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.List;
import javax.swing.ButtonGroup;
import javax.swing.JApplet;
import javax.swing.JCheckBoxMenuItem;
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.Options.CLADOGRAM_TYPE;
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
import org.forester.archaeopteryx.Util.GraphicsExportType;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.data.SequenceRelation;
import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
// Use like this:
//
public class ArchaeopteryxE extends JApplet implements ActionListener {
private final static String NAME = "ArchaeopteryxE";
private static final long serialVersionUID = -1220055577935759443L;
private Configuration _configuration;
private MainPanelApplets _main_panel;
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 TextFrame _textframe;
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_NHX_item;
private JMenuItem _view_as_nexus_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 _infer_common_sn_names_item;
private JCheckBoxMenuItem _show_domain_labels;
private JCheckBoxMenuItem _color_labels_same_as_parent_branch;
private JCheckBoxMenuItem _abbreviate_scientific_names;
private JCheckBoxMenuItem _screen_antialias_cbmi;
private JCheckBoxMenuItem _background_gradient_cbmi;
private JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
private JRadioButtonMenuItem _uniform_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 _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_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;
@Override
public void actionPerformed( final ActionEvent e ) {
final Object o = e.getSource();
if ( o == _midpoint_root_item ) {
getMainPanel().getCurrentTreePanel().midpointRoot();
}
else if ( o == _taxcolor_item ) {
getMainPanel().getCurrentTreePanel().taxColor();
}
else if ( o == _confcolor_item ) {
getMainPanel().getCurrentTreePanel().confColor();
}
else if ( o == _infer_common_sn_names_item ) {
if ( getCurrentTreePanel() != null ) {
getCurrentTreePanel().inferCommonPartOfScientificNames();
}
}
else if ( o == _collapse_species_specific_subtrees ) {
if ( getCurrentTreePanel() != null ) {
getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
}
}
else if ( o == _remove_branch_color_item ) {
removeBranchColors();
}
else if ( o == _switch_colors_mi ) {
switchColors();
}
else if ( o == _view_as_NH_item ) {
viewAsNH();
}
else if ( o == _view_as_NHX_item ) {
viewAsNHX();
}
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(), getCurrentTreePanel() );
}
else if ( o == _cycle_node_shape_mi ) {
MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
}
else if ( o == _non_lined_up_cladograms_rbmi ) {
updateOptions( getOptions() );
_main_panel.getControlPanel().showWhole();
}
else if ( o == _uniform_cladograms_rbmi ) {
updateOptions( getOptions() );
_main_panel.getControlPanel().showWhole();
}
else if ( o == _ext_node_dependent_cladogram_rbmi ) {
updateOptions( getOptions() );
_main_panel.getControlPanel().showWhole();
}
else if ( o == _search_case_senstive_cbmi ) {
updateOptions( getOptions() );
getMainPanel().getControlPanel().search();
}
else if ( o == _search_whole_words_only_cbmi ) {
updateOptions( getOptions() );
getMainPanel().getControlPanel().search();
}
else if ( o == _inverse_search_result_cbmi ) {
updateOptions( getOptions() );
getMainPanel().getControlPanel().search();
}
else if ( o == _show_scale_cbmi ) {
updateOptions( getOptions() );
}
else if ( o == _show_branch_length_values_cbmi ) {
updateOptions( getOptions() );
}
else if ( o == _label_direction_cbmi ) {
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_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 ) {
MainFrame.help( getConfiguration().getWebLinks() );
}
else if ( o == _website_item ) {
try {
Util.openWebsite( Constants.APTX_WEB_SITE, true, this );
}
catch ( final IOException e1 ) {
ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
}
}
else if ( o == _phyloxml_website_item ) {
try {
Util.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
}
catch ( final IOException e1 ) {
ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
}
}
else if ( o == _aptx_ref_item ) {
try {
Util.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
}
catch ( final IOException e1 ) {
ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
}
}
else if ( o == _phyloxml_ref_item ) {
try {
Util.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
}
catch ( final IOException e1 ) {
ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
}
}
repaint();
}
/**
* 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 ) {
removeTextFrame();
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 {
Util.writePhylogenyToGraphicsByteArrayOutputStream( baos,
_main_panel.getWidth(),
_main_panel.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;
}
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( "Help" ) );
_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() ) );
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 );
MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
}
} );
_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( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_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( _uniform_cladograms_rbmi );
_radio_group_1.add( _non_lined_up_cladograms_rbmi );
//
_options_jmenu
.add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL ) );
_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( _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_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
_options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
_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 ) );
_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( _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( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
customizeJMenuItem( _choose_font_mi );
customizeJMenuItem( _choose_minimal_confidence_mi );
customizeJMenuItem( _switch_colors_mi );
customizeJMenuItem( _overview_placment_mi );
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( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
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( _uniform_cladograms_rbmi,
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_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
_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.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
_remove_branch_color_item.setToolTipText( "To delete 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( _infer_common_sn_names_item = new JMenuItem( "Infer Common Parts of Internal Scientific Names" ) );
customizeJMenuItem( _infer_common_sn_names_item );
_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 as Text", getConfiguration() );
_view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
_view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
_view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
_view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
customizeJMenuItem( _view_as_NH_item );
customizeJMenuItem( _view_as_NHX_item );
