- static 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" );
- }
- }
- // + "General remarks\n"
- // + "---------------\n"
- // +
- // "o The application version permits copying to the clipboard \n"
- // +
- // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
- // +
- // "o Changes made to a subtree affect this subtree and its subtrees,\n"
- // + " but not any of its parent tree(s).\n"
- // +
- // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
- // +
- // " are likely to be bootstrap values instead of branch length values.\n\n"
- // +
- // " Remarks regarding SDI (Speciation Duplication Inference):\n"
- // +
- // "o Each external node of the gene tree (in display) needs to be associated with\n"
- // +
- // " a species: either directly through the \"Species\" field, or the species\n"
- // +
- // " is part of the sequence name in the form \"XXXX_SPECIES\"\n"
- // +
- // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
- // +
- // "o A species tree for each species of the gene tree needs to be loaded with\n"
- // +
- // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
- // +
- // "o !External nodes of the gene tree associated with species not present in\n"
- // +
- // " the species tree are REMOVED prior to SDI execution!\n"
- // +
- // "o Both the gene tree and the species tree must be completely binary.\n"
- // +
- // "o Duplications and speciations are a function of the position of the root.\n"
- // +
- // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
- // + " incorrect and need to be inferred again\n"
- // +
- // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\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() );
- }
-
- static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
- if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
- mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );