--- /dev/null
+
+package org.forester.archaeopteryx;
+
+import java.awt.BorderLayout;
+import java.awt.Container;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.IOException;
+import java.net.URL;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.NoSuchElementException;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JApplet;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JFileChooser;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.UIManager;
+import javax.swing.UnsupportedLookAndFeelException;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+import org.apache.commons.codec.binary.Base64;
+import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
+import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
+import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
+import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
+import org.forester.phylogeny.data.SequenceRelation;
+import org.forester.sdi.GSDI;
+import org.forester.sdi.GSDIR;
+import org.forester.sdi.SDIException;
+import org.forester.util.ForesterConstants;
+import org.forester.util.ForesterUtil;
+import org.forester.util.WindowsUtils;
+
+// Use like this:
+// <applet archive="forester.jar"
+// code="org.forester.archaeopteryx.ArchaeopteryxE.class"
+// codebase="http://www.myserver.org/path/to/forester"
+// width="600"
+// height="500"
+// alt="ArchaeopteryxE is not working on your system (requires at least Sun Java 1.5)!">
+// <param name="url_of_tree_to_load"
+// value="http://www.myserver.org/examples/data/apaf.xml">
+// <param name="config_file"
+// value="http://www.myserver.org/examples/config/config_file.txt">
+// </applet>
+public class ArchaeopteryxE extends JApplet implements ActionListener {
+
+ private final static String NAME = "ArchaeopteryxE";
+ private static final long serialVersionUID = -1220055577935759443L;
+ private Configuration _configuration;
+ private MainPanel _mainpanel;
+ private JMenuBar _jmenubar;
+ private JMenu _options_jmenu;
+ private JMenu _font_size_menu;
+ private JMenuItem _super_tiny_fonts_mi;
+ private JMenuItem _tiny_fonts_mi;
+ private JMenuItem _small_fonts_mi;
+ private JMenuItem _medium_fonts_mi;
+ private JMenuItem _large_fonts_mi;
+ private JMenu _tools_menu;
+ private JMenuItem _taxcolor_item;
+ private JMenuItem _confcolor_item;
+ private JMenuItem _midpoint_root_item;
+ private JMenu _view_jmenu;
+ private JMenuItem _view_as_XML_item;
+ private JMenuItem _view_as_NH_item;
+ private JMenuItem _view_as_nexus_item;
+ private JMenuItem _display_basic_information_item;
+ private JMenu _type_menu;
+ private JCheckBoxMenuItem _rectangular_type_cbmi;
+ private JCheckBoxMenuItem _triangular_type_cbmi;
+ private JCheckBoxMenuItem _curved_type_cbmi;
+ private JCheckBoxMenuItem _convex_type_cbmi;
+ private JCheckBoxMenuItem _euro_type_cbmi;
+ private JCheckBoxMenuItem _rounded_type_cbmi;
+ private JCheckBoxMenuItem _unrooted_type_cbmi;
+ private JCheckBoxMenuItem _circular_type_cbmi;
+ private JMenuItem _help_item;
+ private JMenuItem _about_item;
+ private JMenu _help_jmenu;
+ private JMenuItem _website_item;
+ private JMenuItem _phyloxml_website_item;
+ private JMenuItem _phyloxml_ref_item;
+ private JMenuItem _aptx_ref_item;
+ private JMenuItem _remove_branch_color_item;
+ private JMenuItem _remove_visual_styles_item;
+ private JCheckBoxMenuItem _show_domain_labels;
+ private JCheckBoxMenuItem _show_annotation_ref_source;
+ private JCheckBoxMenuItem _color_labels_same_as_parent_branch;
+ private JCheckBoxMenuItem _abbreviate_scientific_names;
+ private JCheckBoxMenuItem _screen_antialias_cbmi;
+ private JCheckBoxMenuItem _background_gradient_cbmi;
+ private JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;
+ private JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
+ private JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
+ private Options _options;
+ private JMenuItem _choose_font_mi;
+ private JMenuItem _switch_colors_mi;
+ JCheckBoxMenuItem _label_direction_cbmi;
+ private JCheckBoxMenuItem _show_scale_cbmi;
+ private JCheckBoxMenuItem _search_case_senstive_cbmi;
+ private JCheckBoxMenuItem _search_whole_words_only_cbmi;
+ private JCheckBoxMenuItem _inverse_search_result_cbmi;
+ private JCheckBoxMenuItem _search_with_regex_cbmi;
+ private JCheckBoxMenuItem _show_overview_cbmi;
+ private JMenuItem _choose_minimal_confidence_mi;
+ private JMenuItem _collapse_species_specific_subtrees;
+ private JMenuItem _overview_placment_mi;
+ private ButtonGroup _radio_group_1;
+ private JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;
+ private JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;
+ private JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi;
+ private JMenuItem _cycle_node_shape_mi;
+ private JMenuItem _cycle_node_fill_mi;
+ private JMenuItem _choose_node_size_mi;
+ private JCheckBoxMenuItem _show_confidence_stddev_cbmi;
+ private final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>();
+ private JMenu _analysis_menu;
+ private JMenuItem _gsdi_item;
+ private JMenuItem _gsdir_item;
+ private Phylogeny _species_tree;
+ private JCheckBoxMenuItem _right_line_up_domains_cbmi;
+ private JCheckBoxMenuItem _line_up_renderable_data_cbmi;
+ // file menu:
+ private JMenuItem _save_item;
+ private JMenuItem _print_item;
+ private JMenuItem _write_to_pdf_item;
+ private JMenuItem _write_to_jpg_item;
+ private JMenuItem _write_to_gif_item;
+ private JMenuItem _write_to_tif_item;
+ private JMenuItem _write_to_png_item;
+ private JMenuItem _write_to_bmp_item;
+ private JMenu _file_jmenu;
+ private JFileChooser _writetopdf_filechooser;
+ private File _current_dir;
+ private JFileChooser _save_filechooser;
+ private JFileChooser _writetographics_filechooser;
+ private JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
+ private JCheckBoxMenuItem _antialias_print_cbmi;
+ private JCheckBoxMenuItem _print_black_and_white_cbmi;
+ private JMenuItem _choose_pdf_width_mi;
+
+ @Override
+ public void actionPerformed( final ActionEvent e ) {
+ final Object o = e.getSource();
+ if ( o == _midpoint_root_item ) {
+ getMainPanel().getCurrentTreePanel().midpointRoot();
+ }
+ else if ( o == _gsdi_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ executeGSDI();
+ }
+ else if ( o == _gsdir_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ executeGSDIR();
+ }
+ else if ( o == _taxcolor_item ) {
+ getMainPanel().getCurrentTreePanel().taxColor();
+ }
+ else if ( o == _confcolor_item ) {
+ getMainPanel().getCurrentTreePanel().confColor();
+ }
+ else if ( o == _collapse_species_specific_subtrees ) {
+ if ( getCurrentTreePanel() != null ) {
+ getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
+ }
+ }
+ else if ( o == _remove_branch_color_item ) {
+ removeBranchColors();
+ }
+ else if ( o == _remove_visual_styles_item ) {
+ removeVisualStyles();
+ }
+ else if ( o == _switch_colors_mi ) {
+ switchColors();
+ }
+ else if ( o == _display_basic_information_item ) {
+ displayBasicInformation();
+ }
+ else if ( o == _view_as_NH_item ) {
+ viewAsNH();
+ }
+ else if ( o == _view_as_XML_item ) {
+ viewAsXML();
+ }
+ else if ( o == _view_as_nexus_item ) {
+ viewAsNexus();
+ }
+ else if ( o == _super_tiny_fonts_mi ) {
+ if ( getCurrentTreePanel() != null ) {
+ getCurrentTreePanel().setSuperTinyFonts();
+ getCurrentTreePanel().repaint();
+ }
+ }
+ else if ( o == _tiny_fonts_mi ) {
+ if ( getCurrentTreePanel() != null ) {
+ getCurrentTreePanel().setTinyFonts();
+ getCurrentTreePanel().repaint();
+ }
+ }
+ else if ( o == _small_fonts_mi ) {
+ if ( getCurrentTreePanel() != null ) {
+ getCurrentTreePanel().setSmallFonts();