customizeJMenuItem( _view_as_XML_item );
customizeJMenuItem( _view_as_nexus_item );
_jmenubar.add( _view_jmenu );
}
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 );
}
}
}
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 ) {
jmi.setFont( MainFrame.menu_font );
if ( !getConfiguration().isUseNativeUI() ) {
jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
}
jmi.addActionListener( this );
}
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 );
}
}
@Override
public void destroy() {
Util.printAppletMessage( NAME, "going to be destroyed " );
removeTextFrame();
if ( getMainPanel() != null ) {
getMainPanel().terminate();
}
}
Configuration getConfiguration() {
return _configuration;
}
TreePanel getCurrentTreePanel() {
return getMainPanel().getCurrentTreePanel();
}
JCheckBoxMenuItem getlabelDirectionCbmi() {
return _label_direction_cbmi;
}
private MainPanel getMainPanel() {
return _main_panel;
}
public Options getOptions() {
return _options;
}
Options getOtions() {
return _options;
}
@Override
public void init() {
final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
Util.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
final Configuration configuration = new Configuration( config_filename, true, true );
setConfiguration( configuration );
setOptions( Options.createInstance( configuration ) );
setupUI();
URL phys_url = null;
Phylogeny[] phys = null;
final String phys_url_string = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
Util.printAppletMessage( NAME, "URL for phylogenies is " + phys_url_string );
// Get URL to tree file
if ( phys_url_string != null ) {
try {
phys_url = new URL( phys_url_string );
}
catch ( final Exception e ) {
ForesterUtil.printErrorMessage( NAME, "error: " + e );
e.printStackTrace();
JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + phys_url_string
+ "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
}
}
// Load the tree from URL
if ( phys_url != null ) {
try {
phys = Util.readPhylogeniesFromUrl( phys_url, getConfiguration().isValidatePhyloXmlAgainstSchema() );
}
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" );
JOptionPane.showMessageDialog( this,
NAME + ": phylogenies from [" + phys_url + "] are null or empty",
"Failed to read phylogenies",
JOptionPane.ERROR_MESSAGE );
return;
}
else {
Util.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
}
setVisible( false );
setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
_jmenubar = new JMenuBar();
if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
if ( !getConfiguration().isUseNativeUI() ) {
_jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
}
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().setParametersForPainting( getMainPanel().getCurrentTreePanel()
.getWidth(),
getMainPanel().getCurrentTreePanel()
.getHeight(),
false );
}
}
} );
if ( getConfiguration().isUseTabbedDisplay() ) {
Util.printAppletMessage( NAME, "using tabbed display" );
Util.addPhylogeniesToTabs( phys,
new File( phys_url.getFile() ).getName(),
phys_url.toString(),
getConfiguration(),
getMainPanel() );
}
else {
Util.printAppletMessage( NAME, "not using tabbed display" );
Util.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
}
validate();
setName( NAME );
getMainPanel().getControlPanel().showWholeAll();
getMainPanel().getControlPanel().showWhole();
System.gc();
Util.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_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
if ( default_sequence != null ) {
getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
/* GUILHEM_END */
}
setVisible( true );
}
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.
}
}
private boolean isScreenAntialias() {
return true;
}
private void removeBranchColors() {
if ( getMainPanel().getCurrentPhylogeny() != null ) {
Util.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
}
}
void removeTextFrame() {
if ( _textframe != null ) {
_textframe.close();
_textframe = null;
}
}
void setConfiguration( final Configuration configuration ) {
_configuration = configuration;
}
private void setMainPanel( final MainPanelApplets main_panel ) {
_main_panel = main_panel;
}
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 );
}
}
private void setupUI() {
try {
if ( getConfiguration().isUseNativeUI() ) {
UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
}
else {
UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
}
}
catch ( final UnsupportedLookAndFeelException e ) {
Util.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
}
catch ( final ClassNotFoundException e ) {
Util.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
}
catch ( final InstantiationException e ) {
Util.dieWithSystemError( "InstantiationException: " + e.toString() );
}
catch ( final IllegalAccessException e ) {
Util.dieWithSystemError( "IllegalAccessException: " + e.toString() );
}
catch ( final Exception e ) {
Util.dieWithSystemError( e.toString() );
}
}
@Override
public void start() {
if ( getMainPanel() != null ) {
getMainPanel().validate();
}
requestFocus();
requestFocusInWindow();
requestFocus();
Util.printAppletMessage( NAME, "started" );
}
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.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.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
&& _show_default_node_shapes_cbmi.isSelected() );
options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
&& _taxonomy_colorize_node_shapes_cbmi.isSelected() );
if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
}
else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
}
else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
}
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() );
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.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
&& _inverse_search_result_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 );
}
}
void updateTypeCheckboxes( final Options options, final Object o ) {
setTypeMenuToAllUnselected();
( ( JCheckBoxMenuItem ) o ).setSelected( true );
}
void viewAsNexus() {
removeTextFrame();
if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
|| ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
return;
}
_textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNexus() );
}
void viewAsNH() {
removeTextFrame();
if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
|| ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
return;
}
_textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNewHampshire( false ) );
}
void viewAsNHX() {
removeTextFrame();
if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
|| ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
return;
}
_textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNewHampshireX() );
}
void viewAsXML() {
removeTextFrame();
if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
|| ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
return;
}
_textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ) );
}
static void setupScreenTextAntialias( final List treepanels, final boolean antialias ) {
for( final TreePanel tree_panel : treepanels ) {
tree_panel.setTextAntialias();
}
}
}