import org.forester.util.ForesterUtil;\r
import org.forester.util.WindowsUtils;\r
\r
-class DefaultFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
- || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )\r
- || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )\r
- || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )\r
- || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )\r
- || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )\r
- || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )\r
- || file_name.endsWith( ".con" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";\r
- }\r
-}\r
-\r
-class GraphicsFileFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )\r
- || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";\r
- }\r
-}\r
-\r
-public abstract class MainFrame extends JFrame implements ActionListener {\r
-\r
- /**\r
- * Display the about box.\r
- */\r
- static void about() {\r
- final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );\r
- about.append( "Copyright (C) 2014 Christian M Zmasek\n" );\r
- about.append( "All Rights Reserved\n" );\r
- about.append( "License: GNU Lesser General Public License (LGPL)\n" );\r
- about.append( "Last modified: " + Constants.PRG_DATE + "\n" );\r
- about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );\r
- about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
- about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );\r
- if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {\r
- about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );\r
- }\r
- if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )\r
- && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {\r
- about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "\r
- + ForesterUtil.OS_VERSION + "]\n" );\r
- }\r
- final Runtime rt = java.lang.Runtime.getRuntime();\r
- final long free_memory = rt.freeMemory() / 1000000;\r
- final long total_memory = rt.totalMemory() / 1000000;\r
- about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );\r
- about.append( "[locale: " + Locale.getDefault() + "]\n" );\r
- about.append( "References:\n" );\r
- about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );\r
- about.append( "For more information & download:\n" );\r
- about.append( Constants.APTX_WEB_SITE + "\n" );\r
- about.append( "Documentation:\n" );\r
- about.append( Constants.APTX_DOC_SITE + "\n" );\r
- about.append( "Comments: " + Constants.AUTHOR_EMAIL );\r
- JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );\r
- }\r
-\r
- static void chooseNodeSize( final Options options, final Component parent ) {\r
- final String s = ( String ) JOptionPane.showInputDialog( parent,\r
- "Please enter the default size for node shapes.\n"\r
- + "[current value: "\r
- + options.getDefaultNodeShapeSize() + "]\n",\r
- "Node Shape Size",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- options.getDefaultNodeShapeSize() );\r
- if ( !ForesterUtil.isEmpty( s ) ) {\r
- boolean success = true;\r
- double m = 0.0;\r
- final String m_str = s.trim();\r
- if ( !ForesterUtil.isEmpty( m_str ) ) {\r
- try {\r
- m = Double.parseDouble( m_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( m >= 0.0 ) ) {\r
- final short size = ForesterUtil.roundToShort( m );\r
- if ( size >= 0.0 ) {\r
- options.setDefaultNodeShapeSize( size );\r
- }\r
- }\r
- }\r
- }\r
-\r
- static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {\r
- return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();\r
- }\r
-\r
- static JMenu createMenu( final String title, final Configuration conf ) {\r
- final JMenu jmenu = new JMenu( title );\r
- if ( !conf.isUseNativeUI() ) {\r
- jmenu.setFont( MainFrame.menu_font );\r
- jmenu.setBackground( conf.getGuiMenuBackgroundColor() );\r
- jmenu.setForeground( conf.getGuiMenuTextColor() );\r
- }\r
- return jmenu;\r
- }\r
-\r
- static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {\r
- label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );\r
- if ( !configuration.isUseNativeUI() ) {\r
- label.setBackground( configuration.getGuiMenuBackgroundColor() );\r
- label.setForeground( configuration.getGuiMenuTextColor() );\r
- label.setOpaque( true );\r
- }\r
- label.setSelected( false );\r
- label.setEnabled( false );\r
- return label;\r
- }\r
-\r
- private static void cycleNodeDataReturn( final Options op, final Configuration conf ) {\r
- switch ( op.getExtDescNodeDataToReturn() ) {\r
- case UNKNOWN:\r
- op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );\r
- break;\r
- case DOMAINS_ALL:\r
- op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );\r
- break;\r
- case DOMAINS_COLLAPSED_PER_PROTEIN:\r
- op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );\r
- break;\r
- case SEQ_ANNOTATIONS:\r
- op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );\r
- break;\r
- case GO_TERM_IDS:\r
- op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );\r
- break;\r
- case SEQUENCE_MOL_SEQ_FASTA:\r
- if ( ( conf != null ) && ( conf.getExtDescNodeDataToReturn() != null )\r
- && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL )\r
- && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN )\r
- && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS )\r
- && ( conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS )\r
- && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA ) ) {\r
- op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );\r
- }\r
- else {\r
- op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
- }\r
- break;\r
- default:\r
- op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
- }\r
- }\r
-\r
- static void cycleNodeFill( final Options op ) {\r
- switch ( op.getDefaultNodeFill() ) {\r
- case GRADIENT:\r
- op.setDefaultNodeFill( NodeFill.SOLID );\r
- break;\r
- case NONE:\r
- op.setDefaultNodeFill( NodeFill.GRADIENT );\r
- break;\r
- case SOLID:\r
- op.setDefaultNodeFill( NodeFill.NONE );\r
- break;\r
- default:\r
- throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );\r
- }\r
- }\r
-\r
- static void cycleNodeShape( final Options op ) {\r
- switch ( op.getDefaultNodeShape() ) {\r
- case CIRCLE:\r
- op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
- break;\r
- case RECTANGLE:\r
- op.setDefaultNodeShape( NodeShape.CIRCLE );\r
- break;\r
- default:\r
- throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );\r
- }\r
- }\r
-\r
- static void cycleOverview( final Options op, final TreePanel tree_panel ) {\r
- switch ( op.getOvPlacement() ) {\r
- case LOWER_LEFT:\r
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );\r
- break;\r
- case LOWER_RIGHT:\r
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );\r
- break;\r
- case UPPER_LEFT:\r
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );\r
- break;\r
- case UPPER_RIGHT:\r
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );\r
- break;\r
- default:\r
- throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );\r
- }\r
- if ( tree_panel != null ) {\r
- tree_panel.updateOvSettings();\r
- }\r
- }\r
-\r
- static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {\r
- if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {\r
- mi.setText( "Cycle Node Return Data... (current: " + options.getExtDescNodeDataToReturn().toString() + ")" );\r
- }\r
- else {\r
- mi.setText( "Cycle Node Return Data..." );\r
- }\r
- }\r
-\r
- static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
- if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
- mi.setText( "Cycle Node Shape Fill Type... (current: "\r
- + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
- }\r
- else {\r
- mi.setText( "Cycle Node Shape Fill Type..." );\r
- }\r
- }\r
-\r
- static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
- if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
- mi.setText( "Cycle Node Shape Fill Type... (current: "\r
- + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
- }\r
- else {\r
- mi.setText( "Cycle Node Shape Fill Type..." );\r
- }\r
- }\r
-\r
- static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
- if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
- mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
- }\r
- else {\r
- mi.setText( "Cycle Overview Placement..." );\r
- }\r
- }\r
-\r
- static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
- if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
- mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
- + ")" );\r
- }\r
- else {\r
- mi.setText( "Select Color Scheme..." );\r
- }\r
- }\r
-\r
- static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
- mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
- }\r
-\r
- static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {\r
- mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "\r
- + o.getPrintSizeY() + ")" );\r
- }\r
-\r
- static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {\r
- mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );\r
- }\r
-\r
- static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
- if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
- mi.setEnabled( true );\r
- }\r
- else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
- mi.setEnabled( true );\r
- }\r
- else {\r
- mi.setEnabled( false );\r
- }\r
- mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
- }\r
-\r
- static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
- mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
- }\r
+public abstract class MainFrame extends JFrame implements ActionListener {\r
\r
- static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
- for( final TreePanel tree_panel : treepanels ) {\r
- tree_panel.setTextAntialias();\r
- }\r
- }\r
final static NHFilter nhfilter = new NHFilter();\r
final static NHXFilter nhxfilter = new NHXFilter();\r
final static XMLFilter xmlfilter = new XMLFilter();\r
JCheckBoxMenuItem _curved_type_cbmi;\r
JCheckBoxMenuItem _convex_type_cbmi;\r
JCheckBoxMenuItem _euro_type_cbmi;\r
- JCheckBoxMenuItem _rounded_type_cbmi; ;\r
+ JCheckBoxMenuItem _rounded_type_cbmi;\r
JCheckBoxMenuItem _unrooted_type_cbmi;\r
JCheckBoxMenuItem _circular_type_cbmi;\r
// view as text menu:\r
// Handy pointers to child components:\r
MainPanel _mainpanel;\r
Container _contentpane;\r
- final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>();\r
+ final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;\r
Configuration _configuration;\r
Options _options;\r
private Phylogeny _species_tree;\r
else if ( o == _show_default_node_shapes_for_marked_cbmi ) {\r
updateOptions( getOptions() );\r
}\r
- else if ( o == _non_lined_up_cladograms_rbmi ) {\r
- updateOptions( getOptions() );\r
- showWhole();\r
+ else if ( o == _non_lined_up_cladograms_rbmi ) {\r
+ updateOptions( getOptions() );\r
+ showWhole();\r
+ }\r
+ else if ( o == _uniform_cladograms_rbmi ) {\r
+ updateOptions( getOptions() );\r
+ showWhole();\r
+ }\r
+ else if ( o == _ext_node_dependent_cladogram_rbmi ) {\r
+ updateOptions( getOptions() );\r
+ showWhole();\r
+ }\r
+ else if ( o == _search_case_senstive_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ getMainPanel().getControlPanel().search0();\r
+ getMainPanel().getControlPanel().search1();\r
+ }\r
+ else if ( o == _search_whole_words_only_cbmi ) {\r
+ if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {\r
+ _search_with_regex_cbmi.setSelected( false );\r
+ }\r
+ updateOptions( getOptions() );\r
+ getMainPanel().getControlPanel().search0();\r
+ getMainPanel().getControlPanel().search1();\r
+ }\r
+ else if ( o == _inverse_search_result_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ getMainPanel().getControlPanel().search0();\r
+ getMainPanel().getControlPanel().search1();\r
+ }\r
+ else if ( o == _search_with_regex_cbmi ) {\r
+ if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {\r
+ _search_whole_words_only_cbmi.setSelected( false );\r
+ }\r
+ if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {\r
+ _search_case_senstive_cbmi.setSelected( true );\r
+ }\r
+ updateOptions( getOptions() );\r
+ getMainPanel().getControlPanel().search0();\r
+ getMainPanel().getControlPanel().search1();\r
+ }\r
+ else if ( o == _show_scale_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _color_by_taxonomic_group_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _show_confidence_stddev_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {\r
+ if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
+ _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );\r
+ }\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {\r
+ if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
+ _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );\r
+ }\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _label_direction_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _show_overview_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ if ( getCurrentTreePanel() != null ) {\r
+ getCurrentTreePanel().updateOvSizes();\r
+ }\r
+ }\r
+ else if ( o == _line_up_renderable_data_cbmi ) {\r
+ if ( !_line_up_renderable_data_cbmi.isSelected() ) {\r
+ _right_line_up_domains_cbmi.setSelected( false );\r
+ }\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _right_line_up_domains_cbmi ) {\r
+ if ( _right_line_up_domains_cbmi.isSelected() ) {\r
+ _line_up_renderable_data_cbmi.setSelected( true );\r
+ }\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )\r
+ || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )\r
+ || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {\r
+ typeChanged( o );\r
+ }\r
+ else if ( o == _about_item ) {\r
+ about();\r
+ }\r
+ else if ( o == _help_item ) {\r
+ try {\r
+ AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet );\r
+ }\r
+ catch ( final IOException e1 ) {\r
+ ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
+ }\r
+ }\r
+ else if ( o == _website_item ) {\r
+ try {\r
+ AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );\r
+ }\r
+ catch ( final IOException e1 ) {\r
+ ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
+ }\r
+ }\r
+ else if ( o == _phyloxml_website_item ) {\r
+ try {\r
+ AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );\r
+ }\r
+ catch ( final IOException e1 ) {\r
+ ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
+ }\r
+ }\r
+ else if ( o == _aptx_ref_item ) {\r
+ try {\r
+ AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );\r
+ }\r
+ catch ( final IOException e1 ) {\r
+ ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
+ }\r
+ }\r
+ else if ( o == _phyloxml_ref_item ) {\r
+ try {\r
+ AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );\r
+ }\r
+ catch ( final IOException e1 ) {\r
+ ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
+ }\r
+ }\r
+ else if ( o == _write_to_pdf_item ) {\r
+ writeToPdf( _mainpanel.getCurrentPhylogeny() );\r
+ }\r
+ else if ( o == _save_all_item ) {\r
+ writeAllToFile();\r
+ }\r
+ else if ( o == _write_to_jpg_item ) {\r
+ writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG );\r
+ }\r
+ else if ( o == _write_to_gif_item ) {\r
+ writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF );\r
+ }\r
+ else if ( o == _write_to_tif_item ) {\r
+ writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF );\r
+ }\r
+ else if ( o == _write_to_bmp_item ) {\r
+ writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP );\r
+ }\r
+ else if ( o == _print_item ) {\r
+ print( getCurrentTreePanel(),\r
+ getOptions(),\r
+ \r
+ this );\r
+ }\r
+ else if ( o == _save_item ) {\r
+ writeToFile( _mainpanel.getCurrentPhylogeny() );\r
+ }\r
+ else if ( o == _write_to_png_item ) {\r
+ writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );\r
+ }\r
+ else if ( o == _graphics_export_visible_only_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _antialias_print_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _print_black_and_white_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _print_using_actual_size_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _graphics_export_using_actual_size_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _print_size_mi ) {\r
+ choosePrintSize();\r
+ }\r
+ else if ( o == _choose_pdf_width_mi ) {\r
+ choosePdfWidth();\r
+ }\r
+ else {\r
+ if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
+ for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
+ if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {\r
+ readPhylogeniesFromWebservice( i );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ _contentpane.repaint();\r
+ }\r
+\r
+ public Configuration getConfiguration() {\r
+ return _configuration;\r
+ }\r
+\r
+ /**\r
+ * This method returns the current external node data which\r
+ * has been selected by the user by clicking the "Return ..."\r
+ * menu item. This method is expected to be called from Javascript or\r
+ * something like it.\r
+ *\r
+ * @return current external node data as String\r
+ */\r
+ public String getCurrentExternalNodesDataBuffer() {\r
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();\r
+ }\r
+\r
+ public int getCurrentExternalNodesDataBufferChangeCounter() {\r
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();\r
+ }\r
+\r
+ public int getCurrentExternalNodesDataBufferLength() {\r
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();\r
+ }\r
+\r
+ public InferenceManager getInferenceManager() {\r
+ return _inference_manager;\r
+ }\r
+\r
+ public MainPanel getMainPanel() {\r
+ return _mainpanel;\r
+ }\r
+\r
+ public Options getOptions() {\r
+ return _options;\r
+ }\r
+\r
+ public ProcessPool getProcessPool() {\r
+ return _process_pool;\r
+ }\r
+\r
+ public void showTextFrame( final String s, final String title ) {\r
+ checkTextFrames();\r
+ _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );\r
+ }\r
+\r
+ public void showWhole() {\r
+ _mainpanel.getControlPanel().showWhole();\r
+ }\r
+\r
+ public void updateProcessMenu() {\r
+ // In general Swing is not thread safe.\r
+ // See "Swing's Threading Policy".\r
+ SwingUtilities.invokeLater( new Runnable() {\r
+\r
+ @Override\r
+ public void run() {\r
+ doUpdateProcessMenu();\r
+ }\r
+ } );\r
+ }\r
+\r
+ void activateSaveAllIfNeeded() {\r
+ if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {\r
+ _save_all_item.setEnabled( true );\r
+ }\r
+ else {\r
+ _save_all_item.setEnabled( false );\r
}\r
- else if ( o == _uniform_cladograms_rbmi ) {\r
- updateOptions( getOptions() );\r
- showWhole();\r
+ }\r
+\r
+ void buildFileMenu() {\r
+ _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );\r
+ _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );\r
+ if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {\r
+ _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );\r
}\r
- else if ( o == _ext_node_dependent_cladogram_rbmi ) {\r
- updateOptions( getOptions() );\r
- showWhole();\r
+ _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );\r
+ _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );\r
+ if ( AptxUtil.canWriteFormat( "gif" ) ) {\r
+ _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );\r
}\r
- else if ( o == _search_case_senstive_cbmi ) {\r
- updateOptions( getOptions() );\r
- getMainPanel().getControlPanel().search0();\r
- getMainPanel().getControlPanel().search1();\r
+ if ( AptxUtil.canWriteFormat( "bmp" ) ) {\r
+ _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );\r
}\r
- else if ( o == _search_whole_words_only_cbmi ) {\r
- if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {\r
- _search_with_regex_cbmi.setSelected( false );\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
+ customizeJMenuItem( _save_item );\r
+ customizeJMenuItem( _write_to_pdf_item );\r
+ customizeJMenuItem( _write_to_png_item );\r
+ customizeJMenuItem( _write_to_jpg_item );\r
+ customizeJMenuItem( _write_to_gif_item );\r
+ customizeJMenuItem( _write_to_tif_item );\r
+ customizeJMenuItem( _write_to_bmp_item );\r
+ customizeJMenuItem( _print_item );\r
+ customizeJMenuItem( _exit_item );\r
+ _jmenubar.add( _file_jmenu );\r
+ }\r
+\r
+ void buildFontSizeMenu() {\r
+ _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );\r
+ _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );\r
+ _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );\r
+ _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );\r
+ _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );\r
+ _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );\r
+ customizeJMenuItem( _super_tiny_fonts_item );\r
+ customizeJMenuItem( _tiny_fonts_item );\r
+ customizeJMenuItem( _small_fonts_item );\r
+ customizeJMenuItem( _medium_fonts_item );\r
+ customizeJMenuItem( _large_fonts_item );\r
+ _jmenubar.add( _font_size_menu );\r
+ }\r
+\r
+ void buildHelpMenu() {\r
+ _help_jmenu = createMenu( "Help", getConfiguration() );\r
+ _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );\r
+ _help_jmenu.addSeparator();\r
+ _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );\r
+ _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...\r
+ _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );\r
+ _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );\r
+ _help_jmenu.addSeparator();\r
+ _help_jmenu.add( _about_item = new JMenuItem( "About" ) );\r
+ customizeJMenuItem( _help_item );\r
+ customizeJMenuItem( _website_item );\r
+ customizeJMenuItem( _phyloxml_website_item );\r
+ customizeJMenuItem( _aptx_ref_item );\r
+ customizeJMenuItem( _phyloxml_ref_item );\r
+ customizeJMenuItem( _about_item );\r
+ _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );\r
+ _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );\r
+ _jmenubar.add( _help_jmenu );\r
+ }\r
+\r
+ void buildTypeMenu() {\r
+ _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );\r
+ _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );\r
+ customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _triangular_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _euro_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _rounded_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _curved_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _convex_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _circular_type_cbmi, false );\r
+ _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
+ _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
+ initializeTypeMenu( getOptions() );\r
+ _jmenubar.add( _type_menu );\r
+ }\r
+\r
+ void buildViewMenu() {\r
+ _view_jmenu = createMenu( "View", getConfiguration() );\r
+ _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );\r
+ _view_jmenu.addSeparator();\r
+ _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );\r
+ _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );\r
+ _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );\r
+ customizeJMenuItem( _display_basic_information_item );\r
+ customizeJMenuItem( _view_as_NH_item );\r
+ customizeJMenuItem( _view_as_XML_item );\r
+ customizeJMenuItem( _view_as_nexus_item );\r
+ _jmenubar.add( _view_jmenu );\r
+ }\r
+\r
+ void checkTextFrames() {\r
+ if ( _textframes.size() > 5 ) {\r
+ try {\r
+ if ( _textframes.getFirst() != null ) {\r
+ _textframes.getFirst().removeMe();\r
+ }\r
+ else {\r
+ _textframes.removeFirst();\r
+ }\r
+ }\r
+ catch ( final NoSuchElementException e ) {\r
+ // Ignore.\r
}\r
- updateOptions( getOptions() );\r
- getMainPanel().getControlPanel().search0();\r
- getMainPanel().getControlPanel().search1();\r
- }\r
- else if ( o == _inverse_search_result_cbmi ) {\r
- updateOptions( getOptions() );\r
- getMainPanel().getControlPanel().search0();\r
- getMainPanel().getControlPanel().search1();\r
}\r
- else if ( o == _search_with_regex_cbmi ) {\r
- if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {\r
- _search_whole_words_only_cbmi.setSelected( false );\r
+ }\r
+\r
+ void choosePdfWidth() {\r
+ final String s = ( String ) JOptionPane.showInputDialog( this,\r
+ "Please enter the default line width for PDF export.\n"\r
+ + "[current value: "\r
+ + getOptions().getPrintLineWidth() + "]\n",\r
+ "Line Width for PDF Export",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getPrintLineWidth() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ float f = 0.0f;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+ try {\r
+ f = Float.parseFloat( m_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
}\r
- if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {\r
- _search_case_senstive_cbmi.setSelected( true );\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( f > 0.0 ) ) {\r
+ getOptions().setPrintLineWidth( f );\r
}\r
- updateOptions( getOptions() );\r
- getMainPanel().getControlPanel().search0();\r
- getMainPanel().getControlPanel().search1();\r
}\r
- else if ( o == _show_scale_cbmi ) {\r
- updateOptions( getOptions() );\r
+ }\r
+\r
+ void choosePrintSize() {\r
+ final String s = ( String ) JOptionPane.showInputDialog( this,\r
+ "Please enter values for width and height,\nseparated by a comma.\n"\r
+ + "[current values: "\r
+ + getOptions().getPrintSizeX() + ", "\r
+ + getOptions().getPrintSizeY() + "]\n"\r
+ + "[A4: " + Constants.A4_SIZE_X + ", "\r
+ + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "\r
+ + Constants.US_LETTER_SIZE_X + ", "\r
+ + Constants.US_LETTER_SIZE_Y + "]",\r
+ "Default Size for Graphics Export",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getPrintSizeX() + ", "\r
+ + getOptions().getPrintSizeY() );\r
+ if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {\r
+ boolean success = true;\r
+ int x = 0;\r
+ int y = 0;\r
+ final String[] str_ary = s.split( "," );\r
+ if ( str_ary.length == 2 ) {\r
+ final String x_str = str_ary[ 0 ].trim();\r
+ final String y_str = str_ary[ 1 ].trim();\r
+ if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {\r
+ try {\r
+ x = Integer.parseInt( x_str );\r
+ y = Integer.parseInt( y_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( x > 1 ) && ( y > 1 ) ) {\r
+ getOptions().setPrintSizeX( x );\r
+ getOptions().setPrintSizeY( y );\r
+ }\r
}\r
- else if ( o == _color_by_taxonomic_group_cbmi ) {\r
- updateOptions( getOptions() );\r
+ }\r
+\r
+ void close() {\r
+ removeAllTextFrames();\r
+ if ( _mainpanel != null ) {\r
+ _mainpanel.terminate();\r
}\r
- else if ( o == _show_confidence_stddev_cbmi ) {\r
- updateOptions( getOptions() );\r
+ if ( _contentpane != null ) {\r
+ _contentpane.removeAll();\r
}\r
- else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {\r
- if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
- _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );\r
+ setVisible( false );\r
+ dispose();\r
+ }\r
+\r
+ void colorRank() {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ final String[] ranks = AptxUtil.getAllPossibleRanks();\r
+ final String rank = ( String ) JOptionPane\r
+ .showInputDialog( this,\r
+ "What rank should the colorization be based on",\r
+ "Rank Selection",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ ranks,\r
+ null );\r
+ if ( !ForesterUtil.isEmpty( rank ) ) {\r
+ _mainpanel.getCurrentTreePanel().colorRank( rank );\r
}\r
- updateOptions( getOptions() );\r
}\r
- else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {\r
- if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
- _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );\r
- }\r
- updateOptions( getOptions() );\r
+ }\r
+\r
+ void confColor() {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().confColor();\r
}\r
- else if ( o == _label_direction_cbmi ) {\r
- updateOptions( getOptions() );\r
+ }\r
+\r
+ void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {\r
+ if ( item != null ) {\r
+ item.setFont( MainFrame.menu_font );\r
+ if ( !getConfiguration().isUseNativeUI() ) {\r
+ item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
+ item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
+ }\r
+ item.setSelected( is_selected );\r
+ item.addActionListener( this );\r
}\r
- else if ( o == _show_overview_cbmi ) {\r
- updateOptions( getOptions() );\r
- if ( getCurrentTreePanel() != null ) {\r
- getCurrentTreePanel().updateOvSizes();\r
+ }\r
+\r
+ JMenuItem customizeJMenuItem( final JMenuItem jmi ) {\r
+ if ( jmi != null ) {\r
+ jmi.setFont( MainFrame.menu_font );\r
+ if ( !getConfiguration().isUseNativeUI() ) {\r
+ jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
+ jmi.setForeground( getConfiguration().getGuiMenuTextColor() );\r
}\r
+ jmi.addActionListener( this );\r
}\r
- else if ( o == _line_up_renderable_data_cbmi ) {\r
- if ( !_line_up_renderable_data_cbmi.isSelected() ) {\r
- _right_line_up_domains_cbmi.setSelected( false );\r
+ return jmi;\r
+ }\r
+\r
+ void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {\r
+ if ( item != null ) {\r
+ item.setFont( MainFrame.menu_font );\r
+ if ( !getConfiguration().isUseNativeUI() ) {\r
+ item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
+ item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
}\r
- updateOptions( getOptions() );\r
+ item.setSelected( is_selected );\r
+ item.addActionListener( this );\r
}\r
- else if ( o == _right_line_up_domains_cbmi ) {\r
- if ( _right_line_up_domains_cbmi.isSelected() ) {\r
- _line_up_renderable_data_cbmi.setSelected( true );\r
+ }\r
+\r
+ void displayBasicInformation( final File treefile ) {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ String title = "Basic Information";\r
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+ title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";\r
}\r
- updateOptions( getOptions() );\r
+ showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );\r
}\r
- else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )\r
- || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )\r
- || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {\r
- typeChanged( o );\r
+ }\r
+\r
+ void exceptionOccuredDuringOpenFile( final Exception e ) {\r
+ try {\r
+ _mainpanel.getCurrentTreePanel().setArrowCursor();\r
}\r
- else if ( o == _about_item ) {\r
- about();\r
+ catch ( final Exception ex ) {\r
+ // Do nothing.\r
}\r
- else if ( o == _help_item ) {\r
- try {\r
- AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet );\r
- }\r
- catch ( final IOException e1 ) {\r
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
- }\r
+ JOptionPane.showMessageDialog( this,\r
+ ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
+ "Error during File|Open",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+\r
+ void exceptionOccuredDuringSaveAs( final Exception e ) {\r
+ try {\r
+ _mainpanel.getCurrentTreePanel().setArrowCursor();\r
}\r
- else if ( o == _website_item ) {\r
- try {\r
- AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );\r
- }\r
- catch ( final IOException e1 ) {\r
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
- }\r
+ catch ( final Exception ex ) {\r
+ // Do nothing.\r
}\r
- else if ( o == _phyloxml_website_item ) {\r
- try {\r
- AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );\r
- }\r
- catch ( final IOException e1 ) {\r
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
- }\r
+ JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );\r
+ }\r
+\r
+ void executeGSDI() {\r
+ if ( !isOKforSDI( false, true ) ) {\r
+ return;\r
}\r
- else if ( o == _aptx_ref_item ) {\r