+ getCurrentTreePanel().repaint();
+ }
+ }
+ else if ( o == _medium_fonts_mi ) {
+ if ( getCurrentTreePanel() != null ) {
+ getCurrentTreePanel().setMediumFonts();
+ getCurrentTreePanel().repaint();
+ }
+ }
+ else if ( o == _large_fonts_mi ) {
+ if ( getCurrentTreePanel() != null ) {
+ getCurrentTreePanel().setLargeFonts();
+ getCurrentTreePanel().repaint();
+ }
+ }
+ else if ( o == _choose_font_mi ) {
+ chooseFont();
+ }
+ else if ( o == _choose_minimal_confidence_mi ) {
+ chooseMinimalConfidence();
+ }
+ else if ( o == _choose_node_size_mi ) {
+ MainFrame.chooseNodeSize( getOptions(), this );
+ }
+ else if ( o == _overview_placment_mi ) {
+ MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
+ }
+ else if ( o == _cycle_node_fill_mi ) {
+ MainFrame.cycleNodeFill( getOptions() );
+ }
+ else if ( o == _cycle_node_shape_mi ) {
+ MainFrame.cycleNodeShape( getOptions() );
+ }
+ else if ( o == _non_lined_up_cladograms_rbmi ) {
+ updateOptions( getOptions() );
+ _mainpanel.getControlPanel().showWhole();
+ }
+ else if ( o == _ext_node_dependent_cladogram_rbmi ) {
+ updateOptions( getOptions() );
+ _mainpanel.getControlPanel().showWhole();
+ }
+ else if ( o == _search_case_senstive_cbmi ) {
+ updateOptions( getOptions() );
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
+ }
+ else if ( o == _search_whole_words_only_cbmi ) {
+ if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {
+ _search_with_regex_cbmi.setSelected( false );
+ }
+ updateOptions( getOptions() );
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
+ }
+ else if ( o == _inverse_search_result_cbmi ) {
+ updateOptions( getOptions() );
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
+ }
+ else if ( o == _search_with_regex_cbmi ) {
+ if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
+ _search_whole_words_only_cbmi.setSelected( false );
+ }
+ if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
+ _search_case_senstive_cbmi.setSelected( true );
+ }
+ updateOptions( getOptions() );
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
+ }
+ else if ( o == _show_scale_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_confidence_stddev_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _label_direction_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _abbreviate_scientific_names ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_overview_cbmi ) {
+ updateOptions( getOptions() );
+ if ( getCurrentTreePanel() != null ) {
+ getCurrentTreePanel().updateOvSizes();
+ }
+ }
+ else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
+ || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
+ || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
+ typeChanged( o );
+ }
+ else if ( o == _screen_antialias_cbmi ) {
+ updateOptions( getOptions() );
+ setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
+ }
+ else if ( o == _background_gradient_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_domain_labels ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _color_labels_same_as_parent_branch ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_default_node_shapes_internal_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_default_node_shapes_external_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _about_item ) {
+ getMainPanel().getMainFrame().about();
+ }
+ else if ( o == _help_item ) {
+ try {
+ AptxUtil.openWebsite( AptxConstants.APTX_DOC_SITE, true, this );
+ }
+ catch ( final IOException e1 ) {
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
+ }
+ }
+ else if ( o == _website_item ) {
+ try {
+ AptxUtil.openWebsite( AptxConstants.APTX_WEB_SITE, true, this );
+ }
+ catch ( final IOException e1 ) {
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
+ }
+ }
+ else if ( o == _phyloxml_website_item ) {
+ try {
+ AptxUtil.openWebsite( AptxConstants.PHYLOXML_WEB_SITE, true, this );
+ }
+ catch ( final IOException e1 ) {
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
+ }
+ }
+ else if ( o == _aptx_ref_item ) {
+ try {
+ AptxUtil.openWebsite( AptxConstants.APTX_REFERENCE_URL, true, this );
+ }
+ catch ( final IOException e1 ) {
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
+ }
+ }
+ else if ( o == _phyloxml_ref_item ) {
+ try {
+ AptxUtil.openWebsite( AptxConstants.PHYLOXML_REFERENCE_URL, true, this );
+ }
+ catch ( final IOException e1 ) {
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
+ }
+ }
+ else if ( o == _color_by_taxonomic_group_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _line_up_renderable_data_cbmi ) {
+ if ( !_line_up_renderable_data_cbmi.isSelected() ) {
+ _right_line_up_domains_cbmi.setSelected( false );
+ }
+ updateOptions( getOptions() );
+ }
+ else if ( o == _right_line_up_domains_cbmi ) {
+ if ( _right_line_up_domains_cbmi.isSelected() ) {
+ _line_up_renderable_data_cbmi.setSelected( true );
+ }
+ updateOptions( getOptions() );
+ }
+ else if ( o == _write_to_pdf_item ) {
+ final File curr_dir = MainFrame.writeToPdf( _mainpanel.getCurrentPhylogeny(),
+ getMainPanel(),
+ _writetopdf_filechooser,
+ _current_dir,
+ getContentPane(),
+ this );
+ if ( curr_dir != null ) {
+ setCurrentDir( curr_dir );
+ }
+ }
+ else if ( o == _write_to_jpg_item ) {
+ final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
+ GraphicsExportType.JPG,
+ _mainpanel,
+ _writetographics_filechooser,
+ this,
+ getContentPane(),
+ _current_dir );
+ if ( curr_dir != null ) {
+ setCurrentDir( curr_dir );
+ }
+ }
+ else if ( o == _write_to_gif_item ) {
+ final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
+ GraphicsExportType.GIF,
+ _mainpanel,
+ _writetographics_filechooser,
+ this,
+ getContentPane(),
+ _current_dir );
+ if ( curr_dir != null ) {
+ setCurrentDir( curr_dir );
+ }
+ }
+ else if ( o == _write_to_tif_item ) {
+ final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
+ GraphicsExportType.TIFF,
+ _mainpanel,
+ _writetographics_filechooser,
+ this,
+ getContentPane(),
+ _current_dir );
+ if ( curr_dir != null ) {
+ setCurrentDir( curr_dir );
+ }
+ }
+ else if ( o == _write_to_bmp_item ) {
+ final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
+ GraphicsExportType.BMP,
+ _mainpanel,
+ _writetographics_filechooser,
+ this,
+ getContentPane(),
+ _current_dir );
+ if ( curr_dir != null ) {
+ setCurrentDir( curr_dir );
+ }
+ }
+ else if ( o == _write_to_png_item ) {
+ final File curr_dir = MainFrame.writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),
+ GraphicsExportType.PNG,
+ _mainpanel,
+ _writetographics_filechooser,
+ this,
+ getContentPane(),
+ _current_dir );
+ if ( curr_dir != null ) {
+ setCurrentDir( curr_dir );
+ }
+ }
+ else if ( o == _print_item ) {
+ MainFrame.print( getCurrentTreePanel(), getOptions(), this );
+ }
+ else if ( o == _save_item ) {
+ final File new_dir = MainFrame.writeToFile( _mainpanel.getCurrentPhylogeny(),
+ getMainPanel(),
+ _save_filechooser,
+ _current_dir,
+ getContentPane(),
+ this );
+ if ( new_dir != null ) {
+ setCurrentDir( new_dir );
+ }
+ }
+ else if ( o == _graphics_export_visible_only_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _antialias_print_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _print_black_and_white_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _choose_pdf_width_mi ) {
+ choosePdfWidth();
+ }
+ repaint();
+ }
+
+ @Override
+ public void destroy() {
+ AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
+ removeAllTextFrames();
+ if ( getMainPanel() != null ) {
+ getMainPanel().terminate();
+ }
+ }
+
+ /**
+ * This method returns the current external node data which
+ * has been selected by the user by clicking the "Return ..."
