import java.awt.event.ActionListener;
import java.awt.event.ComponentAdapter;
import java.awt.event.ComponentEvent;
+import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.IOException;
import java.net.URL;
+import java.util.LinkedList;
import java.util.List;
+import java.util.Map;
+import java.util.NoSuchElementException;
import javax.swing.ButtonGroup;
import javax.swing.JApplet;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
+import org.apache.commons.codec.binary.Base64;
+import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.data.SequenceRelation;
+import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
// Use like this:
// </applet>
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_node_boxes_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 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 JMenu _tools_menu;
+ private JMenuItem _taxcolor_item;
+ private JMenuItem _confcolor_item;
+ private JMenuItem _midpoint_root_item;
+ private JMenu _view_jmenu;
+ private JMenuItem _view_as_XML_item;
+ private JMenuItem _view_as_NH_item;
+ private JMenuItem _view_as_nexus_item;
+ private JMenuItem _display_basic_information_item;
+ private JMenu _type_menu;
+ private JCheckBoxMenuItem _rectangular_type_cbmi;
+ private JCheckBoxMenuItem _triangular_type_cbmi;
+ private JCheckBoxMenuItem _curved_type_cbmi;
+ private JCheckBoxMenuItem _convex_type_cbmi;
+ private JCheckBoxMenuItem _euro_type_cbmi;
+ private JCheckBoxMenuItem _rounded_type_cbmi;
+ private JCheckBoxMenuItem _unrooted_type_cbmi;
+ private JCheckBoxMenuItem _circular_type_cbmi;
+ private JMenuItem _help_item;
+ private JMenuItem _about_item;
+ private JMenu _help_jmenu;
+ private JMenuItem _website_item;
+ private JMenuItem _phyloxml_website_item;
+ private JMenuItem _phyloxml_ref_item;
+ private JMenuItem _aptx_ref_item;
+ private JMenuItem _remove_branch_color_item;
+ private 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_internal_cbmi;
+ private JCheckBoxMenuItem _show_default_node_shapes_external_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 String _ext_node_data_buffer = "";
+ // private int _ext_node_data_buffer_change_counter = 0;
@Override
public void actionPerformed( final ActionEvent e ) {
final Object o = e.getSource();
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 == _switch_colors_mi ) {
switchColors();
}
+ else if ( o == _display_basic_information_item ) {
+ displayBasicInformation();
+ }
else if ( o == _view_as_NH_item ) {
viewAsNH();
}
- else if ( o == _view_as_NHX_item ) {
- viewAsNHX();
- }
else if ( o == _view_as_XML_item ) {
viewAsXML();
}
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 == _show_node_boxes_cbmi ) {
- updateOptions( getOptions() );
+ 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() );
else if ( o == _show_branch_length_values_cbmi ) {
updateOptions( getOptions() );
}
+ else if ( o == _show_confidence_stddev_cbmi ) {
+ updateOptions( getOptions() );
+ }
else if ( o == _label_direction_cbmi ) {
updateOptions( getOptions() );
}
else if ( o == _color_labels_same_as_parent_branch ) {
updateOptions( getOptions() );
}
+ else if ( o == _show_default_node_shapes_internal_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_default_node_shapes_external_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
+ updateOptions( getOptions() );
+ }
else if ( o == _about_item ) {
MainFrame.about();
}
else if ( o == _help_item ) {
- MainFrame.help( getConfiguration().getWebLinks() );
+ help( getConfiguration().getWebLinks() );
}
else if ( o == _website_item ) {
try {
- Util.openWebsite( Constants.APTX_WEB_SITE, true, this );
+ AptxUtil.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 );
+ AptxUtil.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 );
+ AptxUtil.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 );
+ AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
}
catch ( final IOException e1 ) {
ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
repaint();
}
+ @Override
+ public void destroy() {
+ AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
+ removeAllTextFrames();
+ if ( getMainPanel() != null ) {
+ getMainPanel().terminate();
+ }
+ }
+
+ /**
+ * This method returns the current external node data which
+ * has been selected by the user by clicking the "Return ..."