- try {\r
- AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );\r
- }\r
- catch ( final IOException e1 ) {\r
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
- }\r
+ if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Gene tree is not rooted.",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
}\r
- else if ( o == _phyloxml_ref_item ) {\r
- try {\r
- AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );\r
- }\r
- catch ( final IOException e1 ) {\r
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
- }\r
+ final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
+ gene_tree.setAllNodesToNotCollapse();\r
+ gene_tree.recalculateNumberOfExternalDescendants( false );\r
+ GSDI gsdi = null;\r
+ final Phylogeny species_tree = getSpeciesTree().copy();\r
+ try {\r
+ gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );\r
}\r
- else if ( o == _write_to_pdf_item ) {\r
- writeToPdf( _mainpanel.getCurrentPhylogeny() );\r
+ catch ( final SDIException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Error during GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
}\r
- else if ( o == _save_item ) {\r
- writeToFile( _mainpanel.getCurrentPhylogeny() );\r
- // If subtree currently displayed, save it, instead of complete\r
- // tree.\r
+ catch ( final Exception e ) {\r
+ AptxUtil.unexpectedException( e );\r
+ return;\r
}\r
- else if ( o == _write_to_png_item ) {\r
- writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );\r
+ gene_tree.setRerootable( false );\r
+ gene_tree.clearHashIdToNodeMap();\r
+ gene_tree.recalculateNumberOfExternalDescendants( true );\r
+ _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );\r
+ getMainPanel().getControlPanel().setShowEvents( true );\r
+ showWhole();\r
+ final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
+ showWhole();\r
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
+ showWhole();\r
+ _mainpanel.getCurrentTreePanel().setEdited( true );\r
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
+ if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
+ + "Potential duplications: "\r
+ + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
+ + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
+ + "Stripped gene tree nodes: "\r
+ + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
+ + "Number of polytomies in species tree used: " + poly + "\n",\r
+ "GSDI successfully completed",\r
+ JOptionPane.WARNING_MESSAGE );\r
}\r
- else if ( o == _graphics_export_visible_only_cbmi ) {\r
- updateOptions( getOptions() );\r
+ else {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
+ + "Potential duplications: "\r
+ + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
+ + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
+ + "Stripped gene tree nodes: "\r
+ + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
+ + "Number of polytomies in species tree used: " + poly + "\n",\r
+ "GSDI successfully completed",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
}\r
- else if ( o == _antialias_print_cbmi ) {\r
- updateOptions( getOptions() );\r
+ }\r
+\r
+ void executeGSDIR() {\r
+ if ( !isOKforSDI( false, false ) ) {\r
+ return;\r
}\r
- else if ( o == _print_black_and_white_cbmi ) {\r
- updateOptions( getOptions() );\r
+ final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );\r
+ if ( ( p > 0 )\r
+ && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Gene tree is not completely binary",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
}\r
- else if ( o == _print_using_actual_size_cbmi ) {\r
- updateOptions( getOptions() );\r
+ final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
+ gene_tree.setAllNodesToNotCollapse();\r
+ gene_tree.recalculateNumberOfExternalDescendants( false );\r
+ GSDIR gsdir = null;\r
+ final Phylogeny species_tree = getSpeciesTree().copy();\r
+ try {\r
+ gsdir = new GSDIR( gene_tree, species_tree, true, true, true );\r
}\r
- else if ( o == _graphics_export_using_actual_size_cbmi ) {\r
- updateOptions( getOptions() );\r
+ catch ( final SDIException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Error during GSDIR",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
}\r
- else if ( o == _print_size_mi ) {\r
- choosePrintSize();\r
+ catch ( final Exception e ) {\r
+ AptxUtil.unexpectedException( e );\r
+ return;\r
}\r
- else if ( o == _choose_pdf_width_mi ) {\r
- choosePdfWidth();\r
+ final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();\r
+ result_gene_tree.setRerootable( false );\r
+ result_gene_tree.clearHashIdToNodeMap();\r
+ result_gene_tree.recalculateNumberOfExternalDescendants( true );\r
+ PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );\r
+ _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );\r
+ getMainPanel().getControlPanel().setShowEvents( true );\r
+ showWhole();\r
+ final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
+ showWhole();\r
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
+ showWhole();\r
+ _mainpanel.getCurrentTreePanel().setEdited( true );\r
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
+ if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
+ + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
+ + "Stripped gene tree nodes: "\r
+ + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
+ + "Number of polytomies in species tree used: " + poly + "\n",\r
+ "GSDIR successfully completed",\r
+ JOptionPane.WARNING_MESSAGE );\r
}\r
else {\r
- if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
- for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
- if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {\r
- readPhylogeniesFromWebservice( i );\r
- }\r
- }\r
- }\r
+ JOptionPane.showMessageDialog( this,\r
+ "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
+ + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
+ + "Stripped gene tree nodes: "\r
+ + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
+ + "Number of polytomies in species tree used: " + poly + "\n",\r
+ "GSDIR successfully completed",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
}\r
- _contentpane.repaint();\r
}\r
\r
- void activateSaveAllIfNeeded() {\r
- if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {\r
- _save_all_item.setEnabled( true );\r
+ boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {\r
+ if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Gene tree and species tree have no species in common.",\r
+ "Error during SDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
+ }\r
+ else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Gene tree and species tree have only one species in common.",\r
+ "Error during SDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
}\r
else {\r
- _save_all_item.setEnabled( false );\r
+ return true;\r
}\r
}\r
\r
- private void annotateSequences() {\r
- if ( getCurrentTreePanel() != null ) {\r
- List<PhylogenyNode> nodes = null;\r
- if ( ( getCurrentTreePanel().getFoundNodes0() != null )\r
- || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
- nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
+ ControlPanel getControlPanel() {\r
+ return getMainPanel().getControlPanel();\r
+ }\r
+\r
+ File getCurrentDir() {\r
+ if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
+ if ( ForesterUtil.isWindows() ) {\r
+ try {\r
+ _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );\r
+ }\r
+ catch ( final Exception e ) {\r
+ _current_dir = null;\r
+ }\r
}\r
- if ( ( nodes == null ) || nodes.isEmpty() ) {\r
- JOptionPane\r
- .showMessageDialog( this,\r
- "Need to select nodes, either via direct selection or via the \"Search\" function",\r
- "No nodes selected for annotation",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ }\r
+ if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
+ if ( System.getProperty( "user.home" ) != null ) {\r
+ _current_dir = new File( System.getProperty( "user.home" ) );\r
}\r
- final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- final JTextField ref_field = new JTextField( 10 );\r
- final JTextField desc_filed = new JTextField( 20 );\r
- ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
- : getPreviousNodeAnnotationReference() );\r
- final JPanel my_panel = new JPanel();\r
- my_panel.add( new JLabel( "Reference " ) );\r
- my_panel.add( ref_field );\r
- my_panel.add( Box.createHorizontalStrut( 15 ) );\r
- my_panel.add( new JLabel( "Description " ) );\r
- my_panel.add( desc_filed );\r
- final int result = JOptionPane.showConfirmDialog( null,\r
- my_panel,\r
- "Enter the sequence annotation(s) for the "\r
- + nodes.size() + " selected nodes",\r
- JOptionPane.OK_CANCEL_OPTION );\r
- if ( result == JOptionPane.OK_OPTION ) {\r
- String ref = ref_field.getText();\r
- String desc = desc_filed.getText();\r
- if ( !ForesterUtil.isEmpty( ref ) ) {\r
- ref = ref.trim();\r
- ref = ref.replaceAll( "\\s+", " " );\r
- if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
- || ( ref.length() < 3 ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Reference needs to be in the form of \"GO:1234567\"",\r
- "Illegal Format for Annotation Reference",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- }\r
- if ( ref != null ) {\r
- setPreviousNodeAnnotationReference( ref );\r
- }\r
- if ( desc != null ) {\r
- desc = desc.trim();\r
- desc = desc.replaceAll( "\\s+", " " );\r
- }\r
- if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
- for( final PhylogenyNode n : nodes ) {\r
- ForesterUtil.ensurePresenceOfSequence( n );\r
- final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
- : new Annotation( ref );\r
- if ( !ForesterUtil.isEmpty( desc ) ) {\r
- ann.setDesc( desc );\r
- }\r
- n.getNodeData().getSequence().addAnnotation( ann );\r
- }\r
- }\r
- getMainPanel().getControlPanel().showAnnotations();\r
- }\r
+ else if ( System.getProperty( "user.dir" ) != null ) {\r
+ _current_dir = new File( System.getProperty( "user.dir" ) );\r
}\r
}\r
+ return _current_dir;\r
}\r
\r
- // void buildFileMenu() {\r
- // _file_jmenu = createMenu( "File", getConfiguration() );\r
- // _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
- // customizeJMenuItem( _exit_item );\r
- // _jmenubar.add( _file_jmenu );\r
- // }\r
- void buildFileMenu() {\r
- _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );\r
- _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );\r
- // _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );\r
- // _save_all_item.setToolTipText( "Write all phylogenies to one file." );\r
- // _save_all_item.setEnabled( false );\r
- // _file_jmenu.addSeparator();\r
- _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );\r
- // if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {\r
- // _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );\r
- // }\r
- _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );\r
- // _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );\r
- // if ( AptxUtil.canWriteFormat( "gif" ) ) {\r
- // _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );\r
- // }\r
- // if ( AptxUtil.canWriteFormat( "bmp" ) ) {\r
- // _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );\r
- // }\r
- // _file_jmenu.addSeparator();\r
- // _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
- customizeJMenuItem( _save_item );\r
- // customizeJMenuItem( _close_item );\r
- //customizeJMenuItem( _save_all_item );\r
- customizeJMenuItem( _write_to_pdf_item );\r
- customizeJMenuItem( _write_to_png_item );\r
- // customizeJMenuItem( _write_to_jpg_item );\r
- // customizeJMenuItem( _write_to_gif_item );\r
- // customizeJMenuItem( _write_to_tif_item );\r
- // customizeJMenuItem( _write_to_bmp_item );\r
- // customizeJMenuItem( _print_item );\r
- customizeJMenuItem( _exit_item );\r
- _jmenubar.add( _file_jmenu );\r
+ TreePanel getCurrentTreePanel() {\r
+ return getMainPanel().getCurrentTreePanel();\r
}\r
\r
- void buildFontSizeMenu() {\r
- _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );\r
- _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );\r
- _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );\r
- _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );\r
- _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );\r
- _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );\r
- customizeJMenuItem( _super_tiny_fonts_item );\r
- customizeJMenuItem( _tiny_fonts_item );\r
- customizeJMenuItem( _small_fonts_item );\r
- customizeJMenuItem( _medium_fonts_item );\r
- customizeJMenuItem( _large_fonts_item );\r
- _jmenubar.add( _font_size_menu );\r
+ JMenu getHelpMenu() {\r
+ return _help_jmenu;\r
}\r
\r
- void buildHelpMenu() {\r
- _help_jmenu = createMenu( "Help", getConfiguration() );\r
- _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );\r
- _help_jmenu.addSeparator();\r
- _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );\r
- _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...\r
- _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );\r
- _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );\r
- _help_jmenu.addSeparator();\r
- _help_jmenu.add( _about_item = new JMenuItem( "About" ) );\r
- customizeJMenuItem( _help_item );\r
- customizeJMenuItem( _website_item );\r
- customizeJMenuItem( _phyloxml_website_item );\r
- customizeJMenuItem( _aptx_ref_item );\r
- customizeJMenuItem( _phyloxml_ref_item );\r
- customizeJMenuItem( _about_item );\r
- _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );\r
- _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );\r
- _jmenubar.add( _help_jmenu );\r
+ JCheckBoxMenuItem getlabelDirectionCbmi() {\r
+ return _label_direction_cbmi;\r
}\r
\r
- void buildTypeMenu() {\r
- _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );\r
- _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );\r
- customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _triangular_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _euro_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _rounded_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _curved_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _convex_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _circular_type_cbmi, false );\r
- _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
- _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
- initializeTypeMenu( getOptions() );\r
- _jmenubar.add( _type_menu );\r
+ JMenuBar getMenuBarOfMainFrame() {\r
+ return _jmenubar;\r
}\r
\r
- void buildViewMenu() {\r
- _view_jmenu = createMenu( "View", getConfiguration() );\r
- _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );\r
- _view_jmenu.addSeparator();\r
- _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );\r
- _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );\r
- _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );\r
- customizeJMenuItem( _display_basic_information_item );\r
- customizeJMenuItem( _view_as_NH_item );\r
- customizeJMenuItem( _view_as_XML_item );\r
- customizeJMenuItem( _view_as_nexus_item );\r
- _jmenubar.add( _view_jmenu );\r
+ final Phylogeny getSpeciesTree() {\r
+ return _species_tree;\r
+ }\r
+\r
+ void initializeTypeMenu( final Options options ) {\r
+ setTypeMenuToAllUnselected();\r
+ switch ( options.getPhylogenyGraphicsType() ) {\r
+ case CONVEX:\r
+ _convex_type_cbmi.setSelected( true );\r
+ break;\r
+ case CURVED:\r
+ _curved_type_cbmi.setSelected( true );\r
+ break;\r
+ case EURO_STYLE:\r
+ _euro_type_cbmi.setSelected( true );\r
+ break;\r
+ case ROUNDED:\r
+ _rounded_type_cbmi.setSelected( true );\r
+ break;\r
+ case TRIANGULAR:\r
+ _triangular_type_cbmi.setSelected( true );\r