+ * menu item. This method is expected to be called from Javascript or
+ * something like it.
+ *
+ * @return current external node data as String
+ */
+ public String getCurrentExternalNodesDataBuffer() {
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
+ }
+
+ public int getCurrentExternalNodesDataBufferChangeCounter() {
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
+ }
+
+ public int getCurrentExternalNodesDataBufferLength() {
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
+ }
+
+ /**
+ * This method returns the current phylogeny as a string in the chosen format
+ *
+ * @param format must be NH, NHX, NEXUS or PHYLOXML
+ * @return the phylogeny string
+ * @author Herve Menager
+ */
+ public String getCurrentPhylogeny( final String format ) {
+ removeAllTextFrames();
+ if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
+ || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
+ return new String();
+ }
+ switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
+ case NH:
+ return getMainPanel().getCurrentPhylogeny().toNewHampshire();
+ case NHX:
+ return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
+ case NEXUS:
+ return getMainPanel().getCurrentPhylogeny().toNexus();
+ case PHYLOXML:
+ return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
+ default:
+ break;
+ }
+ return new String();
+ }
+
+ /**
+ * This method returns a view of the current phylogeny in a chosen
+ * graphics format, base64-encoded in a string so that in can be used
+ * from javascript.
+ *
+ * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
+ * @return the phylogeny string
+ * @author Herve Menager
+ */
+ public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
+ final ByteArrayOutputStream baos = new ByteArrayOutputStream();
+ try {
+ AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
+ _mainpanel.getWidth(),
+ _mainpanel.getHeight(),
+ getCurrentTreePanel(),
+ getCurrentTreePanel().getControlPanel(),
+ GraphicsExportType.valueOf( format ),
+ getOptions() );
+ }
+ catch ( final IOException ioe ) {
+ ForesterUtil.printErrorMessage( NAME, ioe.toString() );
+ ioe.printStackTrace();
+ JOptionPane.showMessageDialog( this,
+ NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
+ "Failed to generate graphics",
+ JOptionPane.ERROR_MESSAGE );
+ return null;
+ }
+ final byte[] bytes = baos.toByteArray();
+ final String dataImg = Base64.encodeBase64String( bytes );
+ return dataImg;
+ }
+
+ public Options getOptions() {
+ return _options;
+ }
+
+ @Override
+ public void init() {
+ _writetopdf_filechooser = new JFileChooser();
+ _writetopdf_filechooser.setMultiSelectionEnabled( false );
+ _writetopdf_filechooser.addChoosableFileFilter( MainFrame.pdffilter );
+ _writetographics_filechooser = new JFileChooser();
+ _writetographics_filechooser.setMultiSelectionEnabled( false );
+ _writetographics_filechooser.addChoosableFileFilter( MainFrame.graphicsfilefilter );
+ _save_filechooser = new JFileChooser();
+ _save_filechooser.setMultiSelectionEnabled( false );
+ _save_filechooser.setFileFilter( MainFrame.xmlfilter );
+ _save_filechooser.addChoosableFileFilter( MainFrame.nhfilter );
+ _save_filechooser.addChoosableFileFilter( MainFrame.nexusfilter );
+ _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
+ try {
+ final String home_dir = System.getProperty( "user.home" );
+ _save_filechooser.setCurrentDirectory( new File( home_dir ) );
+ _writetopdf_filechooser.setCurrentDirectory( new File( home_dir ) );
+ _writetographics_filechooser.setCurrentDirectory( new File( home_dir ) );
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ // Do nothing. Not important.
