+ 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 );
+ }
+
+ /**
+ * 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;
+ }
+