+ break;\r
+ case UNROOTED:\r
+ _unrooted_type_cbmi.setSelected( true );\r
+ break;\r
+ case CIRCULAR:\r
+ _circular_type_cbmi.setSelected( true );\r
+ break;\r
+ default:\r
+ _rectangular_type_cbmi.setSelected( true );\r
+ break;\r
+ }\r
+ }\r
+\r
+ boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ return false;\r
+ }\r
+ else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "No species tree loaded",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
+ }\r
+ else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Species tree is not completely binary",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
+ }\r
+ else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Gene tree is not completely binary",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
+ }\r
+ else {\r
+ return true;\r
+ }\r
}\r
\r
- void checkTextFrames() {\r
- if ( _textframes.size() > 5 ) {\r
- try {\r
- if ( _textframes.getFirst() != null ) {\r
- _textframes.getFirst().removeMe();\r
- }\r
- else {\r
- _textframes.removeFirst();\r
- }\r
- }\r
- catch ( final NoSuchElementException e ) {\r
- // Ignore.\r
+ boolean isSubtreeDisplayed() {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
+ "Operation can not be exectuted on a sub-tree",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ return true;\r
}\r
}\r
+ return false;\r
}\r
\r
- private void chooseFont() {\r
- final FontChooser fc = new FontChooser();\r
- fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
- fc.showDialog( this, "Select the Base Font" );\r
- getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
+ void midpointRoot() {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().midpointRoot();\r
+ }\r
}\r
\r
- private void chooseMinimalConfidence() {\r
- final String s = ( String ) JOptionPane\r
- .showInputDialog( this,\r
- "Please enter the minimum for confidence values to be displayed.\n"\r
- + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
- "Minimal Confidence Value",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getMinConfidenceValue() );\r
- if ( !ForesterUtil.isEmpty( s ) ) {\r
- boolean success = true;\r
- double m = 0.0;\r
- final String m_str = s.trim();\r
- if ( !ForesterUtil.isEmpty( m_str ) ) {\r
- try {\r
- m = Double.parseDouble( m_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
+ void printPhylogenyToPdf( final String file_name ) {\r
+ if ( !getOptions().isPrintUsingActualSize() ) {\r
+ getCurrentTreePanel()\r
+ .calcParametersForPainting( getOptions().getPrintSizeX(), getOptions().getPrintSizeY() );\r
+ getCurrentTreePanel().resetPreferredSize();\r
+ getCurrentTreePanel().repaint();\r
+ }\r
+ String pdf_written_to = "";\r
+ boolean error = false;\r
+ try {\r
+ if ( getOptions().isPrintUsingActualSize() ) {\r
+ pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,\r
+ getCurrentTreePanel(),\r
+ getCurrentTreePanel().getWidth(),\r
+ getCurrentTreePanel().getHeight() );\r
}\r
else {\r
- success = false;\r
- }\r
- if ( success && ( m >= 0.0 ) ) {\r
- getOptions().setMinConfidenceValue( m );\r
+ pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()\r
+ .getPrintSizeX(), getOptions().getPrintSizeY() );\r
}\r
}\r
- }\r
-\r
- void choosePdfWidth() {\r
- final String s = ( String ) JOptionPane.showInputDialog( this,\r
- "Please enter the default line width for PDF export.\n"\r
- + "[current value: "\r
- + getOptions().getPrintLineWidth() + "]\n",\r
- "Line Width for PDF Export",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getPrintLineWidth() );\r
- if ( !ForesterUtil.isEmpty( s ) ) {\r
- boolean success = true;\r
- float f = 0.0f;\r
- final String m_str = s.trim();\r
- if ( !ForesterUtil.isEmpty( m_str ) ) {\r
- try {\r
- f = Float.parseFloat( m_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
+ catch ( final IOException e ) {\r
+ error = true;\r
+ JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ if ( !error ) {\r
+ if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Wrote PDF to: " + pdf_written_to,\r
+ "Information",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
}\r
else {\r
- success = false;\r
- }\r
- if ( success && ( f > 0.0 ) ) {\r
- getOptions().setPrintLineWidth( f );\r
+ JOptionPane.showMessageDialog( this,\r
+ "There was an unknown problem when attempting to write to PDF file: \""\r
+ + file_name + "\"",\r
+ "Error",\r
+ JOptionPane.ERROR_MESSAGE );\r
}\r
}\r
+ if ( !getOptions().isPrintUsingActualSize() ) {\r
+ getControlPanel().showWhole();\r
+ }\r
}\r
\r
- void choosePrintSize() {\r
- final String s = ( String ) JOptionPane.showInputDialog( this,\r
- "Please enter values for width and height,\nseparated by a comma.\n"\r
- + "[current values: "\r
- + getOptions().getPrintSizeX() + ", "\r
- + getOptions().getPrintSizeY() + "]\n"\r
- + "[A4: " + Constants.A4_SIZE_X + ", "\r
- + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "\r
- + Constants.US_LETTER_SIZE_X + ", "\r
- + Constants.US_LETTER_SIZE_Y + "]",\r
- "Default Size for Graphics Export",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getPrintSizeX() + ", "\r
- + getOptions().getPrintSizeY() );\r
- if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {\r
- boolean success = true;\r
- int x = 0;\r
- int y = 0;\r
- final String[] str_ary = s.split( "," );\r
- if ( str_ary.length == 2 ) {\r
- final String x_str = str_ary[ 0 ].trim();\r
- final String y_str = str_ary[ 1 ].trim();\r
- if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {\r
- try {\r
- x = Integer.parseInt( x_str );\r
- y = Integer.parseInt( y_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( x > 1 ) && ( y > 1 ) ) {\r
- getOptions().setPrintSizeX( x );\r
- getOptions().setPrintSizeY( y );\r
+ void readPhylogeniesFromWebservice( final int i ) {\r
+ final UrlTreeReader reader = new UrlTreeReader( this, i );\r
+ new Thread( reader ).start();\r
+ }\r
+\r
+ void removeAllTextFrames() {\r
+ for( final TextFrame tf : _textframes ) {\r
+ if ( tf != null ) {\r
+ tf.close();\r
}\r
}\r
+ _textframes.clear();\r
}\r
\r
- void close() {\r
- removeAllTextFrames();\r
- if ( _mainpanel != null ) {\r
- _mainpanel.terminate();\r
- }\r
- if ( _contentpane != null ) {\r
- _contentpane.removeAll();\r
- }\r
- setVisible( false );\r
- dispose();\r
+ void resetSearch() {\r
+ getMainPanel().getCurrentTreePanel().setFoundNodes0( null );\r
+ getMainPanel().getCurrentTreePanel().setFoundNodes1( null );\r
+ getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );\r
+ getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );\r
+ getMainPanel().getControlPanel().getSearchTextField0().setText( "" );\r
+ getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );\r
+ getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );\r
+ getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );\r
+ getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );\r
+ getMainPanel().getControlPanel().getSearchTextField1().setText( "" );\r
+ getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );\r
+ getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );\r
}\r
\r
- void colorRank() {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- final String[] ranks = AptxUtil.getAllPossibleRanks();\r
- final String rank = ( String ) JOptionPane\r
- .showInputDialog( this,\r
- "What rank should the colorization be based on",\r
- "Rank Selection",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- ranks,\r
- null );\r
- if ( !ForesterUtil.isEmpty( rank ) ) {\r
- _mainpanel.getCurrentTreePanel().colorRank( rank );\r
- }\r
+ void setConfiguration( final Configuration configuration ) {\r
+ _configuration = configuration;\r
+ }\r
+\r
+ void setCurrentDir( final File current_dir ) {\r
+ _current_dir = current_dir;\r
+ }\r
+\r
+ void setInferenceManager( final InferenceManager i ) {\r
+ _inference_manager = i;\r
+ }\r
+\r
+ void setOptions( final Options options ) {\r
+ _options = options;\r
+ }\r
+\r
+ void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {\r
+ setTypeMenuToAllUnselected();\r
+ switch ( type ) {\r
+ case CIRCULAR:\r
+ _circular_type_cbmi.setSelected( true );\r
+ break;\r
+ case CONVEX:\r
+ _convex_type_cbmi.setSelected( true );\r
+ break;\r
+ case CURVED:\r
+ _curved_type_cbmi.setSelected( true );\r
+ break;\r
+ case EURO_STYLE:\r
+ _euro_type_cbmi.setSelected( true );\r
+ break;\r
+ case ROUNDED:\r
+ _rounded_type_cbmi.setSelected( true );\r
+ break;\r
+ case RECTANGULAR:\r
+ _rectangular_type_cbmi.setSelected( true );\r
+ break;\r
+ case TRIANGULAR:\r
+ _triangular_type_cbmi.setSelected( true );\r
+ break;\r
+ case UNROOTED:\r
+ _unrooted_type_cbmi.setSelected( true );\r
+ break;\r
+ default:\r
+ throw new IllegalArgumentException( "unknown type: " + type );\r
}\r
}\r
\r
- void confColor() {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().confColor();\r
- }\r
+ final void setSpeciesTree( final Phylogeny species_tree ) {\r
+ _species_tree = species_tree;\r
}\r
\r
- void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {\r
- if ( item != null ) {\r
- item.setFont( MainFrame.menu_font );\r
- if ( !getConfiguration().isUseNativeUI() ) {\r
- item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
- item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
- }\r
- item.setSelected( is_selected );\r
- item.addActionListener( this );\r
- }\r
+ void setTypeMenuToAllUnselected() {\r
+ _convex_type_cbmi.setSelected( false );\r
+ _curved_type_cbmi.setSelected( false );\r
+ _euro_type_cbmi.setSelected( false );\r
+ _rounded_type_cbmi.setSelected( false );\r
+ _triangular_type_cbmi.setSelected( false );\r
+ _rectangular_type_cbmi.setSelected( false );\r
+ _unrooted_type_cbmi.setSelected( false );\r
+ _circular_type_cbmi.setSelected( false );\r
}\r
\r
- JMenuItem customizeJMenuItem( final JMenuItem jmi ) {\r
- if ( jmi != null ) {\r
- jmi.setFont( MainFrame.menu_font );\r
- if ( !getConfiguration().isUseNativeUI() ) {\r
- jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
- jmi.setForeground( getConfiguration().getGuiMenuTextColor() );\r
- }\r
- jmi.addActionListener( this );\r
- }\r
- return jmi;\r
+ void switchColors() {\r
+ final TreeColorSet colorset = _mainpanel.getTreeColorSet();\r
+ final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );\r
+ csc.setVisible( true );\r
}\r
\r
- void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {\r
- if ( item != null ) {\r
- item.setFont( MainFrame.menu_font );\r
- if ( !getConfiguration().isUseNativeUI() ) {\r
- item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
- item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
- }\r
- item.setSelected( is_selected );\r
- item.addActionListener( this );\r
+ void taxColor() {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().taxColor();\r
}\r
}\r
\r
- private void deleteSelectedNodes( final boolean delete ) {\r
- final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
- if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {\r
- return;\r
- }\r
- final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
- if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
- final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
- for( final PhylogenyNode n : all_selected_nodes ) {\r
- if ( n.isExternal() ) {\r
- nodes.add( n );\r
- }\r
+ void typeChanged( final Object o ) {\r
+ updateTypeCheckboxes( getOptions(), o );\r
+ updateOptions( getOptions() );\r
+ if ( getCurrentTreePanel() != null ) {\r
+ final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();\r
+ final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();\r
+ if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
+ || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )\r
+ || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
+ || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {\r
+ getCurrentTreePanel().getControlPanel().showWhole();\r
}\r
- }\r
- String function = "Retain";\r
- if ( delete ) {\r
- function = "Delete";\r
- }\r
- if ( ( nodes == null ) || nodes.isEmpty() ) {\r
- JOptionPane\r
- .showMessageDialog( this,\r
- "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
- "No external nodes selected to " + function.toLowerCase(),\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- final int todo = nodes.size();\r
- final int ext = phy.getNumberOfExternalNodes();\r
- int res = todo;\r
- if ( delete ) {\r
- res = ext - todo;\r
- }\r
- if ( res < 1 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Cannot delete all nodes",\r
- "Attempt to delete all nodes ",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
- + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
- + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
- if ( result == JOptionPane.OK_OPTION ) {\r
- if ( !delete ) {\r
- final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
- for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
- final PhylogenyNode n = it.next();\r
- if ( !nodes.contains( n ) ) {\r
- to_delete.add( n );\r
- }\r
- }\r
- for( final PhylogenyNode n : to_delete ) {\r
- phy.deleteSubtree( n, true );\r
- }\r
+ if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
+ getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );\r
}\r
else {\r
- for( final PhylogenyNode n : nodes ) {\r
- phy.deleteSubtree( n, true );\r
- }\r
- }\r
- resetSearch();\r
- getCurrentTreePanel().setNodeInPreorderToNull();\r
- phy.externalNodesHaveChanged();\r
- phy.clearHashIdToNodeMap();\r
- phy.recalculateNumberOfExternalDescendants( true );\r
- getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
- getCurrentTreePanel().setEdited( true );\r
- repaint();\r
- }\r
- }\r
-\r
- void displayBasicInformation( final File treefile ) {\r
- if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
- String title = "Basic Information";\r
- if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
- title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";\r
- }\r
- showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );\r
- }\r
- }\r
-\r
- private void doUpdateProcessMenu() {\r
- if ( _process_pool.size() > 0 ) {\r
- if ( _process_menu == null ) {\r
- _process_menu = createMenu( "", getConfiguration() );\r
- _process_menu.setForeground( Color.RED );\r
- }\r
- _process_menu.removeAll();\r
- final String text = "processes running: " + _process_pool.size();\r
- _process_menu.setText( text );\r
- _jmenubar.add( _process_menu );\r
- for( int i = 0; i < _process_pool.size(); ++i ) {\r
- final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
- _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
+ getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );\r
}\r
- }\r
- else {\r
- if ( _process_menu != null ) {\r
- _process_menu.removeAll();\r
- _jmenubar.remove( _process_menu );\r
+ getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );\r
+ updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
+ if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {\r
+ if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {\r
+ getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );\r
+ }\r
+ else {\r
+ getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );\r
+ }\r
}\r
}\r
- _jmenubar.validate();\r
- _jmenubar.repaint();\r
- repaint();\r
- }\r
-\r
- void exceptionOccuredDuringOpenFile( final Exception e ) {\r
- try {\r
- _mainpanel.getCurrentTreePanel().setArrowCursor();\r
- }\r
- catch ( final Exception ex ) {\r
- // Do nothing.\r
- }\r
- JOptionPane.showMessageDialog( this,\r
- ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
- "Error during File|Open",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
-\r