+ * menu item. This method is expected to be called from Javascript or
+ * something like it.
+ *
+ * @return current external node data as String
+ */
+ public String getCurrentExternalNodesDataBuffer() {
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
+ }
+
+ public int getCurrentExternalNodesDataBufferChangeCounter() {
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
+ }
+
+ public int getCurrentExternalNodesDataBufferLength() {
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
+ }
+
+ /**
+ * This method returns the current phylogeny as a string in the chosen format
+ *
+ * @param format must be NH, NHX, NEXUS or PHYLOXML
+ * @return the phylogeny string
+ * @author Herve Menager
+ */
+ public String getCurrentPhylogeny( final String format ) {
+ removeAllTextFrames();
+ if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
+ || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
+ return new String();
+ }
+ switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
+ case NH:
+ return getMainPanel().getCurrentPhylogeny().toNewHampshire();
+ case NHX:
+ return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
+ case NEXUS:
+ return getMainPanel().getCurrentPhylogeny().toNexus();
+ case PHYLOXML:
+ return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
+ default:
+ break;
+ }
+ return new String();
+ }
+
+ /**
+ * This method returns a view of the current phylogeny in a chosen
+ * graphics format, base64-encoded in a string so that in can be used
+ * from javascript.
+ *
+ * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
+ * @return the phylogeny string
+ * @author Herve Menager
+ */
+ public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
+ final ByteArrayOutputStream baos = new ByteArrayOutputStream();
+ try {
+ AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
+ _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;
+ }
+
+ public Options getOptions() {
+ return _options;
+ }
+
+ @Override
+ public void init() {
+ final String config_filename = getParameter( Constants.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 phys_url_string = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+ AptxUtil.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 = AptxUtil.readPhylogeniesFromUrl( phys_url,
+ getConfiguration().isValidatePhyloXmlAgainstSchema(),
+ getConfiguration().isReplaceUnderscoresInNhParsing(),
+ getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
+ getConfiguration().getTaxonomyExtraction() );
+ }
+ 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 {
+ AptxUtil.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() ) {
+ 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" );
+ 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_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
+ if ( default_sequence != null ) {
+ getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
+ /* GUILHEM_END */
+ }
+ setVisible( true );
+ }
+
+ public void showTextFrame( final String s, final String title ) {
+ checkTextFrames();
+ _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
+ }
+
+ @Override
+ public void start() {
+ if ( getMainPanel() != null ) {
+ getMainPanel().validate();
+ }
+ requestFocus();
+ requestFocusInWindow();
+ requestFocus();
+ AptxUtil.printAppletMessage( NAME, "started" );
+ }
+
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" ) );
@Override
public void stateChanged( final ChangeEvent e ) {
- MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getCurrentTreePanel() );
+ MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
MainFrame
.setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
_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 ),
_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_node_boxes_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL ) );
+ _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_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_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 ) );
_options_jmenu
.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
customizeJMenuItem( _choose_minimal_confidence_mi );
customizeJMenuItem( _switch_colors_mi );
customizeJMenuItem( _overview_placment_mi );
- customizeCheckBoxMenuItem( _show_node_boxes_cbmi, getOptions().getDefaultNodeShape() );
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_external_cbmi, getOptions()
+ .isShowDefaultNodeShapesExternal() );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
+ .isShowDefaultNodeShapesInternal() );
+ 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() );
customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
+ customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
_jmenubar.add( _options_jmenu );
}
_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 buildViewMenu() {
- _view_jmenu = MainFrame.createMenu( "View as Text", getConfiguration() );
+ _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
+ _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
+ _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_NHX_item = new JMenuItem( "View as NHX" ) );
_view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
+ customizeJMenuItem( _display_basic_information_item );
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 );
+ void checkTextFrames() {
+ if ( _textframes.size() > 5 ) {
+ try {
+ if ( _textframes.getFirst() != null ) {
+ _textframes.getFirst().removeMe();
}
- catch ( final Exception ex ) {
- success = false;
+ else {
+ _textframes.removeFirst();
}
}
- else {
- success = false;
- }
- if ( success && ( m >= 0.0 ) ) {
- getOptions().setMinConfidenceValue( m );
+ catch ( final NoSuchElementException e ) {
+ // Ignore.