+ }
+ final String config_filename = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
+ AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
+ final Configuration configuration = new Configuration( config_filename, true, true, true );
+ setConfiguration( configuration );
+ setOptions( Options.createInstance( configuration ) );
+ setupUI();
+ final String tree_url_str = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+ if ( ForesterUtil.isEmpty( tree_url_str ) ) {
+ ForesterUtil.printErrorMessage( NAME, "could not get tree URL from "
+ + AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+ JOptionPane.showMessageDialog( this, NAME + ": could not get tree URL from "
+ + AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
+ // Get URL to tree file
+ URL phys_url = null;
+ try {
+ phys_url = new URL( tree_url_str );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.printErrorMessage( NAME, "error: " + e );
+ e.printStackTrace();
+ JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
+ + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
+ }
+ if ( phys_url == null ) {
+ ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from "
+ + AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+ JOptionPane.showMessageDialog( this,
+ NAME + ": Could not create URL from: \"" + tree_url_str,
+ "Failed to create URL",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ // Load the tree from URL
+ Phylogeny[] phys = null;
+ try {
+ phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
+ getConfiguration().isValidatePhyloXmlAgainstSchema(),
+ getConfiguration().isReplaceUnderscoresInNhParsing(),
+ getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
+ getConfiguration().getTaxonomyExtraction(),
+ getConfiguration().isMidpointReroot() );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.printErrorMessage( NAME, e.toString() );
+ e.printStackTrace();
+ JOptionPane.showMessageDialog( this,
+ NAME + ": Failed to read phylogenies: " + "\nException: " + e,
+ "Failed to read phylogenies",
+ JOptionPane.ERROR_MESSAGE );
+ }
+ if ( phys == null ) {
+ ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null" );
+ JOptionPane.showMessageDialog( this,
+ NAME + ": phylogenies from [" + phys_url + "] are null",
+ "Failed to read phylogenies",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ else if ( phys.length < 1 ) {
+ ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are empty" );
+ JOptionPane.showMessageDialog( this,
+ NAME + ": phylogenies from [" + phys_url + "] are empty",
+ "Failed to read phylogenies",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ else {
+ AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
+ }
+ //
+ final String species_tree_url_str = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
+ if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
+ AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" );
+ Phylogeny[] species_trees = null;
+ try {
+ final URL species_tree_url = new URL( species_tree_url_str );
+ species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
+ configuration.isValidatePhyloXmlAgainstSchema(),
+ configuration.isReplaceUnderscoresInNhParsing(),
+ false,
+ TAXONOMY_EXTRACTION.NO,
+ false );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.printErrorMessage( NAME, "could not read species tree from [" + species_tree_url_str
+ + "]" );
+ JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from ["
+ + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE );
+ }
+ if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
+ AptxUtil.printAppletMessage( NAME, "successfully read species tree" );
+ if ( species_trees[ 0 ].isEmpty() ) {
+ ForesterUtil.printErrorMessage( NAME, "species tree is empty" );
+ }
+ else if ( !species_trees[ 0 ].isRooted() ) {
+ ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" );
+ }
+ else {
+ setSpeciesTree( species_trees[ 0 ] );
+ AptxUtil.printAppletMessage( NAME, "species tree OK" );
+ }
+ }
+ }
+ try {
+ setVisible( false );
+ setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
+ _jmenubar = new JMenuBar();
+ if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
+ buildFileMenu();
+ if ( !getConfiguration().isUseNativeUI() ) {
+ _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
+ }
+ if ( getSpeciesTree() != null ) {
+ buildAnalysisMenu();
+ }
+ buildToolsMenu();
+ buildViewMenu();
+ buildFontSizeMenu();
+ buildOptionsMenu();
+ buildTypeMenu();
+ buildHelpMenu();
+ setJMenuBar( _jmenubar );
+ }
+ final Container contentpane = getContentPane();
+ contentpane.setLayout( new BorderLayout() );
+ contentpane.add( getMainPanel(), BorderLayout.CENTER );
+ addComponentListener( new ComponentAdapter() {
+
+ @Override
+ public void componentResized( final ComponentEvent e ) {
+ if ( getMainPanel().getCurrentTreePanel() != null ) {
+ getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
+ .getCurrentTreePanel()
+ .getWidth(),
+ getMainPanel()
+ .getCurrentTreePanel()
+ .getHeight() );
+ }
+ }
+ } );
+ if ( getConfiguration().isUseTabbedDisplay() ) {
+ try {
+ AptxUtil.printAppletMessage( NAME, "using tabbed display" );
+ AptxUtil.addPhylogeniesToTabs( phys,
+ new File( phys_url.getFile() ).getName(),
+ phys_url.toString(),
+ getConfiguration(),
+ getMainPanel() );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.printErrorMessage( NAME, e.toString() );
+ e.printStackTrace();
+ }
+ }
+ else {
+ AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
+ if ( getSpeciesTree() != null ) {
+ AptxUtil.printAppletMessage( NAME,
+ "Warning: gsdi (gene duplication inference) only available tabbed display" );
+ }
+ AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
+ }
+ validate();
+ setName( NAME );
+ getMainPanel().getControlPanel().showWholeAll();
+ getMainPanel().getControlPanel().showWhole();
+ /* GUILHEM_BEG */
+ getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
+ for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
+ .getRelevantSequenceRelationTypes() ) {
+ getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
+ }
+ final String default_relation = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
+ if ( default_relation != null ) {
+ getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
+ }
+ final String default_sequence = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
+ if ( default_sequence != null ) {
+ getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
+ }
+ /* GUILHEM_END */
+ System.gc();
+ AptxUtil.printAppletMessage( NAME, "successfully initialized" );
+ setVisible( true );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.printErrorMessage( NAME, e.toString() );
+ e.printStackTrace();
+ }
+ }
+
+ public void showTextFrame( final String s, final String title ) {
+ checkTextFrames();
+ _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
+ }
+
+ @Override
+ public void start() {
+ if ( getMainPanel() != null ) {
+ getMainPanel().validate();
+ }
+ requestFocus();
+ requestFocusInWindow();
+ requestFocus();
+ AptxUtil.printAppletMessage( NAME, "started" );
+ }
+
+ private void chooseFont() {
+ final FontChooser fc = new FontChooser();
+ fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
+ fc.showDialog( this, "Select the Base Font" );
+ getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
+ }
+
+ private void chooseMinimalConfidence() {
+ final String s = ( String ) JOptionPane
+ .showInputDialog( this,
+ "Please the minimum for confidence values to be displayed.\n" + "[current value: "
+ + getOptions().getMinConfidenceValue() + "]\n",
+ "Minimal Confidence Value",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ getOptions().getMinConfidenceValue() );
+ if ( !ForesterUtil.isEmpty( s ) ) {
+ boolean success = true;
+ double m = 0.0;
+ final String m_str = s.trim();
+ if ( !ForesterUtil.isEmpty( m_str ) ) {
+ try {
+ m = Double.parseDouble( m_str );
+ }
+ catch ( final Exception ex ) {
+ success = false;
+ }
+ }
+ else {
+ success = false;
+ }
+ if ( success && ( m >= 0.0 ) ) {
+ getOptions().setMinConfidenceValue( m );
+ }
+ }
+ }
+
+ private void choosePdfWidth() {
+ final String s = ( String ) JOptionPane.showInputDialog( this,
+ "Please enter the default line width for PDF export.\n"
+ + "[current value: "
+ + getOptions().getPrintLineWidth() + "]\n",
+ "Line Width for PDF Export",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ getOptions().getPrintLineWidth() );
+ if ( !ForesterUtil.isEmpty( s ) ) {
+ boolean success = true;
+ float f = 0.0f;
+ final String m_str = s.trim();
+ if ( !ForesterUtil.isEmpty( m_str ) ) {
+ try {
+ f = Float.parseFloat( m_str );
+ }
+ catch ( final Exception ex ) {
+ success = false;
+ }
+ }
+ else {
+ success = false;
+ }
+ if ( success && ( f > 0.0 ) ) {
+ getOptions().setPrintLineWidth( f );
+ }
+ }
+ }
+
+ private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
+ if ( item != null ) {
+ item.setFont( MainFrame.menu_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
+ item.setForeground( getConfiguration().getGuiMenuTextColor() );
+ }
+ item.setSelected( is_selected );
+ item.addActionListener( this );
+ }
+ }
+
+ private Phylogeny getSpeciesTree() {
+ return _species_tree;
+ }
+
+ private boolean isScreenAntialias() {
+ return true;
+ }
+
+ private void removeBranchColors() {
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {
+ AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
+ }
+ }
+
+ private void removeVisualStyles() {
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {
+ AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
+ }
+ }
+
+ private void setMainPanel( final MainPanelApplets main_panel ) {
+ _mainpanel = main_panel;
+ }
+
+ private void setSpeciesTree( final Phylogeny species_tree ) {
+ _species_tree = species_tree;
+ }
+
+ private void setupUI() {
+ try {
+ if ( getConfiguration().isUseNativeUI() ) {
+ UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
+ }
+ else {
+ UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
+ }
+ }
+ catch ( final UnsupportedLookAndFeelException e ) {
+ AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
+ }
+ catch ( final ClassNotFoundException e ) {
+ AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
+ }
+ catch ( final InstantiationException e ) {
+ AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
+ }
+ catch ( final IllegalAccessException e ) {
+ AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
+ }
+ catch ( final Exception e ) {
+ AptxUtil.dieWithSystemError( e.toString() );
+ }
+ }
+
+ void buildAnalysisMenu() {
+ _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
+ _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
+ _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
+ customizeJMenuItem( _gsdi_item );
+ customizeJMenuItem( _gsdir_item );
+ _analysis_menu.addSeparator();
+ _jmenubar.add( _analysis_menu );
+ }
+
+ void buildFileMenu() {
+ _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
+ _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
+ _file_jmenu.addSeparator();
+ _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
+ if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
+ _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
+ }
+ _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
+ _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
+ if ( AptxUtil.canWriteFormat( "gif" ) ) {
+ _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
+ }
+ if ( AptxUtil.canWriteFormat( "bmp" ) ) {
+ _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
+ }
+ _file_jmenu.addSeparator();
+ _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
+ customizeJMenuItem( _save_item );
+ customizeJMenuItem( _write_to_pdf_item );
+ customizeJMenuItem( _write_to_png_item );
+ customizeJMenuItem( _write_to_jpg_item );
+ customizeJMenuItem( _write_to_gif_item );
+ customizeJMenuItem( _write_to_tif_item );
+ customizeJMenuItem( _write_to_bmp_item );
+ customizeJMenuItem( _print_item );
+ _jmenubar.add( _file_jmenu );
+ }
+
+ void buildFontSizeMenu() {
+ _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
+ _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
+ _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
+ _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
+ _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
+ _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
+ customizeJMenuItem( _super_tiny_fonts_mi );
+ customizeJMenuItem( _tiny_fonts_mi );
+ customizeJMenuItem( _small_fonts_mi );
+ customizeJMenuItem( _medium_fonts_mi );
+ customizeJMenuItem( _large_fonts_mi );
+ _jmenubar.add( _font_size_menu );
+ }
+
+ void buildHelpMenu() {
+ _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
+ _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
+ _help_jmenu.addSeparator();
+ _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
+ _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
+ _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
+ _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
+ _help_jmenu.addSeparator();
+ _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
+ customizeJMenuItem( _help_item );
+ customizeJMenuItem( _website_item );
+ customizeJMenuItem( _phyloxml_website_item );
+ customizeJMenuItem( _aptx_ref_item );
+ customizeJMenuItem( _phyloxml_ref_item );
+ customizeJMenuItem( _about_item );
+ _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
+ _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
+ _jmenubar.add( _help_jmenu );
+ }
+
+ void buildOptionsMenu() {
+ _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
+ _options_jmenu.addChangeListener( new ChangeListener() {
+
+ @Override
+ public void stateChanged( final ChangeEvent e ) {
+ MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
+ MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
+ MainFrame
+ .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
+ MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
+ .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
+ setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
+ MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
+ MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
+ MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
+ try {
+ getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
+ getMainPanel().getControlPanel().setVisibilityOfX();
+ }
+ catch ( final Exception ignore ) {
+ // do nothing, not important.
+ }
+ }
+ } );
+ _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
+ getConfiguration() ) );
+ _options_jmenu
+ .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
+ _options_jmenu
+ .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
+ _radio_group_1 = new ButtonGroup();
+ _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
+ _radio_group_1.add( _non_lined_up_cladograms_rbmi );
+ _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
+ _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
+ _options_jmenu
+ .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
+ _options_jmenu
+ .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
+ _options_jmenu
+ .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
+ _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
+ if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
+ _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
+ _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
+ }
+ _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
+ _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
+ _options_jmenu
+ .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
+ _options_jmenu
+ .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
+ _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
+ _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
+ _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
+ _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
+ _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
+ _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
+ _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
+ _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
+ _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
+ _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
+ _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
+ _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
+ _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
+ _options_jmenu.addSeparator();
+ _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
+ getConfiguration() ) );
+ _options_jmenu
+ .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
+ _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
+ _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
+ _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );
+ _options_jmenu
+ .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
+ //
+ _options_jmenu.addSeparator();
+ _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
+ getConfiguration() ) );
+ _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
+ _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
+ _options_jmenu
+ .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
+ _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
+ //
+ customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
+ customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
+ customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
+ customizeJMenuItem( _choose_pdf_width_mi );
+ //
+ customizeJMenuItem( _choose_font_mi );
+ customizeJMenuItem( _choose_minimal_confidence_mi );
+ customizeJMenuItem( _switch_colors_mi );
+ customizeJMenuItem( _overview_placment_mi );
+ customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
+ customizeCheckBoxMenuItem( _label_direction_cbmi,
+ getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
+ customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
+ customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
+ customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
+ customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
+ customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
+ .isShowDefaultNodeShapesExternal() );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
+ .isShowDefaultNodeShapesInternal() );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
+ .isShowDefaultNodeShapesForMarkedNodes() );
+ customizeJMenuItem( _cycle_node_shape_mi );
+ customizeJMenuItem( _cycle_node_fill_mi );
+ customizeJMenuItem( _choose_node_size_mi );
+ customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
+ customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
+ customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
+ customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
+ customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.LINED_UP );
+ customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
+ customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );
+ customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
+ customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
+ customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
+ customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
+ customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
+ _jmenubar.add( _options_jmenu );
+ }
+
+ void buildToolsMenu() {
+ _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
+ _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
+ customizeJMenuItem( _confcolor_item );
+ _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
+ customizeJMenuItem( _taxcolor_item );
+ _tools_menu.addSeparator();
+ _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
+ _remove_visual_styles_item
+ .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
+ customizeJMenuItem( _remove_visual_styles_item );
+ _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
+ _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
+ customizeJMenuItem( _remove_branch_color_item );
+ _tools_menu.addSeparator();
+ _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
+ customizeJMenuItem( _midpoint_root_item );
+ _tools_menu.addSeparator();
+ _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
+ customizeJMenuItem( _collapse_species_specific_subtrees );
+ _jmenubar.add( _tools_menu );
+ }
+
+ void buildTypeMenu() {
+ _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
+ _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
+ _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
+ _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
+ _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
+ _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
+ _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
+ _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
+ _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
+ customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
+ customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
+ customizeCheckBoxMenuItem( _euro_type_cbmi, false );
+ customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
+ customizeCheckBoxMenuItem( _curved_type_cbmi, false );
+ customizeCheckBoxMenuItem( _convex_type_cbmi, false );
+ customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
+ customizeCheckBoxMenuItem( _circular_type_cbmi, false );
+ _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
+ _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
+ initializeTypeMenu( getOptions() );
+ _jmenubar.add( _type_menu );
+ }
+
+ void buildViewMenu() {
+ _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
+ _view_jmenu
+ .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
+ _view_jmenu.addSeparator();
+ _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
+ _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
+ _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
+ customizeJMenuItem( _display_basic_information_item );
+ customizeJMenuItem( _view_as_NH_item );
+ customizeJMenuItem( _view_as_XML_item );
+ customizeJMenuItem( _view_as_nexus_item );
+ _jmenubar.add( _view_jmenu );
+ }
+
+ void checkTextFrames() {
+ if ( _textframes.size() > 5 ) {
+ try {
+ if ( _textframes.getFirst() != null ) {
+ _textframes.getFirst().removeMe();
+ }
+ else {
+ _textframes.removeFirst();
+ }
+ }
+ catch ( final NoSuchElementException e ) {
+ // Ignore.
