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 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"
private final static String NAME = "ArchaeopteryxE";
private static final long serialVersionUID = -1220055577935759443L;
private Configuration _configuration;
- private MainPanelApplets _mainpanel;
+ private MainPanel _mainpanel;
private JMenuBar _jmenubar;
private JMenu _options_jmenu;
private JMenu _font_size_menu;
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 _uniform_cladograms_rbmi;
private JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
private JCheckBoxMenuItem _search_case_senstive_cbmi;
private JCheckBoxMenuItem _search_whole_words_only_cbmi;
private JCheckBoxMenuItem _inverse_search_result_cbmi;
+ private JCheckBoxMenuItem _search_with_regex_cbmi;
private JCheckBoxMenuItem _show_overview_cbmi;
private JMenuItem _choose_minimal_confidence_mi;
- private JCheckBoxMenuItem _show_branch_length_values_cbmi;
private JMenuItem _collapse_species_specific_subtrees;
private JMenuItem _overview_placment_mi;
private ButtonGroup _radio_group_1;
private JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;
private JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;
+ private JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi;
private JMenuItem _cycle_node_shape_mi;
private JMenuItem _cycle_node_fill_mi;
private JMenuItem _choose_node_size_mi;
- private JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi;
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 JCheckBoxMenuItem _print_using_actual_size_cbmi;
+ private JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;
+ private JMenuItem _print_size_mi;
+ private JMenuItem _choose_pdf_width_mi;
@Override
public void actionPerformed( final ActionEvent e ) {
else if ( o == _remove_branch_color_item ) {
removeBranchColors();
}
+ else if ( o == _remove_visual_styles_item ) {
+ removeVisualStyles();
+ }
else if ( o == _switch_colors_mi ) {
switchColors();
}
MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
}
else if ( o == _cycle_node_fill_mi ) {
- MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
+ MainFrame.cycleNodeFill( getOptions() );
}
else if ( o == _cycle_node_shape_mi ) {
- MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
+ MainFrame.cycleNodeShape( getOptions() );
}
else if ( o == _non_lined_up_cladograms_rbmi ) {
updateOptions( getOptions() );
}
else if ( o == _search_case_senstive_cbmi ) {
updateOptions( getOptions() );
- getMainPanel().getControlPanel().search();
+ 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().search();
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
}
else if ( o == _inverse_search_result_cbmi ) {
updateOptions( getOptions() );
- getMainPanel().getControlPanel().search();
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
}
- else if ( o == _show_scale_cbmi ) {
+ else if ( o == _search_with_regex_cbmi ) {
+ if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
+ _search_whole_words_only_cbmi.setSelected( false );
+ }
+ if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
+ _search_case_senstive_cbmi.setSelected( true );
+ }
updateOptions( getOptions() );
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
}
- else if ( o == _show_branch_length_values_cbmi ) {
+ else if ( o == _show_scale_cbmi ) {
updateOptions( getOptions() );
}
else if ( o == _show_confidence_stddev_cbmi ) {
else if ( o == _show_default_node_shapes_external_cbmi ) {
updateOptions( getOptions() );
}
- else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
- updateOptions( getOptions() );
- }
else if ( o == _about_item ) {
MainFrame.about();
}
else if ( o == _help_item ) {
- help();
+ 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( Constants.APTX_WEB_SITE, true, this );
+ AptxUtil.openWebsite( AptxConstants.APTX_WEB_SITE, true, this );
}
catch ( final IOException e1 ) {
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
}
}
else if ( o == _phyloxml_website_item ) {
try {
- AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
+ AptxUtil.openWebsite( AptxConstants.PHYLOXML_WEB_SITE, true, this );
}
catch ( final IOException e1 ) {
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
}
}
else if ( o == _aptx_ref_item ) {
try {
- AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
+ AptxUtil.openWebsite( AptxConstants.APTX_REFERENCE_URL, true, this );
}
catch ( final IOException e1 ) {
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
}
}
else if ( o == _phyloxml_ref_item ) {
try {
- AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
+ AptxUtil.openWebsite( AptxConstants.PHYLOXML_REFERENCE_URL, true, this );
}
catch ( final IOException e1 ) {
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
+ 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 == _print_using_actual_size_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _graphics_export_using_actual_size_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _print_size_mi ) {
+ choosePrintSize();
+ }
+ else if ( o == _choose_pdf_width_mi ) {
+ choosePdfWidth();
+ }
repaint();
}
* 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() {
/**
* 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
}
/**
- * This method returns a view of the current phylogeny in a chosen
+ * This method returns a view of the current phylogeny in a chosen
* graphics format, base64-encoded in a string so that in can be used
* from javascript.
