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;
// </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_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;
+ 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_NHX_item;
+ private JMenuItem _view_as_nexus_item;
+ private JMenuItem _display_basic_information_item;
+ private JMenu _type_menu;
+ private JCheckBoxMenuItem _rectangular_type_cbmi;
+ private JCheckBoxMenuItem _triangular_type_cbmi;
+ private JCheckBoxMenuItem _curved_type_cbmi;
+ private JCheckBoxMenuItem _convex_type_cbmi;
+ private JCheckBoxMenuItem _euro_type_cbmi;
+ private JCheckBoxMenuItem _rounded_type_cbmi;
+ private JCheckBoxMenuItem _unrooted_type_cbmi;
+ private JCheckBoxMenuItem _circular_type_cbmi;
+ private JMenuItem _help_item;
+ private JMenuItem _about_item;
+ private JMenu _help_jmenu;
+ private JMenuItem _website_item;
+ private JMenuItem _phyloxml_website_item;
+ private JMenuItem _phyloxml_ref_item;
+ private JMenuItem _aptx_ref_item;
+ private JMenuItem _remove_branch_color_item;
+ private JMenuItem _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;
+ private JCheckBoxMenuItem _show_confidence_stddev_cbmi;
+ private final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>();
+ private String _ext_node_data_buffer = "";
@Override
public void actionPerformed( final ActionEvent e ) {
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 == _show_branch_length_values_cbmi ) {
updateOptions( getOptions() );
}
+ else if ( o == _show_confidence_stddev_cbmi ) {
+ updateOptions( getOptions() );
+ }
else if ( o == _label_direction_cbmi ) {
updateOptions( getOptions() );
}
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();
}
+ 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" );
+ }
+ }
+ 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 setCurrentExternalNodesDataBuffer( final String s ) {
+ if ( !ForesterUtil.isEmpty( s ) ) {
+ _ext_node_data_buffer = s.trim();
+ }
+ else {
+ _ext_node_data_buffer = "";
+ }
+ }
+
+ /**
+ * 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 _ext_node_data_buffer;
+ }
+
/**
* This method returns the current phylogeny as a string in the chosen format
*
* @author Herve Menager
*/
public String getCurrentPhylogeny( final String format ) {
- removeTextFrame();
+ removeAllTextFrames();
if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
|| ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
return new String();
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;
+ }
+
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" ) );
_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_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_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL ) );
_options_jmenu
_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 ) );
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 );
}
}
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 );
@Override
public void destroy() {
- Util.printAppletMessage( NAME, "going to be destroyed " );
- removeTextFrame();
+ AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
+ removeAllTextFrames();
if ( getMainPanel() != null ) {
getMainPanel().terminate();
}
@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 );
+ 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 );
- Util.printAppletMessage( NAME, "URL for phylogenies is " + phys_url_string );
+ AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + phys_url_string );
// Get URL to tree file
if ( phys_url_string != null ) {
try {
// Load the tree from URL
if ( phys_url != null ) {
try {
- phys = Util.readPhylogeniesFromUrl( phys_url, getConfiguration().isValidatePhyloXmlAgainstSchema() );
+ phys = AptxUtil.readPhylogeniesFromUrl( phys_url, getConfiguration().isValidatePhyloXmlAgainstSchema() );
}
catch ( final Exception e ) {
ForesterUtil.printErrorMessage( NAME, e.toString() );
return;
}
else {
- Util.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
+ AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
}
setVisible( false );
setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
}
} );
if ( getConfiguration().isUseTabbedDisplay() ) {
- Util.printAppletMessage( NAME, "using tabbed display" );
- Util.addPhylogeniesToTabs( phys,
- new File( phys_url.getFile() ).getName(),
- phys_url.toString(),
- getConfiguration(),
- getMainPanel() );
+ AptxUtil.printAppletMessage( NAME, "using tabbed display" );
+ AptxUtil.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() );
+ AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
+ AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
}
validate();
setName( NAME );
getMainPanel().getControlPanel().showWholeAll();
getMainPanel().getControlPanel().showWhole();
System.gc();
- Util.printAppletMessage( NAME, "successfully initialized" );
+ AptxUtil.printAppletMessage( NAME, "successfully initialized" );
/* GUILHEM_BEG */
getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
private void removeBranchColors() {
if ( getMainPanel().getCurrentPhylogeny() != null ) {
- Util.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
- }
- }
-
- void removeTextFrame() {
- if ( _textframe != null ) {
- _textframe.close();
- _textframe = null;
+ AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
}
}
}
}
catch ( final UnsupportedLookAndFeelException e ) {
- Util.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
+ AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
}
catch ( final ClassNotFoundException e ) {
- Util.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
+ AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
}
catch ( final InstantiationException e ) {
- Util.dieWithSystemError( "InstantiationException: " + e.toString() );
+ AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
}
catch ( final IllegalAccessException e ) {
- Util.dieWithSystemError( "IllegalAccessException: " + e.toString() );
+ AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
}
catch ( final Exception e ) {
- Util.dieWithSystemError( e.toString() );
+ AptxUtil.dieWithSystemError( e.toString() );
}
}
requestFocus();
requestFocusInWindow();
requestFocus();
- Util.printAppletMessage( NAME, "started" );
+ AptxUtil.printAppletMessage( NAME, "started" );
}
void switchColors() {
}
}
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() );
}
( ( JCheckBoxMenuItem ) o ).setSelected( true );
}
+ void displayBasicInformation() {
+ if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
+ String title = "Basic Information";
+ if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
+ title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
+ }
+ showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title );
+ }
+ }
+
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;
+ if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
+ String title = "NHX";
+ if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
+ title = getMainPanel().getCurrentPhylogeny().getName() + " " + title;
+ }
+ showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshireX(), title );
}
- _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNewHampshireX() );
}
void viewAsXML() {
- removeTextFrame();
- if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
- || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
- return;
+ 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 );
+ }
+ }
+
+ public void showTextFrame( final String s, final String title ) {
+ checkTextFrames();
+ _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
+ }
+
+ void checkTextFrames() {
+ if ( _textframes.size() > 5 ) {
+ try {
+ if ( _textframes.getFirst() != null ) {
+ _textframes.getFirst().removeMe();
+ }
+ else {
+ _textframes.removeFirst();
+ }
+ }
+ catch ( final NoSuchElementException e ) {
+ // Ignore.
+ }
+ }
+ }
+
+ void removeAllTextFrames() {
+ for( final TextFrame tf : _textframes ) {
+ if ( tf != null ) {
+ tf.close();
+ }
}
- _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ) );
+ _textframes.clear();
}
static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
git://source.jalview.org / jalview.git / blobdiff