+ }
+ }
+ }
+
+ void clearCurrentExternalNodesDataBuffer() {
+ getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
+ }
+
+ void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
+ if ( item != null ) {
+ item.setFont( MainFrame.menu_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
+ item.setForeground( getConfiguration().getGuiMenuTextColor() );
+ }
+ item.setSelected( is_selected );
+ item.addActionListener( this );
+ }
+ }
+
+ void customizeJMenuItem( final JMenuItem jmi ) {
+ if ( jmi != null ) {
+ jmi.setFont( MainFrame.menu_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
+ jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
+ }
+ jmi.addActionListener( this );
+ }
+ }
+
+ void displayBasicInformation() {
+ if ( ( getMainPanel() != null ) && ( getMainPanel().getCurrentPhylogeny() != null )
+ && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
+ String title = "Basic Information";
+ if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
+ title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
+ }
+ showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title );
+ }
+ }
+
+ void executeGSDI() {
+ if ( !isOKforSDI( false, true ) ) {
+ return;
+ }
+ if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
+ JOptionPane.showMessageDialog( this,
+ "Gene tree is not rooted.",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
+ gene_tree.setAllNodesToNotCollapse();
+ gene_tree.recalculateNumberOfExternalDescendants( false );
+ GSDI gsdi = null;
+ final Phylogeny species_tree = _species_tree.copy();
+ try {
+ gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
+ }
+ catch ( final SDIException e ) {
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Error during GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final Exception e ) {
+ AptxUtil.unexpectedException( e );
+ return;
+ }
+ gene_tree.setRerootable( false );
+ gene_tree.clearHashIdToNodeMap();
+ gene_tree.recalculateNumberOfExternalDescendants( true );
+ _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
+ getMainPanel().getControlPanel().setShowEvents( true );
+ showWhole();
+ final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
+ showWhole();
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );
+ showWhole();
+ _mainpanel.getCurrentTreePanel().setEdited( true );
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
+ if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
+ JOptionPane.showMessageDialog( this,
+ "Duplications: " + gsdi.getDuplicationsSum() + "\n"
+ + "Potential duplications: "
+ + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
+ + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
+ + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
+ + "Number of polytomies in species tree used: " + poly + "\n",
+ "GSDI successfully completed",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ else {
+ JOptionPane.showMessageDialog( this,
+ "Duplications: " + gsdi.getDuplicationsSum() + "\n"
+ + "Potential duplications: "
+ + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
+ + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
+ + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
+ + "Number of polytomies in species tree used: " + poly + "\n",
+ "GSDI successfully completed",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ }
+
+ void executeGSDIR() {
+ if ( !isOKforSDI( false, false ) ) {
+ return;
+ }
+ final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
+ if ( ( p > 0 )
+ && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
+ JOptionPane.showMessageDialog( this,
+ "Gene tree is not completely binary",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
+ gene_tree.setAllNodesToNotCollapse();
+ gene_tree.recalculateNumberOfExternalDescendants( false );
+ GSDIR gsdir = null;
+ final Phylogeny species_tree = _species_tree.copy();
+ try {
+ gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
+ }
+ catch ( final SDIException e ) {
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Error during GSDIR",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final Exception e ) {
+ AptxUtil.unexpectedException( e );
+ return;
+ }
+ final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
+ result_gene_tree.setRerootable( false );
+ result_gene_tree.clearHashIdToNodeMap();
+ result_gene_tree.recalculateNumberOfExternalDescendants( true );
+ PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
+ _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
+ getMainPanel().getControlPanel().setShowEvents( true );
+ showWhole();
+ final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
+ showWhole();
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );
+ showWhole();
+ _mainpanel.getCurrentTreePanel().setEdited( true );
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
+ if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
+ JOptionPane.showMessageDialog( this,
+ "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
+ + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
+ + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
+ + "Number of polytomies in species tree used: " + poly + "\n",
+ "GSDIR successfully completed",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ else {
+ JOptionPane.showMessageDialog( this,
+ "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
+ + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
+ + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
+ + "Number of polytomies in species tree used: " + poly + "\n",
+ "GSDIR successfully completed",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ }
+
+ Configuration getConfiguration() {
+ return _configuration;
+ }
+
+ File getCurrentDir() {
+ if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
+ if ( ForesterUtil.isWindows() ) {
+ try {
+ _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
+ }
+ catch ( final Exception e ) {
+ _current_dir = null;
+ }
+ }
+ }
+ if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
+ if ( System.getProperty( "user.home" ) != null ) {
+ _current_dir = new File( System.getProperty( "user.home" ) );
+ }
+ else if ( System.getProperty( "user.dir" ) != null ) {
+ _current_dir = new File( System.getProperty( "user.dir" ) );
+ }
+ }
+ return _current_dir;
+ }
+
+ TreePanel getCurrentTreePanel() {
+ return getMainPanel().getCurrentTreePanel();
+ }
+
+ JCheckBoxMenuItem getlabelDirectionCbmi() {
+ return _label_direction_cbmi;
+ }
+
+ MainPanel getMainPanel() {
+ return _mainpanel;
+ }
+
+ Options getOtions() {
+ return _options;
+ }
+
+ void initializeTypeMenu( final Options options ) {
+ setTypeMenuToAllUnselected();
+ try {
+ switch ( options.getPhylogenyGraphicsType() ) {
+ case CONVEX:
+ _convex_type_cbmi.setSelected( true );
+ break;
+ case CURVED:
+ _curved_type_cbmi.setSelected( true );
+ break;
+ case EURO_STYLE:
+ _euro_type_cbmi.setSelected( true );
+ break;
+ case ROUNDED:
+ _rounded_type_cbmi.setSelected( true );
+ break;
+ case TRIANGULAR:
+ _triangular_type_cbmi.setSelected( true );
+ break;
+ case UNROOTED:
+ _unrooted_type_cbmi.setSelected( true );
+ break;
+ case CIRCULAR:
+ _circular_type_cbmi.setSelected( true );
+ break;
+ default:
+ _rectangular_type_cbmi.setSelected( true );
+ break;
+ }
+ }
+ catch ( final NullPointerException np ) {
+ // In all likelihood, this is caused by menu-less display.