- void exceptionOccuredDuringSaveAs( final Exception e ) {\r
- try {\r
- _mainpanel.getCurrentTreePanel().setArrowCursor();\r
- }\r
- catch ( final Exception ex ) {\r
- // Do nothing.\r
- }\r
- JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );\r
}\r
\r
- void executeGSDI() {\r
- if ( !isOKforSDI( false, true ) ) {\r
- return;\r
- }\r
- if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Gene tree is not rooted.",\r
- "Cannot execute GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
- gene_tree.setAllNodesToNotCollapse();\r
- gene_tree.recalculateNumberOfExternalDescendants( false );\r
- GSDI gsdi = null;\r
- final Phylogeny species_tree = getSpeciesTree().copy();\r
- try {\r
- gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );\r
- }\r
- catch ( final SDIException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Error during GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final Exception e ) {\r
- AptxUtil.unexpectedException( e );\r
- return;\r
- }\r
- gene_tree.setRerootable( false );\r
- gene_tree.clearHashIdToNodeMap();\r
- gene_tree.recalculateNumberOfExternalDescendants( true );\r
- _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );\r
- getMainPanel().getControlPanel().setShowEvents( true );\r
- showWhole();\r
- final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
- _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
- showWhole();\r
- _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
- showWhole();\r
- _mainpanel.getCurrentTreePanel().setEdited( true );\r
- final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
- if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
- + "Potential duplications: "\r
- + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
- + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
- + "Stripped gene tree nodes: "\r
- + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
- + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
- + "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDI successfully completed",\r
- JOptionPane.WARNING_MESSAGE );\r
+ void updateOptions( final Options options ) {\r
+ options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
+ options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
+ && _background_gradient_cbmi.isSelected() );\r
+ options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
+ options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
+ && _show_annotation_ref_source.isSelected() );\r
+ options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
+ && _abbreviate_scientific_names.isSelected() );\r
+ options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
+ && _color_labels_same_as_parent_branch.isSelected() );\r
+ options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
+ && _show_default_node_shapes_internal_cbmi.isSelected() );\r
+ options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
+ && _show_default_node_shapes_external_cbmi.isSelected() );\r
+ options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )\r
+ && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
+ if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
+ options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
}\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
- + "Potential duplications: "\r
- + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
- + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
- + "Stripped gene tree nodes: "\r
- + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
- + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
- + "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDI successfully completed",\r
- JOptionPane.INFORMATION_MESSAGE );\r
+ else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {\r
+ options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
}\r
- }\r
-\r
- void executeGSDIR() {\r
- if ( !isOKforSDI( false, false ) ) {\r
- return;\r
+ else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {\r
+ options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
}\r
- final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );\r
- if ( ( p > 0 )\r
- && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Gene tree is not completely binary",\r
- "Cannot execute GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
+ && _search_case_senstive_cbmi.isSelected() );\r
+ if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
+ options.setShowScale( _show_scale_cbmi.isSelected() );\r
}\r
- final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
- gene_tree.setAllNodesToNotCollapse();\r
- gene_tree.recalculateNumberOfExternalDescendants( false );\r
- GSDIR gsdir = null;\r
- final Phylogeny species_tree = getSpeciesTree().copy();\r
- try {\r
- gsdir = new GSDIR( gene_tree, species_tree, true, true, true );\r
+ if ( _label_direction_cbmi != null ) {\r
+ if ( _label_direction_cbmi.isSelected() ) {\r
+ options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );\r
+ }\r
+ else {\r
+ options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );\r
+ }\r
}\r
- catch ( final SDIException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Error during GSDIR",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
+ options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
+ && _show_confidence_stddev_cbmi.isSelected() );\r
+ if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
+ options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
}\r
- catch ( final Exception e ) {\r
- AptxUtil.unexpectedException( e );\r
- return;\r
+ options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
+ && ( _print_using_actual_size_cbmi.isSelected() ) );\r
+ options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
+ && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
+ options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
+ if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
+ && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
}\r
- final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();\r
- result_gene_tree.setRerootable( false );\r
- result_gene_tree.clearHashIdToNodeMap();\r
- result_gene_tree.recalculateNumberOfExternalDescendants( true );\r
- PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );\r
- _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );\r
- getMainPanel().getControlPanel().setShowEvents( true );\r
- showWhole();\r
- final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
- _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
- showWhole();\r
- _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
- showWhole();\r
- _mainpanel.getCurrentTreePanel().setEdited( true );\r
- final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
- if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
- + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
- + "Stripped gene tree nodes: "\r
- + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
- + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
- + "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDIR successfully completed",\r
- JOptionPane.WARNING_MESSAGE );\r
+ else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )\r
+ && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
}\r
else {\r
- JOptionPane.showMessageDialog( this,\r
- "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
- + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
- + "Stripped gene tree nodes: "\r
- + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
- + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
- + "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDIR successfully completed",\r
- JOptionPane.INFORMATION_MESSAGE );\r
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
}\r
- }\r
-\r
- boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {\r
- if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Gene tree and species tree have no species in common.",\r
- "Error during SDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return false;\r
+ options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
+ && _print_black_and_white_cbmi.isSelected() );\r
+ options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
+ && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
+ if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
}\r
- else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Gene tree and species tree have only one species in common.",\r
- "Error during SDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return false;\r
+ else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {\r
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
}\r
- else {\r
- return true;\r
+ else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {\r
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );\r
}\r
- }\r
-\r
- public Configuration getConfiguration() {\r
- return _configuration;\r
- }\r
-\r
- ControlPanel getControlPanel() {\r
- return getMainPanel().getControlPanel();\r
- }\r
-\r
- File getCurrentDir() {\r
- if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
- if ( ForesterUtil.isWindows() ) {\r
- try {\r
- _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );\r
- }\r
- catch ( final Exception e ) {\r
- _current_dir = null;\r
- }\r
- }\r
+ else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {\r
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
}\r
- if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
- if ( System.getProperty( "user.home" ) != null ) {\r
- _current_dir = new File( System.getProperty( "user.home" ) );\r
+ options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
+ && _replace_underscores_cbmi.isSelected() );\r
+ options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
+ && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
+ options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
+ && _search_whole_words_only_cbmi.isSelected() );\r
+ options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );\r
+ options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
+ && _inverse_search_result_cbmi.isSelected() );\r
+ if ( _graphics_export_visible_only_cbmi != null ) {\r
+ options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
+ if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
+ _graphics_export_using_actual_size_cbmi.setSelected( true );\r
+ _graphics_export_using_actual_size_cbmi.setEnabled( false );\r
}\r
- else if ( System.getProperty( "user.dir" ) != null ) {\r
- _current_dir = new File( System.getProperty( "user.dir" ) );\r
+ else {\r
+ _graphics_export_using_actual_size_cbmi.setEnabled( true );\r
}\r
}\r
- return _current_dir;\r
- }\r
-\r
- /**\r
- * This method returns the current external node data which\r
- * has been selected by the user by clicking the "Return ..."\r
- * menu item. This method is expected to be called from Javascript or\r
- * something like it.\r
- *\r
- * @return current external node data as String\r
- */\r
- public String getCurrentExternalNodesDataBuffer() {\r
- return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();\r
- }\r
-\r
- public int getCurrentExternalNodesDataBufferChangeCounter() {\r
- return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();\r
- }\r
-\r
- public int getCurrentExternalNodesDataBufferLength() {\r
- return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();\r
- }\r
-\r
- TreePanel getCurrentTreePanel() {\r
- return getMainPanel().getCurrentTreePanel();\r
- }\r
-\r
- JMenu getHelpMenu() {\r
- return _help_jmenu;\r
- }\r
-\r
- public InferenceManager getInferenceManager() {\r
- return _inference_manager;\r
+ if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
+ }\r
+ else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );\r
+ }\r
+ else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );\r
+ }\r
+ else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );\r
+ }\r
+ else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );\r
+ }\r
+ else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );\r
+ }\r
+ else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );\r
+ }\r
+ else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );\r
+ }\r
+ if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {\r
+ options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );\r
+ }\r
+ if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {\r
+ options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );\r
+ }\r
}\r
\r
- JCheckBoxMenuItem getlabelDirectionCbmi() {\r
- return _label_direction_cbmi;\r
+ void updateTypeCheckboxes( final Options options, final Object o ) {\r
+ setTypeMenuToAllUnselected();\r
+ ( ( JCheckBoxMenuItem ) o ).setSelected( true );\r
}\r
\r
- public MainPanel getMainPanel() {\r
- return _mainpanel;\r
+ void viewAsNexus() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ String title = "Nexus";\r
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+ }\r
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),\r
+ title );\r
+ }\r
}\r
\r
- JMenuBar getMenuBarOfMainFrame() {\r
- return _jmenubar;\r
+ void viewAsNH() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ String title = "New Hampshire";\r
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+ }\r
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
+ .getNhConversionSupportValueStyle() ),\r
+ title );\r
+ }\r
}\r
\r
- public Options getOptions() {\r
- return _options;\r
+ void viewAsXML() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ String title = "phyloXML";\r
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+ }\r
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );\r
+ }\r
}\r
\r
- private String getPreviousNodeAnnotationReference() {\r
- return _previous_node_annotation_ref;\r
+ boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {\r
+ try {\r
+ final PhylogenyWriter writer = new PhylogenyWriter();\r
+ writer.toNewHampshire( t, true, getOptions().getNhConversionSupportValueStyle(), file );\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringSaveAs( e );\r
+ }\r
+ return exception;\r
}\r
\r
- public ProcessPool getProcessPool() {\r
- return _process_pool;\r
+ boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {\r
+ try {\r
+ final PhylogenyWriter writer = new PhylogenyWriter();\r
+ writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringSaveAs( e );\r
+ }\r
+ return exception;\r
}\r
\r
- final Phylogeny getSpeciesTree() {\r
- return _species_tree;\r
+ boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {\r
+ try {\r
+ final PhylogenyWriter writer = new PhylogenyWriter();\r
+ writer.toPhyloXML( file, t, 0 );\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringSaveAs( e );\r
+ }\r
+ return exception;\r
}\r
\r
- void initializeTypeMenu( final Options options ) {\r
- setTypeMenuToAllUnselected();\r
- switch ( options.getPhylogenyGraphicsType() ) {\r
- case CONVEX:\r
- _convex_type_cbmi.setSelected( true );\r
- break;\r
- case CURVED:\r
- _curved_type_cbmi.setSelected( true );\r
- break;\r
- case EURO_STYLE:\r
- _euro_type_cbmi.setSelected( true );\r
- break;\r
- case ROUNDED:\r
- _rounded_type_cbmi.setSelected( true );\r
- break;\r
- case TRIANGULAR:\r
- _triangular_type_cbmi.setSelected( true );\r
- break;\r
- case UNROOTED:\r
- _unrooted_type_cbmi.setSelected( true );\r
- break;\r
- case CIRCULAR:\r
- _circular_type_cbmi.setSelected( true );\r
- break;\r
- default:\r
- _rectangular_type_cbmi.setSelected( true );\r
- break;\r
+ void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {\r
+ _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),\r
+ _mainpanel.getCurrentTreePanel().getHeight() );\r