- *
+ *
* @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
* @return the phylogeny string
* @author Herve Menager
@Override
public void init() {
- final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
+ _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();
- URL phys_url = null;
- Phylogeny[] phys = null;
- final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+ 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
- if ( tree_url_str != 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 );
- }
+ 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
- if ( phys_url != 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 ) || ( phys.length < 1 ) ) {
- ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null or empty" );
+ 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 or empty",
+ 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;
AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
}
//
- final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
+ 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;
}
}
}
- //
- setVisible( false );
- setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
- _jmenubar = new JMenuBar();
- if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
- if ( !getConfiguration().isUseNativeUI() ) {
- _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
+ try {
+ setVisible( false );
+ setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
+ _jmenubar = new JMenuBar();
+ if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
+ buildFileMenu();
+ if ( !getConfiguration().isUseNativeUI() ) {
+ _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
+ }
+ if ( getSpeciesTree() != null ) {
+ buildAnalysisMenu();
+ }
+ buildToolsMenu();
+ buildViewMenu();
+ buildFontSizeMenu();
+ buildOptionsMenu();
+ buildTypeMenu();
+ buildHelpMenu();
+ setJMenuBar( _jmenubar );
}
- if ( getSpeciesTree() != null ) {
- buildAnalysisMenu();
+ final Container contentpane = getContentPane();
+ contentpane.setLayout( new BorderLayout() );
+ contentpane.add( getMainPanel(), BorderLayout.CENTER );
+ addComponentListener( new ComponentAdapter() {
+
+ @Override
+ public void componentResized( final ComponentEvent e ) {
+ if ( getMainPanel().getCurrentTreePanel() != null ) {
+ getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
+ .getCurrentTreePanel()
+ .getWidth(),
+ getMainPanel()
+ .getCurrentTreePanel()
+ .getHeight() );
+ }
+ }
+ } );
+ if ( getConfiguration().isUseTabbedDisplay() ) {
+ try {
+ AptxUtil.printAppletMessage( NAME, "using tabbed display" );
+ AptxUtil.addPhylogeniesToTabs( phys,
+ new File( phys_url.getFile() ).getName(),
+ phys_url.toString(),
+ getConfiguration(),
+ getMainPanel() );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.printErrorMessage( NAME, e.toString() );
+ e.printStackTrace();
+ }
}
- buildToolsMenu();
- buildViewMenu();
- buildFontSizeMenu();
- buildOptionsMenu();
- buildTypeMenu();
- buildHelpMenu();
- setJMenuBar( _jmenubar );
- }
- final Container contentpane = getContentPane();
- contentpane.setLayout( new BorderLayout() );
- contentpane.add( getMainPanel(), BorderLayout.CENTER );
- addComponentListener( new ComponentAdapter() {
-
- @Override
- public void componentResized( final ComponentEvent e ) {
- if ( getMainPanel().getCurrentTreePanel() != null ) {
- getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
- .getCurrentTreePanel()
- .getWidth(),
- getMainPanel()
- .getCurrentTreePanel()
- .getHeight(),
- getOptions()
- .isAllowFontSizeChange() );
+ else {
+ AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
+ if ( getSpeciesTree() != null ) {
+ AptxUtil.printAppletMessage( NAME,
+ "Warning: gsdi (gene duplication inference) only available tabbed display" );
}
+ AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
}
- } );
- if ( getConfiguration().isUseTabbedDisplay() ) {
- AptxUtil.printAppletMessage( NAME, "using tabbed display" );
- AptxUtil.addPhylogeniesToTabs( phys,
- new File( phys_url.getFile() ).getName(),
- phys_url.toString(),
- getConfiguration(),
- getMainPanel() );
- }
- else {
- AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
- if ( getSpeciesTree() != null ) {
- AptxUtil.printAppletMessage( NAME,
- "Warning: gsdi (gene duplication inference) only available tabbed display" );
+ validate();
+ setName( NAME );
+ getMainPanel().getControlPanel().showWholeAll();
+ getMainPanel().getControlPanel().showWhole();
+ /* GUILHEM_BEG */
+ getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
+ for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
+ .getRelevantSequenceRelationTypes() ) {
+ getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
}
- AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
- }
- validate();
- setName( NAME );
- getMainPanel().getControlPanel().showWholeAll();
- getMainPanel().getControlPanel().showWhole();
- System.gc();
- AptxUtil.printAppletMessage( NAME, "successfully initialized" );
- /* GUILHEM_BEG */
- getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
- for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
- .getRelevantSequenceRelationTypes() ) {
- getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
- }
- final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
- if ( default_relation != null ) {
- getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
+ final String default_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 );
}
- final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
- if ( default_sequence != null ) {
- getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
+ catch ( final Exception e ) {
+ ForesterUtil.printErrorMessage( NAME, e.toString() );
+ e.printStackTrace();
}
- /* GUILHEM_END */
- setVisible( true );
}
public void showTextFrame( final String s, final String title ) {
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 choosePrintSize() {