+ }
+ }
+
+ boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
+ if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
+ return false;
+ }
+ else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
+ JOptionPane.showMessageDialog( this,
+ "No species tree loaded",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
+ JOptionPane.showMessageDialog( this,
+ "Species tree is not completely binary",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
+ JOptionPane.showMessageDialog( this,
+ "Gene tree is not completely binary",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else {
+ return true;
+ }
+ }
+
+ boolean isSubtreeDisplayed() {
+ if ( getCurrentTreePanel() != null ) {
+ if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
+ JOptionPane
+ .showMessageDialog( this,
+ "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
+ "Operation can not be exectuted on a sub-tree",
+ JOptionPane.WARNING_MESSAGE );
+ return true;
+ }
+ }
+ return false;
+ }
+
+ void removeAllTextFrames() {
+ for( final TextFrame tf : _textframes ) {
+ if ( tf != null ) {
+ tf.close();
+ }
+ }
+ _textframes.clear();
+ }
+
+ void setConfiguration( final Configuration configuration ) {
+ _configuration = configuration;
+ }
+
+ void setCurrentDir( final File current_dir ) {
+ _current_dir = current_dir;
+ }
+
+ void setOptions( final Options options ) {
+ _options = options;
+ }
+
+ void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
+ setTypeMenuToAllUnselected();
+ try {
+ switch ( type ) {
+ case CIRCULAR:
+ _circular_type_cbmi.setSelected( true );
+ break;
+ case CONVEX:
+ _convex_type_cbmi.setSelected( true );
+ break;
+ case CURVED:
+ _curved_type_cbmi.setSelected( true );
+ break;
+ case EURO_STYLE:
+ _euro_type_cbmi.setSelected( true );
+ break;
+ case ROUNDED:
+ _rounded_type_cbmi.setSelected( true );
+ break;
+ case RECTANGULAR:
+ _rectangular_type_cbmi.setSelected( true );
+ break;
+ case TRIANGULAR:
+ _triangular_type_cbmi.setSelected( true );
+ break;
+ case UNROOTED:
+ _unrooted_type_cbmi.setSelected( true );
+ break;
+ default:
+ throw new IllegalArgumentException( "unknown type: " + type );
+ }
+ }
+ catch ( final NullPointerException np ) {
+ // In all likelihood, this is caused by menu-less display.
+ }
+ }
+
+ void setTypeMenuToAllUnselected() {
+ if ( _convex_type_cbmi != null ) {
+ _convex_type_cbmi.setSelected( false );
+ }
+ if ( _curved_type_cbmi != null ) {
+ _curved_type_cbmi.setSelected( false );
+ }
+ if ( _euro_type_cbmi != null ) {
+ _euro_type_cbmi.setSelected( false );
+ }
+ if ( _rounded_type_cbmi != null ) {
+ _rounded_type_cbmi.setSelected( false );
+ }
+ if ( _triangular_type_cbmi != null ) {
+ _triangular_type_cbmi.setSelected( false );
+ }
+ if ( _rectangular_type_cbmi != null ) {
+ _rectangular_type_cbmi.setSelected( false );
+ }
+ if ( _unrooted_type_cbmi != null ) {
+ _unrooted_type_cbmi.setSelected( false );
+ }
+ if ( _circular_type_cbmi != null ) {
+ _circular_type_cbmi.setSelected( false );
+ }
+ }
+
+ void showWhole() {
+ _mainpanel.getControlPanel().showWhole();
+ }
+
+ void switchColors() {
+ final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
+ final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
+ csc.setVisible( true );
+ getMainPanel().setTreeColorSet( colorset );
+ }
+
+ void typeChanged( final Object o ) {
+ updateTypeCheckboxes( getOptions(), o );
+ updateOptions( getOptions() );
+ if ( getCurrentTreePanel() != null ) {
+ final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
+ final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
+ if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
+ || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
+ || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
+ || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
+ getCurrentTreePanel().getControlPanel().showWhole();
+ }
+ if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
+ getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
+ }
+ else {
+ getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
+ }
+ getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
+ MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
+ }
+ }
+
+ void updateOptions( final Options options ) {
+ options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
+ options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
+ && _background_gradient_cbmi.isSelected() );
+ options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
+ options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
+ && _show_annotation_ref_source.isSelected() );
+ options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
+ && _abbreviate_scientific_names.isSelected() );
+ options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
+ && _color_labels_same_as_parent_branch.isSelected() );
+ options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
+ && _show_default_node_shapes_internal_cbmi.isSelected() );
+ options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
+ && _show_default_node_shapes_external_cbmi.isSelected() );
+ options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
+ && _show_default_node_shapes_for_marked_cbmi.isSelected() );
+ if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
+ options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
+ }
+
+ else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
+ options.setCladogramType( CLADOGRAM_TYPE.LINED_UP );
+ }
+ options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
+ && _search_case_senstive_cbmi.isSelected() );
+ if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
+ options.setShowScale( _show_scale_cbmi.isSelected() );
+ }
+ if ( _label_direction_cbmi != null ) {
+ if ( _label_direction_cbmi.isSelected() ) {
+ options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
+ }
+ else {
+ options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
+ }
+ }
+ options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
+ options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
+ && _show_confidence_stddev_cbmi.isSelected() );
+ options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
+ && _search_whole_words_only_cbmi.isSelected() );
+ options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );
+ options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
+ && _inverse_search_result_cbmi.isSelected() );
+ options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
+ options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
+ && _print_black_and_white_cbmi.isSelected() );
+ if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
+ }
+ else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
+ }
+ else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
+ }
+ else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
+ }
+ else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
+ }
+ else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
+ }
+ else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
+ }
+ else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
+ }
+ if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
+ options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
+ }
+ if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
+ options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
+ }
+ if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
+ options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
+ }
+ if ( _graphics_export_visible_only_cbmi != null ) {
+ options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
+ }
+ }
+
+ void updateTypeCheckboxes( final Options options, final Object o ) {
+ setTypeMenuToAllUnselected();
+ ( ( JCheckBoxMenuItem ) o ).setSelected( true );
+ }
+
+ void viewAsNexus() {
+ if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
+ String title = "Nexus";
+ if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
+ }
+ showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
+ .getNhConversionSupportValueStyle() ),
+ title );
+ }
+ }
+
+ void viewAsNH() {
+ if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
+ String title = "New Hampshire";
+ if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
+ }
+ showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions()
+ .getNhConversionSupportValueStyle() ),
+ title );
+ }
+ }
+
+ void viewAsXML() {
+ if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
+ String title = "phyloXML";
+ if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
+ }
+ showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
+ }
+ }
+
+ static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {
+ mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );
+ }
+
+ static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
+ for( final TreePanel tree_panel : treepanels ) {
+ tree_panel.setTextAntialias();
+ }
+ }
+}
\ No newline at end of file
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// Copyright (C) 2000-2001 Washington University School of Medicine
+// and Howard Hughes Medical Institute
+// Copyright (C) 2003-2007 Ethalinda K.S. Cannon
+// All rights reserved
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+//
+// Contact: phylosoft @ gmail . com
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
+
+package org.forester.archaeopteryx;
+
+import java.awt.BorderLayout;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JApplet;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
+import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.util.ForesterUtil;
+
+public final class MainFrameApplet extends MainFrame {
+
+ private static final long serialVersionUID = 1941019292746717053L;
+ private final static int DEFAULT_FRAME_X_SIZE = 640;
+ private final static int DEFAULT_FRAME_Y_SIZE = 580;
+ private final ArchaeopteryxA _applet;
+ private ButtonGroup _radio_group_1;
+
+ MainFrameApplet( final ArchaeopteryxA parent_applet,
+ final Configuration configuration,
+ final String species_tree_url_str ) {
+ setTitle( ArchaeopteryxA.NAME );
+ _applet = parent_applet;
+ setConfiguration( configuration );
+ setOptions( Options.createInstance( configuration ) );
+ _mainpanel = new MainPanelApplets( _configuration, this );
+ if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