}
}
}
+ void clearCurrentExternalNodesDataBuffer() {
+ getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
+ }
+
void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
if ( item != null ) {
item.setFont( MainFrame.menu_font );
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() );
+ void displayBasicInformation() {
+ if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
+ String title = "Basic Information";
+ if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
+ title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
}
- item.setSelected( is_selected );
- item.addActionListener( this );
- }
- }
-
- @Override
- public void destroy() {
- Util.printAppletMessage( NAME, "going to be destroyed " );
- removeTextFrame();
- if ( getMainPanel() != null ) {
- getMainPanel().terminate();
+ showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title );
}
}
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 );
- }
+ void help( final Map<String, WebLink> weblinks ) {
+ 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( "Memory problems (Java heap space error)\n" );
+ sb.append( "---------------------------------------\n" );
+ sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
+ sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
+ sb.append( "the '-Xmx' Java command line option. For example:\n" );
+ sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
+ if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
+ sb.append( "Active web links\n" );
+ sb.append( "--------------------\n" );
+ for( final String key : weblinks.keySet() ) {
+ sb.append( " " + weblinks.get( key ).toString() + "\n" );
}
- } );
- 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 );
+ sb.append( "\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 );
}
void initializeTypeMenu( final Options options ) {
}
}
- 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 removeAllTextFrames() {
+ for( final TextFrame tf : _textframes ) {
+ if ( tf != null ) {
+ tf.close();
+ }
}
+ _textframes.clear();
}
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;
}
}
}
- 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 );
&& _abbreviate_scientific_names.isSelected() );
options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
&& _color_labels_same_as_parent_branch.isSelected() );
- options.setShowNodeBoxes( ( _show_node_boxes_cbmi != null ) && _show_node_boxes_cbmi.isSelected() );
+ options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
+ && _show_default_node_shapes_internal_cbmi.isSelected() );
+ options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
+ && _show_default_node_shapes_external_cbmi.isSelected() );
+ options.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 );
}
}
}
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() );
}
}
void viewAsNexus() {
- removeTextFrame();
- if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
- || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
- return;
+ if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
+ String title = "Nexus";
+ if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
+ title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
+ }
+ showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
+ .getNhConversionSupportValueStyle() ),
+ title );
}
- _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNexus() );
}
void viewAsNH() {
- removeTextFrame();
- if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
- || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
- return;
+ if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
+ String title = "New Hampshire";
+ if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
+ title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
+ }
+ showTextFrame( getMainPanel().getCurrentPhylogeny()
+ .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
+ title );
}
- _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNewHampshire( false ) );
}
- void viewAsNHX() {
- removeTextFrame();
- if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
- || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
- return;
+ void viewAsXML() {
+ if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
+ String title = "phyloXML";
+ if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
+ title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
+ }
+ showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
}
- _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNewHampshireX() );
}
- void viewAsXML() {
- removeTextFrame();
- if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
- || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
- return;
+ 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 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 _main_panel;
+ }
+
+ private boolean isScreenAntialias() {
+ return true;
+ }
+
+ private void removeBranchColors() {
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {
+ AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
+ }
+ }
+
+ private void setMainPanel( final MainPanelApplets main_panel ) {
+ _main_panel = main_panel;
+ }
+
+ 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() );
}
- _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ) );
}
static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
git://source.jalview.org / jalview.git / blobdiff