+ final String s = ( String ) JOptionPane.showInputDialog( this,
+ "Please enter values for width and height,\nseparated by a comma.\n"
+ + "[current values: "
+ + getOptions().getPrintSizeX() + ", "
+ + getOptions().getPrintSizeY() + "]\n"
+ + "[A4: " + AptxConstants.A4_SIZE_X + ", "
+ + AptxConstants.A4_SIZE_Y + "]\n" + "[US Letter: "
+ + AptxConstants.US_LETTER_SIZE_X + ", "
+ + AptxConstants.US_LETTER_SIZE_Y + "]",
+ "Default Size for Graphics Export",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ getOptions().getPrintSizeX() + ", "
+ + getOptions().getPrintSizeY() );
+ if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {
+ boolean success = true;
+ int x = 0;
+ int y = 0;
+ final String[] str_ary = s.split( "," );
+ if ( str_ary.length == 2 ) {
+ final String x_str = str_ary[ 0 ].trim();
+ final String y_str = str_ary[ 1 ].trim();
+ if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {
+ try {
+ x = Integer.parseInt( x_str );
+ y = Integer.parseInt( y_str );
+ }
+ catch ( final Exception ex ) {
+ success = false;
+ }
+ }
+ else {
+ success = false;
+ }
+ }
+ else {
+ success = false;
+ }
+ if ( success && ( x > 1 ) && ( y > 1 ) ) {
+ getOptions().setPrintSizeX( x );
+ getOptions().setPrintSizeY( y );
+ }
+ }
+ }
+
+ 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();
- // _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
- // customizeJMenuItem( _lineage_inference );
- // _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
+ _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" ) );
void buildHelpMenu() {
_help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
- _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
+ _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" ) );
.setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
.createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
- MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
- _show_scale_cbmi,
- _show_branch_length_values_cbmi,
- _non_lined_up_cladograms_rbmi,
- _uniform_cladograms_rbmi,
- _ext_node_dependent_cladogram_rbmi,
- _label_direction_cbmi );
+ 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 ),
_options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
_options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
_options_jmenu
- .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
- _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_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( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_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( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
+ .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 ) );
- if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
- _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_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( _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( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
+ _options_jmenu
+ .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
+ _options_jmenu
+ .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
+ _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
+ _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() );
+ customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
+ customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
+ .isGraphicsExportUsingActualSize() );
+ customizeJMenuItem( _print_size_mi );
+ 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( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
+ 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 );
getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
- customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
+ customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );
customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
+ customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
+ customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
_jmenubar.add( _options_jmenu );
}
customizeJMenuItem( _confcolor_item );
_tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
customizeJMenuItem( _taxcolor_item );
- _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
- _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
+ _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" ) );
_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( "View as phyloXML" ) );
- _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
- _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
+ _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 );
}
void customizeJMenuItem( final JMenuItem jmi ) {
- jmi.setFont( MainFrame.menu_font );
- if ( !getConfiguration().isUseNativeUI() ) {
- jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
- jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
+ if ( jmi != null ) {
+ jmi.setFont( MainFrame.menu_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
+ jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
+ }
+ jmi.addActionListener( this );
}
- jmi.addActionListener( this );
}
void displayBasicInformation() {
- if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
+ if ( ( getMainPanel() != null ) && ( getMainPanel().getCurrentPhylogeny() != null )
+ && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
String title = "Basic Information";
if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
- title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
+ title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
}
- showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title );
+ showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title );
}
}
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();
}
return _label_direction_cbmi;
}
- Options getOtions() {
- return _options;
+ MainPanel getMainPanel() {
+ return _mainpanel;
}
- void help() {
- final StringBuilder sb = new StringBuilder();