+ try {
+ readSpeciesTree( configuration, species_tree_url_str );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "failed to read species tree from "
+ + species_tree_url_str );
+ ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, e.toString() );
+ }
+ }
+ // build the menu bar
+ _jmenubar = new JMenuBar();
+ buildFileMenu();
+ if ( !_configuration.isUseNativeUI() ) {
+ _jmenubar.setBackground( _configuration.getGuiMenuBackgroundColor() );
+ }
+ buildAnalysisMenu();
+ buildToolsMenu();
+ buildViewMenu();
+ buildFontSizeMenu();
+ buildOptionsMenu();
+ buildTypeMenu();
+ buildHelpMenu();
+ setJMenuBar( _jmenubar );
+ _contentpane = getContentPane();
+ _contentpane.setLayout( new BorderLayout() );
+ _contentpane.add( _mainpanel, BorderLayout.CENTER );
+ setSize( getConfiguration().getFrameXSize() > 40 ? getConfiguration().getFrameXSize() : DEFAULT_FRAME_X_SIZE,
+ getConfiguration().getFrameYSize() > 40 ? getConfiguration().getFrameYSize() : DEFAULT_FRAME_Y_SIZE );
+ addWindowListener( new WindowAdapter() {
+
+ @Override
+ public void windowClosing( final WindowEvent e ) {
+ close();
+ }
+ } );
+ addComponentListener( new ComponentAdapter() {
+
+ @Override
+ public void componentResized( final ComponentEvent e ) {
+ if ( _mainpanel.getCurrentTreePanel() != null ) {
+ _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()
+ .getWidth(),
+ _mainpanel.getCurrentTreePanel()
+ .getHeight() );
+ }
+ }
+ } );
+ setFocusable( true );
+ requestFocus();
+ requestFocusInWindow();
+ setVisible( true );
+ System.gc();
+ }
+
+ @Override
+ public MainPanel getMainPanel() {
+ return _mainpanel;
+ }
+
+ private void readSpeciesTree( final Configuration configuration, final String species_tree_url_str )
+ throws MalformedURLException, FileNotFoundException, IOException {
+ final URL species_tree_url = new URL( species_tree_url_str );
+ final Phylogeny[] species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
+ configuration
+ .isValidatePhyloXmlAgainstSchema(),
+ configuration
+ .isReplaceUnderscoresInNhParsing(),
+ false,
+ TAXONOMY_EXTRACTION.NO,
+ false );
+ if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
+ AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "successfully read species tree" );
+ if ( species_trees[ 0 ].isEmpty() ) {
+ ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "species tree is empty" );
+ }
+ else if ( !species_trees[ 0 ].isRooted() ) {
+ ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "species tree is not rooted" );
+ }
+ else {
+ setSpeciesTree( species_trees[ 0 ] );
+ AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "species tree OK" );
+ }
+ }
+ else {
+ ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "failed to read species tree from "
+ + species_tree_url_str );
+ }
+ }
+
+ void buildAnalysisMenu() {
+ _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
+ if ( getSpeciesTree() != null ) {
+ _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
+ _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
+ customizeJMenuItem( _gsdi_item );
+ customizeJMenuItem( _gsdir_item );
+ _analysis_menu.addSeparator();
+ }
+ _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
+ customizeJMenuItem( _lineage_inference );
+ _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
+ _jmenubar.add( _analysis_menu );
+ }
+
+ void buildOptionsMenu() {
+ _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
+ _options_jmenu.addChangeListener( new ChangeListener() {
+
+ @Override
+ public void stateChanged( final ChangeEvent e ) {
+ MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
+ MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
+ MainFrame
+ .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
+ MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, createCurrentFontDesc( getMainPanel()
+ .getTreeFontSet() ) );
+ // setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
+ setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
+ MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
+ MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
+ MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
+ try {
+ getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
+ getMainPanel().getControlPanel().setVisibilityOfX();
+ }
+ catch ( final Exception ignore ) {
+ // do nothing, not important.
+ }
+ }
+ } );
+ _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
+ getConfiguration() ) );
+ _options_jmenu
+ .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
+ _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
+ _radio_group_1 = new ButtonGroup();
+ _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
+ _radio_group_1.add( _non_lined_up_cladograms_rbmi );
+ _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
+ _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
+ _options_jmenu
+ .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
+ _options_jmenu
+ .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
+ _options_jmenu
+ .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
+ _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
+ if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
+ _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
+ _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
+ }
+ _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
+ _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
+ _options_jmenu
+ .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
+ _options_jmenu
+ .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
+ _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
+ _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
+ _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
+ _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
+ _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
+ _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
+ _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
+ _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
+ _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
+ _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
+ _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
+ _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
+ _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
+ _options_jmenu.addSeparator();
+ _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
+ getConfiguration() ) );
+ _options_jmenu
+ .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
+ _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
+ _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
+ _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );
+ _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
+
+ _options_jmenu.addSeparator();
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
+ getConfiguration() ) );
+ _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
+ _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
+ _options_jmenu
+ .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
+ _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
+
+ customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
+ customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
+ customizeJMenuItem( _choose_pdf_width_mi );
+
+ customizeJMenuItem( _choose_font_mi );
+ customizeJMenuItem( _switch_colors_mi );
+ customizeJMenuItem( _choose_minimal_confidence_mi );
+ customizeJMenuItem( _overview_placment_mi );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
+ .isShowDefaultNodeShapesInternal() );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
+ .isShowDefaultNodeShapesExternal() );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
+ .isShowDefaultNodeShapesForMarkedNodes() );
+ customizeJMenuItem( _cycle_node_shape_mi );
+ customizeJMenuItem( _cycle_node_fill_mi );
+ customizeJMenuItem( _choose_node_size_mi );
+ customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
+ customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
+ customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
+ customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
+ customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
+ customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
+ customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
+ customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
+ customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
+ customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
+ customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.LINED_UP );
+ customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
+ customizeCheckBoxMenuItem( _label_direction_cbmi,
+ getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
+ customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );
+ customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
+ customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
+ customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
+ customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
+ customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
+ _jmenubar.add( _options_jmenu );
+ }
+
+ void buildToolsMenu() {
+ _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
+ _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
+ customizeJMenuItem( _confcolor_item );
+ _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
+ customizeJMenuItem( _taxcolor_item );
+ _tools_menu.addSeparator();
+ _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
+ _remove_visual_styles_item
+ .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
+ customizeJMenuItem( _remove_visual_styles_item );
+ _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
+ _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
+ customizeJMenuItem( _remove_branch_color_item );
+ _tools_menu.addSeparator();
+ _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
+ customizeJMenuItem( _midpoint_root_item );
+ _tools_menu.addSeparator();
+ _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
+ customizeJMenuItem( _collapse_species_specific_subtrees );
+ _jmenubar.add( _tools_menu );
+ }
+
+ JApplet getApplet() {
+ return _applet;
+ }
+}
git://source.jalview.org / jalview.git / commitdiff