+ String file_written_to = "";\r
+ boolean error = false;\r
+ try {\r
+ file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,\r
+ _mainpanel.getCurrentTreePanel().getWidth(),\r
+ _mainpanel.getCurrentTreePanel().getHeight(),\r
+ _mainpanel.getCurrentTreePanel(),\r
+ _mainpanel.getControlPanel(),\r
+ type,\r
+ getOptions() );\r
+ }\r
+ catch ( final IOException e ) {\r
+ error = true;\r
+ JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ if ( !error ) {\r
+ if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Wrote image to: " + file_written_to,\r
+ "Graphics Export",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this,\r
+ "There was an unknown problem when attempting to write to an image file: \""\r
+ + file_name + "\"",\r
+ "Error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
}\r
+ _contentpane.repaint();\r
}\r
\r
- boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {\r
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
- return false;\r
- }\r
- else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "No species tree loaded",\r
- "Cannot execute GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return false;\r
+ void writeToFile( final Phylogeny t ) {\r
+ if ( t == null ) {\r
+ return;\r
}\r
- else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Species tree is not completely binary",\r
- "Cannot execute GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return false;\r
+ String initial_filename = null;\r
+ if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
+ try {\r
+ initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();\r
+ }\r
+ catch ( final IOException e ) {\r
+ initial_filename = null;\r
+ }\r
}\r
- else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Gene tree is not completely binary",\r
- "Cannot execute GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return false;\r
+ if ( !ForesterUtil.isEmpty( initial_filename ) ) {\r
+ _save_filechooser.setSelectedFile( new File( initial_filename ) );\r
}\r
else {\r
- return true;\r
+ _save_filechooser.setSelectedFile( new File( "" ) );\r
+ }\r
+ final File my_dir = getCurrentDir();\r
+ if ( my_dir != null ) {\r
+ _save_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _save_filechooser.showSaveDialog( _contentpane );\r
+ final File file = _save_filechooser.getSelectedFile();\r
+ setCurrentDir( _save_filechooser.getCurrentDirectory() );\r
+ boolean exception = false;\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( file.exists() ) {\r
+ final int i = JOptionPane.showConfirmDialog( this,\r
+ file + " already exists.\nOverwrite?",\r
+ "Overwrite?",\r
+ JOptionPane.OK_CANCEL_OPTION,\r
+ JOptionPane.QUESTION_MESSAGE );\r
+ if ( i != JOptionPane.OK_OPTION ) {\r
+ return;\r
+ }\r
+ else {\r
+ final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );\r
+ try {\r
+ ForesterUtil.copyFile( file, to );\r
+ }\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Failed to create backup copy " + to,\r
+ "Failed to Create Backup Copy",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ try {\r
+ file.delete();\r
+ }\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Failed to delete: " + file,\r
+ "Failed to Delete",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
+ }\r
+ if ( _save_filechooser.getFileFilter() == MainFrame.nhfilter ) {\r
+ exception = writeAsNewHampshire( t, exception, file );\r
+ }\r
+ else if ( _save_filechooser.getFileFilter() == MainFrame.xmlfilter ) {\r
+ exception = writeAsPhyloXml( t, exception, file );\r
+ }\r
+ else if ( _save_filechooser.getFileFilter() == MainFrame.nexusfilter ) {\r
+ exception = writeAsNexus( t, exception, file );\r
+ }\r
+ // "*.*":\r
+ else {\r
+ final String file_name = file.getName().trim().toLowerCase();\r
+ if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
+ || file_name.endsWith( ".tree" ) ) {\r
+ exception = writeAsNewHampshire( t, exception, file );\r
+ }\r
+ else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {\r
+ exception = writeAsNexus( t, exception, file );\r
+ }\r
+ // XML is default:\r
+ else {\r
+ exception = writeAsPhyloXml( t, exception, file );\r
+ }\r
+ }\r
+ if ( !exception ) {\r
+ getMainPanel().setTitleOfSelectedTab( file.getName() );\r
+ getMainPanel().getCurrentTreePanel().setTreeFile( file );\r
+ getMainPanel().getCurrentTreePanel().setEdited( false );\r
+ }\r
}\r
}\r
\r
- boolean isSubtreeDisplayed() {\r
- if ( getCurrentTreePanel() != null ) {\r
- if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
- JOptionPane\r
- .showMessageDialog( this,\r
- "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
- "Operation can not be exectuted on a sub-tree",\r
- JOptionPane.WARNING_MESSAGE );\r
- return true;\r
+ void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {\r
+ if ( ( t == null ) || t.isEmpty() ) {\r
+ return;\r
+ }\r
+ String initial_filename = "";\r
+ if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
+ initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();\r
+ }\r
+ if ( initial_filename.indexOf( '.' ) > 0 ) {\r
+ initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
+ }\r
+ initial_filename = initial_filename + "." + type;\r
+ _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );\r
+ final File my_dir = getCurrentDir();\r
+ if ( my_dir != null ) {\r
+ _writetographics_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _writetographics_filechooser.showSaveDialog( _contentpane );\r
+ File file = _writetographics_filechooser.getSelectedFile();\r
+ setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {\r
+ file = new File( file.toString() + "." + type );\r
+ }\r
+ if ( file.exists() ) {\r
+ final int i = JOptionPane.showConfirmDialog( this,\r
+ file + " already exists. Overwrite?",\r
+ "Warning",\r
+ JOptionPane.OK_CANCEL_OPTION,\r
+ JOptionPane.WARNING_MESSAGE );\r
+ if ( i != JOptionPane.OK_OPTION ) {\r
+ return;\r
+ }\r
+ else {\r
+ try {\r
+ file.delete();\r
+ }\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Failed to delete: " + file,\r
+ "Error",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
}\r
+ writePhylogenyToGraphicsFile( file.toString(), type );\r
}\r
- return false;\r
}\r
\r
- void midpointRoot() {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().midpointRoot();\r
+ void writeToPdf( final Phylogeny t ) {\r
+ if ( ( t == null ) || t.isEmpty() ) {\r
+ return;\r
}\r
- }\r
-\r
- void printPhylogenyToPdf( final String file_name ) {\r
- if ( !getOptions().isPrintUsingActualSize() ) {\r
- getCurrentTreePanel()\r
- .calcParametersForPainting( getOptions().getPrintSizeX(), getOptions().getPrintSizeY() );\r
- getCurrentTreePanel().resetPreferredSize();\r
- getCurrentTreePanel().repaint();\r
+ String initial_filename = "";\r
+ if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
+ initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();\r
}\r
- String pdf_written_to = "";\r
- boolean error = false;\r
- try {\r
- if ( getOptions().isPrintUsingActualSize() ) {\r
- pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,\r
- getCurrentTreePanel(),\r
- getCurrentTreePanel().getWidth(),\r
- getCurrentTreePanel().getHeight() );\r
- }\r
- else {\r
- pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()\r
- .getPrintSizeX(), getOptions().getPrintSizeY() );\r
- }\r
+ if ( initial_filename.indexOf( '.' ) > 0 ) {\r
+ initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
}\r
- catch ( final IOException e ) {\r
- error = true;\r
- JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
+ initial_filename = initial_filename + ".pdf";\r
+ _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );\r
+ final File my_dir = getCurrentDir();\r
+ if ( my_dir != null ) {\r
+ _writetopdf_filechooser.setCurrentDirectory( my_dir );\r
}\r
- if ( !error ) {\r
- if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Wrote PDF to: " + pdf_written_to,\r
- "Information",\r
- JOptionPane.INFORMATION_MESSAGE );\r
+ final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );\r
+ File file = _writetopdf_filechooser.getSelectedFile();\r
+ setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {\r
+ file = new File( file.toString() + ".pdf" );\r
}\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "There was an unknown problem when attempting to write to PDF file: \""\r
- + file_name + "\"",\r
- "Error",\r
- JOptionPane.ERROR_MESSAGE );\r
+ if ( file.exists() ) {\r
+ final int i = JOptionPane.showConfirmDialog( this,\r
+ file + " already exists. Overwrite?",\r
+ "WARNING",\r
+ JOptionPane.OK_CANCEL_OPTION,\r
+ JOptionPane.WARNING_MESSAGE );\r
+ if ( i != JOptionPane.OK_OPTION ) {\r
+ return;\r
+ }\r
}\r
+ printPhylogenyToPdf( file.toString() );\r
}\r
- if ( !getOptions().isPrintUsingActualSize() ) {\r
- getControlPanel().showWhole();\r
- }\r
- }\r
-\r
- void readPhylogeniesFromWebservice( final int i ) {\r
- final UrlTreeReader reader = new UrlTreeReader( this, i );\r
- new Thread( reader ).start();\r
}\r
\r
- void removeAllTextFrames() {\r
- for( final TextFrame tf : _textframes ) {\r
- if ( tf != null ) {\r
- tf.close();\r
+ private void annotateSequences() {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ List<PhylogenyNode> nodes = null;\r
+ if ( ( getCurrentTreePanel().getFoundNodes0() != null )\r
+ || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
+ nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
+ }\r
+ if ( ( nodes == null ) || nodes.isEmpty() ) {\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ "Need to select nodes, either via direct selection or via the \"Search\" function",\r
+ "No nodes selected for annotation",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ final JTextField ref_field = new JTextField( 10 );\r
+ final JTextField desc_filed = new JTextField( 20 );\r
+ ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
+ : getPreviousNodeAnnotationReference() );\r
+ final JPanel my_panel = new JPanel();\r
+ my_panel.add( new JLabel( "Reference " ) );\r
+ my_panel.add( ref_field );\r
+ my_panel.add( Box.createHorizontalStrut( 15 ) );\r
+ my_panel.add( new JLabel( "Description " ) );\r
+ my_panel.add( desc_filed );\r
+ final int result = JOptionPane.showConfirmDialog( null,\r
+ my_panel,\r
+ "Enter the sequence annotation(s) for the "\r
+ + nodes.size() + " selected nodes",\r
+ JOptionPane.OK_CANCEL_OPTION );\r
+ if ( result == JOptionPane.OK_OPTION ) {\r
+ String ref = ref_field.getText();\r
+ String desc = desc_filed.getText();\r
+ if ( !ForesterUtil.isEmpty( ref ) ) {\r
+ ref = ref.trim();\r
+ ref = ref.replaceAll( "\\s+", " " );\r
+ if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
+ || ( ref.length() < 3 ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Reference needs to be in the form of \"GO:1234567\"",\r
+ "Illegal Format for Annotation Reference",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ }\r
+ if ( ref != null ) {\r
+ setPreviousNodeAnnotationReference( ref );\r
+ }\r
+ if ( desc != null ) {\r
+ desc = desc.trim();\r
+ desc = desc.replaceAll( "\\s+", " " );\r
+ }\r
+ if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
+ for( final PhylogenyNode n : nodes ) {\r
+ ForesterUtil.ensurePresenceOfSequence( n );\r
+ final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
+ : new Annotation( ref );\r
+ if ( !ForesterUtil.isEmpty( desc ) ) {\r
+ ann.setDesc( desc );\r
+ }\r
+ n.getNodeData().getSequence().addAnnotation( ann );\r
+ }\r
+ }\r
+ getMainPanel().getControlPanel().showAnnotations();\r
+ }\r
}\r
}\r
- _textframes.clear();\r
- }\r
-\r
- private void removeBranchColors() {\r
- if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
- AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
- }\r
- }\r
-\r
- private void removeVisualStyles() {\r
- if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
- AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
- }\r
- }\r
-\r
- void resetSearch() {\r
- getMainPanel().getCurrentTreePanel().setFoundNodes0( null );\r
- getMainPanel().getCurrentTreePanel().setFoundNodes1( null );\r
- getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );\r
- getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );\r
- getMainPanel().getControlPanel().getSearchTextField0().setText( "" );\r
- getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );\r
- getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );\r
- getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );\r
- getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );\r
- getMainPanel().getControlPanel().getSearchTextField1().setText( "" );\r
- getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );\r
- getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );\r
- }\r
-\r
- void setConfiguration( final Configuration configuration ) {\r
- _configuration = configuration;\r
- }\r
-\r
- void setCurrentDir( final File current_dir ) {\r
- _current_dir = current_dir;\r
- }\r
-\r
- void setInferenceManager( final InferenceManager i ) {\r
- _inference_manager = i;\r
- }\r
-\r
- void setOptions( final Options options ) {\r
- _options = options;\r
- }\r
-\r
- private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
- _previous_node_annotation_ref = previous_node_annotation_ref;\r
- }\r
-\r
- void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {\r
- setTypeMenuToAllUnselected();\r
- switch ( type ) {\r
- case CIRCULAR:\r
- _circular_type_cbmi.setSelected( true );\r
- break;\r
- case CONVEX:\r
- _convex_type_cbmi.setSelected( true );\r
- break;\r
- case CURVED:\r
- _curved_type_cbmi.setSelected( true );\r
- break;\r
- case EURO_STYLE:\r
- _euro_type_cbmi.setSelected( true );\r
- break;\r
- case ROUNDED:\r
- _rounded_type_cbmi.setSelected( true );\r
- break;\r
- case RECTANGULAR:\r
- _rectangular_type_cbmi.setSelected( true );\r
- break;\r
- case TRIANGULAR:\r
- _triangular_type_cbmi.setSelected( true );\r
- break;\r
- case UNROOTED:\r
- _unrooted_type_cbmi.setSelected( true );\r
- break;\r
- default:\r
- throw new IllegalArgumentException( "unknown type: " + type );\r
- }\r
- }\r
-\r
- final void setSpeciesTree( final Phylogeny species_tree ) {\r
- _species_tree = species_tree;\r
- }\r
-\r
- void setTypeMenuToAllUnselected() {\r
- _convex_type_cbmi.setSelected( false );\r
- _curved_type_cbmi.setSelected( false );\r
- _euro_type_cbmi.setSelected( false );\r
- _rounded_type_cbmi.setSelected( false );\r
- _triangular_type_cbmi.setSelected( false );\r
- _rectangular_type_cbmi.setSelected( false );\r
- _unrooted_type_cbmi.setSelected( false );\r
- _circular_type_cbmi.setSelected( false );\r
- }\r
-\r
- public void showTextFrame( final String s, final String title ) {\r
- checkTextFrames();\r
- _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );\r
- }\r
-\r
- public void showWhole() {\r
- _mainpanel.getControlPanel().showWhole();\r
- }\r
-\r
- void switchColors() {\r
- final TreeColorSet colorset = _mainpanel.getTreeColorSet();\r
- final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );\r
- csc.setVisible( true );\r
}\r
\r
- void taxColor() {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().taxColor();\r
- }\r
+ private void chooseFont() {\r
+ final FontChooser fc = new FontChooser();\r
+ fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
+ fc.showDialog( this, "Select the Base Font" );\r
+ getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
}\r
\r
- void typeChanged( final Object o ) {\r
- updateTypeCheckboxes( getOptions(), o );\r
- updateOptions( getOptions() );\r
- if ( getCurrentTreePanel() != null ) {\r
- final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();\r