- sb.append( "Display options\n" );
- sb.append( "-------------------\n" );
- sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
- sb.append( "Clickable tree nodes\n" );
- sb.append( "--------------------\n" );
- sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
- sb.append( "or by right clicking:\n" );
- sb.append( "o Display Node Data -- display information for a node\n" );
- sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
- sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
- sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
- sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
- sb.append( "o Colorize Subtree -- color a subtree\n" );
- sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
- sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
- sb.append( "- there may be additional choices depending on this particular setup\n\n" );
- sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
- sb.append( "Zooming\n" );
- sb.append( "---------\n" );
- sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
- sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
- sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
- sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
- sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
- sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
- sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
- sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
- sb.append( "Quick tree manipulation:\n" );
- sb.append( "------------------------\n" );
- sb.append( "Order Subtrees -- order the tree by branch length\n" );
- sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
- sb.append( "phyloXML\n" );
- sb.append( "-------------------\n" );
- sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
- sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
- sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
- sb.append( "\n" );
- sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
- sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
- TextFrame.instantiate( sb.toString(), "Help", _textframes );
+ Options getOtions() {
+ return _options;
}
void initializeTypeMenu( final Options options ) {
_configuration = configuration;
}
+ void setCurrentDir( final File current_dir ) {
+ _current_dir = current_dir;
+ }
+
void setOptions( final Options options ) {
_options = options;
}
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 )
&& _show_default_node_shapes_internal_cbmi.isSelected() );
options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
&& _show_default_node_shapes_external_cbmi.isSelected() );
- options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
- && _taxonomy_colorize_node_shapes_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 );
}
options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
&& _show_confidence_stddev_cbmi.isSelected() );
- if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
- options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
- }
options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
&& _search_whole_words_only_cbmi.isSelected() );
+ options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );
options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
&& _inverse_search_result_cbmi.isSelected() );
+ options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
+ && ( _print_using_actual_size_cbmi.isSelected() ) );
+ options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
+ && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
+ options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
+ 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 ( ( _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() );
+ if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
+ _graphics_export_using_actual_size_cbmi.setSelected( true );
+ _graphics_export_using_actual_size_cbmi.setEnabled( false );
+ }
+ else {
+ _graphics_export_using_actual_size_cbmi.setEnabled( true );
+ }
+ }
}
void updateTypeCheckboxes( final Options options, final Object o ) {
if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
String title = "Nexus";
if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
- title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
}
showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
.getNhConversionSupportValueStyle() ),
if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
String title = "New Hampshire";
if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
- title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
}
- showTextFrame( getMainPanel().getCurrentPhylogeny()
- .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
+ showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions()
+ .getNhConversionSupportValueStyle() ),
title );
}
}
if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
String title = "phyloXML";
if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
- title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
}
showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
}
}
- 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() );
+ static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
+ mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
+ + o.getPrintSizeY() + ")" );
}
- 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 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 MainPanel getMainPanel() {
- return _mainpanel;
- }
-
- private Phylogeny getSpeciesTree() {
- return _species_tree;
- }
-
- private boolean isScreenAntialias() {
- return true;
- }
-
- private void removeBranchColors() {
- if ( getMainPanel().getCurrentPhylogeny() != null ) {
- AptxUtil.removeBranchColors( 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() );
- }
+ 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 ) {
git://source.jalview.org / jalview.git / blobdiff