooseNodeSize( final Options options, final Component parent ) { + final String s = ( String ) JOptionPane.showInputDialog( parent, + "Please enter the default size for node shapes.\n" + + "[current value: " + + options.getDefaultNodeShapeSize() + "]\n", + "Node Shape Size", + JOptionPane.QUESTION_MESSAGE, + null, + null, + options.getDefaultNodeShapeSize() ); + 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 ) ) { + final short size = ForesterUtil.roundToShort( m ); + if ( size >= 0.0 ) { + options.setDefaultNodeShapeSize( size ); + } + } + } + } + void close() { removeTextFrame(); if ( _mainpanel != null ) { @@ -571,6 +715,23 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } + void colorRank() { + if ( _mainpanel.getCurrentTreePanel() != null ) { + final String[] ranks = AptxUtil.getAllPossibleRanks(); + final String rank = ( String ) JOptionPane + .showInputDialog( this, + "What rank should the colorization be based on", + "Rank Selection", + JOptionPane.QUESTION_MESSAGE, + null, + ranks, + null ); + if ( !ForesterUtil.isEmpty( rank ) ) { + _mainpanel.getCurrentTreePanel().colorRank( rank ); + } + } + } + void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) { if ( item != null ) { item.setFont( MainFrame.menu_font ); @@ -583,7 +744,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } - void customizeJMenuItem( final JMenuItem jmi ) { + JMenuItem customizeJMenuItem( final JMenuItem jmi ) { if ( jmi != null ) { jmi.setFont( MainFrame.menu_font ); if ( !getConfiguration().isUseNativeUI() ) { @@ -592,6 +753,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { } jmi.addActionListener( this ); } + return jmi; } void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) { @@ -649,7 +811,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } - Configuration getConfiguration() { + public Configuration getConfiguration() { return _configuration; } @@ -665,7 +827,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { return _label_direction_cbmi; } - MainPanel getMainPanel() { + public MainPanel getMainPanel() { return _mainpanel; } @@ -673,7 +835,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { return _jmenubar; } - Options getOptions() { + public Options getOptions() { return _options; } @@ -722,7 +884,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { private void removeBranchColors() { if ( getMainPanel().getCurrentPhylogeny() != null ) { - Util.removeBranchColors( getMainPanel().getCurrentPhylogeny() ); + AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() ); } } @@ -741,6 +903,14 @@ public abstract class MainFrame extends JFrame implements ActionListener { _options = options; } + void setInferenceManager( final InferenceManager i ) { + _inference_manager = i; + } + + public InferenceManager getInferenceManager() { + return _inference_manager; + } + void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) { setTypeMenuToAllUnselected(); switch ( type ) { @@ -784,7 +954,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { _circular_type_cbmi.setSelected( false ); } - void showWhole() { + public void showWhole() { _mainpanel.getControlPanel().showWhole(); } @@ -840,7 +1010,10 @@ public abstract class MainFrame extends JFrame implements ActionListener { && _abbreviate_scientific_names.isSelected() ); options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null ) && _color_labels_same_as_parent_branch.isSelected() ); - options.setShowNodeBoxes( ( _show_node_boxes_cbmi != null ) && _show_node_boxes_cbmi.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() ); if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) { options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP ); } @@ -864,6 +1037,8 @@ public abstract class MainFrame extends JFrame 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() ); } @@ -872,6 +1047,17 @@ public abstract class MainFrame extends JFrame implements ActionListener { options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null ) && ( _graphics_export_using_actual_size_cbmi.isSelected() ) ); options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() ); + if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null ) + && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) { + options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ); + } + else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null ) + && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) { + options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES ); + } + else { + options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ); + } options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null ) && _print_black_and_white_cbmi.isSelected() ); options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null ) @@ -925,22 +1111,31 @@ public abstract class MainFrame extends JFrame implements ActionListener { ( ( JCheckBoxMenuItem ) o ).setSelected( true ); } + void displayBasicInformation() { + if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) { + return; + } + _textframe = TextFrame.instantiate( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ) ); + } + void viewAsNexus() { removeTextFrame(); if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() - || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) { + || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 20000 ) ) { return; } - _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNexus() ); + _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNexus( getOptions() + .getNhConversionSupportValueStyle() ) ); } void viewAsNH() { removeTextFrame(); if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() - || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) { + || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 20000 ) ) { return; } - _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNewHampshire( false ) ); + _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny() + .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ) ); } void viewAsNHX() { @@ -965,10 +1160,11 @@ public abstract class MainFrame extends JFrame implements ActionListener { */ static void about() { final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" ); - about.append( "Copyright (C) 2007-2011 Christian Zmasek\n" ); + about.append( "Copyright (C) 2007-2012 Christian M. Zmasek\n" ); about.append( "All Rights Reserved\n" ); about.append( "License: GNU Lesser General Public License (LGPL)\n" ); about.append( "Last modified: " + Constants.PRG_DATE + "\n" ); + about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" ); about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" ); about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" ); if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) { @@ -1035,7 +1231,38 @@ public abstract class MainFrame extends JFrame implements ActionListener { default: throw new RuntimeException( "unknown placement: " + op.getOvPlacement() ); } - tree_panel.updateOvSettings(); + if ( tree_panel != null ) { + tree_panel.updateOvSettings(); + } + } + + static void cycleNodeFill( final Options op, final TreePanel tree_panel ) { + switch ( op.getDefaultNodeFill() ) { + case GRADIENT: + op.setDefaultNodeFill( NodeFill.SOLID ); + break; + case NONE: + op.setDefaultNodeFill( NodeFill.GRADIENT ); + break; + case SOLID: + op.setDefaultNodeFill( NodeFill.NONE ); + break; + default: + throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() ); + } + } + + static void cycleNodeShape( final Options op, final TreePanel tree_panel ) { + switch ( op.getDefaultNodeShape() ) { + case CIRCLE: + op.setDefaultNodeShape( NodeShape.RECTANGLE ); + break; + case RECTANGLE: + op.setDefaultNodeShape( NodeShape.CIRCLE ); + break; + default: + throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() ); + } } static void help( final Map weblinks ) { @@ -1136,12 +1363,32 @@ public abstract class MainFrame extends JFrame implements ActionListener { TextFrame.instantiate( sb.toString() ); } - static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) { - if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) { - mi.setText( "Overview Placement... (current: " + tree_panel.getOptions().getOvPlacement() + ")" ); + static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) { + if ( ( options != null ) && ( options.getOvPlacement() != null ) ) { + mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" ); } else { - mi.setText( "Overview Placement..." ); + mi.setText( "Cycle Overview Placement..." ); + } + } + + static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) { + if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) { + mi.setText( "Cycle Node Shape Fill Type... (current: " + + options.getDefaultNodeFill().toString().toLowerCase() + ")" ); + } + else { + mi.setText( "Cycle Node Shape Fill Type..." ); + } + } + + static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) { + if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) { + mi.setText( "Cycle Node Shape Fill Type... (current: " + + options.getDefaultNodeShape().toString().toLowerCase() + ")" ); + } + else { + mi.setText( "Cycle Node Shape Fill Type..." ); } } @@ -1162,7 +1409,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) { mi.setEnabled( true ); } - else if ( ForesterUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) { + else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) { mi.setEnabled( true ); } else { @@ -1171,6 +1418,10 @@ public abstract class MainFrame extends JFrame implements ActionListener { mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" ); } + static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) { + mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" ); + } + static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel, final JCheckBoxMenuItem scale, final JCheckBoxMenuItem branch_lengths,