X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryxE.java;h=b72d1b5536176fd7da06a2a0f6a50b4a2437260b;hb=a07102813fbac79ba1a534dc9954a8500dc5e5ff;hp=51f09b03e5a24a98b239c0d565d0fc8e096d446d;hpb=b606686e01ec42a13f9a91103c7e338925497101;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index 51f09b0..b72d1b5 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -7,10 +7,14 @@ import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ComponentAdapter; import java.awt.event.ComponentEvent; +import java.io.ByteArrayOutputStream; import java.io.File; import java.io.IOException; import java.net.URL; +import java.util.LinkedList; import java.util.List; +import java.util.Map; +import java.util.NoSuchElementException; import javax.swing.ButtonGroup; import javax.swing.JApplet; @@ -25,6 +29,8 @@ import javax.swing.UnsupportedLookAndFeelException; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; +import org.apache.commons.codec.binary.Base64; +import org.forester.archaeopteryx.AptxUtil.GraphicsExportType; import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE; import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION; import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE; @@ -59,7 +65,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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; @@ -69,6 +74,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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; @@ -114,6 +120,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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; + final LinkedList _textframes = new LinkedList(); ; @Override public void actionPerformed( final ActionEvent e ) { @@ -143,6 +151,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { else if ( o == _switch_colors_mi ) { switchColors(); } + else if ( o == _display_basic_information_item ) { + displayBasicInformation(); + } else if ( o == _view_as_NH_item ) { viewAsNH(); } @@ -233,6 +244,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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() ); } @@ -270,11 +284,11 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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() ); @@ -282,7 +296,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } 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() ); @@ -290,7 +304,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } 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() ); @@ -298,7 +312,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } 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() ); @@ -307,6 +321,64 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { repaint(); } + void help( final Map 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 ); + } + /** * This method returns the current phylogeny as a string in the chosen format * @@ -315,7 +387,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { * @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(); @@ -335,6 +407,40 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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" ) ); @@ -405,7 +511,11 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _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 @@ -413,11 +523,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _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 ) ); @@ -469,6 +574,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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 ); } @@ -518,11 +624,14 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } 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 ); @@ -603,8 +712,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { @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(); } @@ -637,15 +746,15 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { @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 { @@ -661,7 +770,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { // 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() ); @@ -681,7 +790,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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 ) ); @@ -715,23 +824,23 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } ); 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() @@ -791,14 +900,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { private void removeBranchColors() { if ( getMainPanel().getCurrentPhylogeny() != null ) { - Util.removeBranchColors( getMainPanel().getCurrentPhylogeny() ); - } - } - - void removeTextFrame() { - if ( _textframe != null ) { - _textframe.close(); - _textframe = null; + AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() ); } } @@ -888,19 +990,19 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } 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() ); } } @@ -912,7 +1014,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { requestFocus(); requestFocusInWindow(); requestFocus(); - Util.printAppletMessage( NAME, "started" ); + AptxUtil.printAppletMessage( NAME, "started" ); } void switchColors() { @@ -981,6 +1083,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } 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() ); } @@ -1019,40 +1123,88 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { ( ( 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 treepanels, final boolean antialias ) {