- final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();\r
- if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
- || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )\r
- || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
- || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {\r
- getCurrentTreePanel().getControlPanel().showWhole();\r
- }\r
- if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
- getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );\r
+ private void chooseMinimalConfidence() {\r
+ final String s = ( String ) JOptionPane\r
+ .showInputDialog( this,\r
+ "Please enter the minimum for confidence values to be displayed.\n"\r
+ + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
+ "Minimal Confidence Value",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getMinConfidenceValue() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ double m = 0.0;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+ try {\r
+ m = Double.parseDouble( m_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
}\r
else {\r
- getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );\r
+ success = false;\r
}\r
- getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );\r
- updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
- if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {\r
- if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {\r
- getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );\r
- }\r
- else {\r
- getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );\r
- }\r
+ if ( success && ( m >= 0.0 ) ) {\r
+ getOptions().setMinConfidenceValue( m );\r
}\r
}\r
}\r
\r
- void updateOptions( final Options options ) {\r
- options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
- options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
- && _background_gradient_cbmi.isSelected() );\r
- options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
- options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
- && _show_annotation_ref_source.isSelected() );\r
- options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
- && _abbreviate_scientific_names.isSelected() );\r
- options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
- && _color_labels_same_as_parent_branch.isSelected() );\r
- options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
- && _show_default_node_shapes_internal_cbmi.isSelected() );\r
- options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
- && _show_default_node_shapes_external_cbmi.isSelected() );\r
- options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )\r
- && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
- if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
- options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
+ private void deleteSelectedNodes( final boolean delete ) {\r
+ final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
+ if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {\r
+ return;\r
}\r
- else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {\r
- options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
+ final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
+ if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
+ final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
+ for( final PhylogenyNode n : all_selected_nodes ) {\r
+ if ( n.isExternal() ) {\r
+ nodes.add( n );\r
+ }\r
+ }\r
}\r
- else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {\r
- options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
+ String function = "Retain";\r
+ if ( delete ) {\r
+ function = "Delete";\r
}\r
- options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
- && _search_case_senstive_cbmi.isSelected() );\r
- if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
- options.setShowScale( _show_scale_cbmi.isSelected() );\r
+ if ( ( nodes == null ) || nodes.isEmpty() ) {\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
+ "No external nodes selected to " + function.toLowerCase(),\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
}\r
- if ( _label_direction_cbmi != null ) {\r
- if ( _label_direction_cbmi.isSelected() ) {\r
- options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );\r
+ final int todo = nodes.size();\r
+ final int ext = phy.getNumberOfExternalNodes();\r
+ int res = todo;\r
+ if ( delete ) {\r
+ res = ext - todo;\r
+ }\r
+ if ( res < 1 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Cannot delete all nodes",\r
+ "Attempt to delete all nodes ",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
+ + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
+ + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
+ if ( result == JOptionPane.OK_OPTION ) {\r
+ if ( !delete ) {\r
+ final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
+ for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !nodes.contains( n ) ) {\r
+ to_delete.add( n );\r
+ }\r
+ }\r
+ for( final PhylogenyNode n : to_delete ) {\r
+ phy.deleteSubtree( n, true );\r
+ }\r
}\r
else {\r
- options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );\r
+ for( final PhylogenyNode n : nodes ) {\r
+ phy.deleteSubtree( n, true );\r
+ }\r
}\r
+ resetSearch();\r
+ getCurrentTreePanel().setNodeInPreorderToNull();\r
+ phy.externalNodesHaveChanged();\r
+ phy.clearHashIdToNodeMap();\r
+ phy.recalculateNumberOfExternalDescendants( true );\r
+ getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
+ getCurrentTreePanel().setEdited( true );\r
+ repaint();\r
}\r
- options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
- options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
- && _show_confidence_stddev_cbmi.isSelected() );\r
- if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
- options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
- }\r
- options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
- && ( _print_using_actual_size_cbmi.isSelected() ) );\r
- options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
- && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
- options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
- if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
- && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
- options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
- }\r
- else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )\r
- && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
- options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
+ }\r
+\r
+ private void doUpdateProcessMenu() {\r
+ if ( _process_pool.size() > 0 ) {\r
+ if ( _process_menu == null ) {\r
+ _process_menu = createMenu( "", getConfiguration() );\r
+ _process_menu.setForeground( Color.RED );\r
+ }\r
+ _process_menu.removeAll();\r
+ final String text = "processes running: " + _process_pool.size();\r
+ _process_menu.setText( text );\r
+ _jmenubar.add( _process_menu );\r
+ for( int i = 0; i < _process_pool.size(); ++i ) {\r
+ final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
+ _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
+ }\r
}\r
else {\r
- options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
+ if ( _process_menu != null ) {\r
+ _process_menu.removeAll();\r
+ _jmenubar.remove( _process_menu );\r
+ }\r
}\r
- options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
- && _print_black_and_white_cbmi.isSelected() );\r
- options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
- && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
- if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
- options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
+ _jmenubar.validate();\r
+ _jmenubar.repaint();\r
+ repaint();\r
+ }\r
+\r
+ private String getPreviousNodeAnnotationReference() {\r
+ return _previous_node_annotation_ref;\r
+ }\r
+\r
+ static void print( final TreePanel tp,\r
+ final Options op,\r
+ \r
+ final Component c\r
+ ) {\r
+ if ( ( tp == null ) || ( tp.getPhylogeny() == null )\r
+ || tp.getPhylogeny().isEmpty() ) {\r
+ return;\r
}\r
- else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {\r
- options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
+ if ( !op.isPrintUsingActualSize() ) {\r
+ tp.calcParametersForPainting( op.getPrintSizeX() - 80,\r
+ op.getPrintSizeY() - 140 );\r
+ tp.resetPreferredSize();\r
+ tp.repaint();\r
}\r
- else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {\r
- options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );\r
+ final String job_name = Constants.PRG_NAME;\r
+ boolean error = false;\r
+ String printer_name = null;\r
+ try {\r
+ printer_name = Printer.print( tp, job_name );\r
}\r
- else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {\r
- options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
+ catch ( final Exception e ) {\r
+ error = true;\r
+ JOptionPane.showMessageDialog( c, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );\r
}\r
- options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
- && _replace_underscores_cbmi.isSelected() );\r
- options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
- && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
- options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
- && _search_whole_words_only_cbmi.isSelected() );\r
- options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );\r
- options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
- && _inverse_search_result_cbmi.isSelected() );\r
- if ( _graphics_export_visible_only_cbmi != null ) {\r
- options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
- if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
- _graphics_export_using_actual_size_cbmi.setSelected( true );\r
- _graphics_export_using_actual_size_cbmi.setEnabled( false );\r
- }\r
- else {\r
- _graphics_export_using_actual_size_cbmi.setEnabled( true );\r
+ if ( !error && ( printer_name != null ) ) {\r
+ String msg = "Printing data sent to printer";\r
+ if ( printer_name.length() > 1 ) {\r
+ msg += " [" + printer_name + "]";\r
}\r
+ JOptionPane.showMessageDialog( c, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );\r
}\r
- if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
- }\r
- else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );\r
- }\r
- else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );\r
+ if ( !op.isPrintUsingActualSize() ) {\r
+ tp.getControlPanel().showWhole();\r
}\r
- else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );\r
+ }\r
+\r
+ private void removeBranchColors() {\r
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
+ AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
}\r
- else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );\r
+ }\r
+\r
+ private void removeVisualStyles() {\r
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
+ AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
}\r
- else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );\r
+ }\r
+\r
+ private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
+ _previous_node_annotation_ref = previous_node_annotation_ref;\r
+ }\r
+\r
+ private void writeAllToFile() {\r
+ if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {\r
+ return;\r
}\r
- else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );\r
+ final File my_dir = getCurrentDir();\r
+ if ( my_dir != null ) {\r
+ _save_filechooser.setCurrentDirectory( my_dir );\r
}\r
- else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );\r
+ _save_filechooser.setSelectedFile( new File( "" ) );\r
+ final int result = _save_filechooser.showSaveDialog( _contentpane );\r
+ final File file = _save_filechooser.getSelectedFile();\r
+ setCurrentDir( _save_filechooser.getCurrentDirectory() );\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( file.exists() ) {\r
+ final int i = JOptionPane.showConfirmDialog( this,\r
+ file + " already exists. Overwrite?",\r
+ "Warning",\r
+ JOptionPane.OK_CANCEL_OPTION,\r
+ JOptionPane.WARNING_MESSAGE );\r
+ if ( i != JOptionPane.OK_OPTION ) {\r
+ return;\r
+ }\r
+ else {\r
+ try {\r
+ file.delete();\r
+ }\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Failed to delete: " + file,\r
+ "Error",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
+ }\r
+ final int count = getMainPanel().getTabbedPane().getTabCount();\r
+ final List<Phylogeny> trees = new ArrayList<Phylogeny>();\r
+ for( int i = 0; i < count; ++i ) {\r
+ final Phylogeny phy = getMainPanel().getPhylogeny( i );\r
+ if ( ForesterUtil.isEmpty( phy.getName() )\r
+ && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) {\r
+ phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) );\r
+ }\r
+ trees.add( phy );\r
+ getMainPanel().getTreePanels().get( i ).setEdited( false );\r
+ }\r
+ final PhylogenyWriter writer = new PhylogenyWriter();\r
+ try {\r
+ writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );\r
+ }\r
+ catch ( final IOException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Failed to write to: " + file,\r
+ "Error",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
}\r
- if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {\r
- options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );\r
+ }\r
+\r
+ /**\r
+ * Display the about box.\r
+ */\r
+ static void about() {\r
+ final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );\r
+ about.append( "Copyright (C) 2014 Christian M Zmasek\n" );\r
+ about.append( "All Rights Reserved\n" );\r
+ about.append( "License: GNU Lesser General Public License (LGPL)\n" );\r
+ about.append( "Last modified: " + Constants.PRG_DATE + "\n" );\r
+ about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );\r
+ about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
+ about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );\r
+ if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {\r
+ about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );\r
}\r
- if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {\r
- options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );\r
+ if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )\r
+ && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {\r
+ about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "\r
+ + ForesterUtil.OS_VERSION + "]\n" );\r
}\r
+ final Runtime rt = java.lang.Runtime.getRuntime();\r
+ final long free_memory = rt.freeMemory() / 1000000;\r
+ final long total_memory = rt.totalMemory() / 1000000;\r
+ about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );\r
+ about.append( "[locale: " + Locale.getDefault() + "]\n" );\r
+ about.append( "References:\n" );\r
+ about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );\r
+ about.append( "For more information & download:\n" );\r
+ about.append( Constants.APTX_WEB_SITE + "\n" );\r
+ about.append( "Documentation:\n" );\r
+ about.append( Constants.APTX_DOC_SITE + "\n" );\r
+ about.append( "Comments: " + Constants.AUTHOR_EMAIL );\r
+ JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );\r
}\r
\r
- public void updateProcessMenu() {\r
- // In general Swing is not thread safe.\r
- // See "Swing's Threading Policy".\r
- SwingUtilities.invokeLater( new Runnable() {\r
-\r
- @Override\r
- public void run() {\r
- doUpdateProcessMenu();\r
+ static void chooseNodeSize( final Options options, final Component parent ) {\r
+ final String s = ( String ) JOptionPane.showInputDialog( parent,\r
+ "Please enter the default size for node shapes.\n"\r
+ + "[current value: "\r
+ + options.getDefaultNodeShapeSize() + "]\n",\r
