+++ /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