+ "Node Shape Size",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ options.getDefaultNodeShapeSize() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ double m = 0.0;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+ try {\r
+ m = Double.parseDouble( m_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
}\r
- } );\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( m >= 0.0 ) ) {\r
+ final short size = ForesterUtil.roundToShort( m );\r
+ if ( size >= 0.0 ) {\r
+ options.setDefaultNodeShapeSize( size );\r
+ }\r
+ }\r
+ }\r
}\r
\r
- void updateTypeCheckboxes( final Options options, final Object o ) {\r
- setTypeMenuToAllUnselected();\r
- ( ( JCheckBoxMenuItem ) o ).setSelected( true );\r
+ static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {\r
+ return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();\r
}\r
\r
- void viewAsNexus() {\r
- if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
- String title = "Nexus";\r
- if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
- title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
- }\r
- showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),\r
- title );\r
+ static JMenu createMenu( final String title, final Configuration conf ) {\r
+ final JMenu jmenu = new JMenu( title );\r
+ if ( !conf.isUseNativeUI() ) {\r
+ jmenu.setFont( MainFrame.menu_font );\r
+ jmenu.setBackground( conf.getGuiMenuBackgroundColor() );\r
+ jmenu.setForeground( conf.getGuiMenuTextColor() );\r
}\r
+ return jmenu;\r
}\r
\r
- void viewAsNH() {\r
- if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
- String title = "New Hampshire";\r
- if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
- title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
- }\r
- showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
- .getNhConversionSupportValueStyle() ),\r
- title );\r
+ static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {\r
+ label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );\r
+ if ( !configuration.isUseNativeUI() ) {\r
+ label.setBackground( configuration.getGuiMenuBackgroundColor() );\r
+ label.setForeground( configuration.getGuiMenuTextColor() );\r
+ label.setOpaque( true );\r
}\r
+ label.setSelected( false );\r
+ label.setEnabled( false );\r
+ return label;\r
}\r
\r
- void viewAsXML() {\r
- if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
- String title = "phyloXML";\r
- if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
- title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
- }\r
- showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );\r
+ static void cycleNodeFill( final Options op ) {\r
+ switch ( op.getDefaultNodeFill() ) {\r
+ case GRADIENT:\r
+ op.setDefaultNodeFill( NodeFill.SOLID );\r
+ break;\r
+ case NONE:\r
+ op.setDefaultNodeFill( NodeFill.GRADIENT );\r
+ break;\r
+ case SOLID:\r
+ op.setDefaultNodeFill( NodeFill.NONE );\r
+ break;\r
+ default:\r
+ throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );\r
}\r
}\r
\r
- boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {\r
- try {\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- writer.toNewHampshire( t, true, getOptions().getNhConversionSupportValueStyle(), file );\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringSaveAs( e );\r
+ static void cycleNodeShape( final Options op ) {\r
+ switch ( op.getDefaultNodeShape() ) {\r
+ case CIRCLE:\r
+ op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
+ break;\r
+ case RECTANGLE:\r
+ op.setDefaultNodeShape( NodeShape.CIRCLE );\r
+ break;\r
+ default:\r
+ throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );\r
}\r
- return exception;\r
}\r
\r
- boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {\r
- try {\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );\r
+ static void cycleOverview( final Options op, final TreePanel tree_panel ) {\r
+ switch ( op.getOvPlacement() ) {\r
+ case LOWER_LEFT:\r
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );\r
+ break;\r
+ case LOWER_RIGHT:\r
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );\r
+ break;\r
+ case UPPER_LEFT:\r
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );\r
+ break;\r
+ case UPPER_RIGHT:\r
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );\r
+ break;\r
+ default:\r
+ throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );\r
}\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringSaveAs( e );\r
+ if ( tree_panel != null ) {\r
+ tree_panel.updateOvSettings();\r
}\r
- return exception;\r
}\r
\r
- boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {\r
- try {\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- writer.toPhyloXML( file, t, 0 );\r
+ static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {\r
+ mi.setText( "Cycle Node Return Data... (current: " + options.getExtDescNodeDataToReturn().toString() + ")" );\r
}\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringSaveAs( e );\r
+ else {\r
+ mi.setText( "Cycle Node Return Data..." );\r
}\r
- return exception;\r
}\r
\r
- void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {\r
- _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),\r
- _mainpanel.getCurrentTreePanel().getHeight() );\r
- String file_written_to = "";\r
- boolean error = false;\r
- try {\r
- file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,\r
- _mainpanel.getCurrentTreePanel().getWidth(),\r
- _mainpanel.getCurrentTreePanel().getHeight(),\r
- _mainpanel.getCurrentTreePanel(),\r
- _mainpanel.getControlPanel(),\r
- type,\r
- getOptions() );\r
- }\r
- catch ( final IOException e ) {\r
- error = true;\r
- JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
+ static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
+ mi.setText( "Cycle Node Shape Fill Type... (current: "\r
+ + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
}\r
- if ( !error ) {\r
- if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Wrote image to: " + file_written_to,\r
- "Graphics Export",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "There was an unknown problem when attempting to write to an image file: \""\r
- + file_name + "\"",\r
- "Error",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
+ else {\r
+ mi.setText( "Cycle Node Shape Fill Type..." );\r
}\r
- _contentpane.repaint();\r
}\r
\r
- void writeToFile( final Phylogeny t ) {\r
- if ( t == null ) {\r
- return;\r
+ static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
+ mi.setText( "Cycle Node Shape Fill Type... (current: "\r
+ + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
}\r
- String initial_filename = null;\r
- if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
- try {\r
- initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();\r
- }\r
- catch ( final IOException e ) {\r
- initial_filename = null;\r
- }\r
+ else {\r
+ mi.setText( "Cycle Node Shape Fill Type..." );\r
}\r
- if ( !ForesterUtil.isEmpty( initial_filename ) ) {\r
- _save_filechooser.setSelectedFile( new File( initial_filename ) );\r
+ }\r
+\r
+ static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
+ mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
}\r
else {\r
- _save_filechooser.setSelectedFile( new File( "" ) );\r
+ mi.setText( "Cycle Overview Placement..." );\r
}\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _save_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+\r
+ static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
+ if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
+ mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
+ + ")" );\r
}\r
- final int result = _save_filechooser.showSaveDialog( _contentpane );\r
- final File file = _save_filechooser.getSelectedFile();\r
- setCurrentDir( _save_filechooser.getCurrentDirectory() );\r
- boolean exception = false;\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( this,\r
- file + " already exists.\nOverwrite?",\r
- "Overwrite?",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.QUESTION_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return;\r
- }\r
- else {\r
- final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );\r
- try {\r
- ForesterUtil.copyFile( file, to );\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Failed to create backup copy " + to,\r
- "Failed to Create Backup Copy",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- try {\r
- file.delete();\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Failed to delete: " + file,\r
- "Failed to Delete",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- }\r
- if ( _save_filechooser.getFileFilter() == MainFrame.nhfilter ) {\r
- exception = writeAsNewHampshire( t, exception, file );\r
- }\r
- else if ( _save_filechooser.getFileFilter() == MainFrame.xmlfilter ) {\r
- exception = writeAsPhyloXml( t, exception, file );\r
- }\r
- else if ( _save_filechooser.getFileFilter() == MainFrame.nexusfilter ) {\r
- exception = writeAsNexus( t, exception, file );\r
- }\r
- // "*.*":\r
- else {\r
- final String file_name = file.getName().trim().toLowerCase();\r
- if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
- || file_name.endsWith( ".tree" ) ) {\r
- exception = writeAsNewHampshire( t, exception, file );\r
- }\r
- else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {\r
- exception = writeAsNexus( t, exception, file );\r
- }\r
- // XML is default:\r
- else {\r
- exception = writeAsPhyloXml( t, exception, file );\r
- }\r
- }\r
- if ( !exception ) {\r
- getMainPanel().setTitleOfSelectedTab( file.getName() );\r
- getMainPanel().getCurrentTreePanel().setTreeFile( file );\r
- getMainPanel().getCurrentTreePanel().setEdited( false );\r
- }\r
+ else {\r
+ mi.setText( "Select Color Scheme..." );\r
}\r
}\r
\r
- void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {\r
- if ( ( t == null ) || t.isEmpty() ) {\r
- return;\r
+ static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
+ mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
+ }\r
+\r
+ static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {\r
+ mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "\r
+ + o.getPrintSizeY() + ")" );\r
+ }\r
+\r
+ static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {\r
+ mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );\r
+ }\r
+\r
+ static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
+ if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
+ mi.setEnabled( true );\r
}\r
- String initial_filename = "";\r
- if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
- initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();\r
+ else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
+ mi.setEnabled( true );\r
}\r
- if ( initial_filename.indexOf( '.' ) > 0 ) {\r
- initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
+ else {\r
+ mi.setEnabled( false );\r
}\r
- initial_filename = initial_filename + "." + type;\r
- _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _writetographics_filechooser.setCurrentDirectory( my_dir );\r
+ mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
+ }\r
+\r
+ static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
+ mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
+ }\r
+\r
+ static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
+ for( final TreePanel tree_panel : treepanels ) {\r
+ tree_panel.setTextAntialias();\r
}\r
- final int result = _writetographics_filechooser.showSaveDialog( _contentpane );\r
- File file = _writetographics_filechooser.getSelectedFile();\r
- setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {\r
- file = new File( file.toString() + "." + type );\r
- }\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( this,\r
- file + " already exists. Overwrite?",\r
- "Warning",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.WARNING_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return;\r
+ }\r
+\r
+ private static void cycleNodeDataReturn( final Options op, final Configuration conf ) {\r
+ switch ( op.getExtDescNodeDataToReturn() ) {\r
+ case UNKNOWN:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );\r
+ break;\r
+ case DOMAINS_ALL:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );\r
+ break;\r
+ case DOMAINS_COLLAPSED_PER_PROTEIN:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );\r
+ break;\r
+ case SEQ_ANNOTATIONS:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );\r
+ break;\r
+ case GO_TERM_IDS:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );\r
+ break;\r
+ case SEQUENCE_MOL_SEQ_FASTA:\r
+ if ( ( conf != null ) && ( conf.getExtDescNodeDataToReturn() != null )\r
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL )\r
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN )\r
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS )\r
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS )\r
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA ) ) {\r
+ op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );\r
}\r
else {\r
- try {\r
- file.delete();\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Failed to delete: " + file,\r
- "Error",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
+ op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
}\r
- }\r
- writePhylogenyToGraphicsFile( file.toString(), type );\r
+ break;\r
+ default:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
}\r
}\r
+}\r
\r
- void writeToPdf( final Phylogeny t ) {\r
- if ( ( t == null ) || t.isEmpty() ) {\r
- return;\r
- }\r
- String initial_filename = "";\r
- if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
- initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();\r
- }\r
- if ( initial_filename.indexOf( '.' ) > 0 ) {\r
- initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
- }\r
- initial_filename = initial_filename + ".pdf";\r
- _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _writetopdf_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );\r
- File file = _writetopdf_filechooser.getSelectedFile();\r
- setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {\r
- file = new File( file.toString() + ".pdf" );\r
- }\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( this,\r
- file + " already exists. Overwrite?",\r
- "WARNING",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.WARNING_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return;\r
- }\r
- }\r
- printPhylogenyToPdf( file.toString() );\r
- }\r
+class DefaultFilter extends FileFilter {\r
+\r
+ @Override\r
+ public boolean accept( final File f ) {\r
+ final String file_name = f.getName().trim().toLowerCase();\r
+ return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
+ || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )\r
+ || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )\r
+ || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )\r
+ || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )\r
+ || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )\r
+ || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )\r
+ || file_name.endsWith( ".con" ) || f.isDirectory();\r
+ }\r
+\r
+ @Override\r
+ public String getDescription() {\r
+ return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";\r
+ }\r
+}\r
+\r
+class GraphicsFileFilter extends FileFilter {\r
+\r
+ @Override\r
+ public boolean accept( final File f ) {\r
+ final String file_name = f.getName().trim().toLowerCase();\r
+ return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )\r
+ || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();\r
+ }\r
+\r
+ @Override\r
+ public String getDescription() {\r
+ return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";\r
}\r
}\r
\r
git://source.jalview.org / jalview.git / commitdiff