Class ExtendedTreeViewer

src/figtree/treeviewer/ExtendedTreeViewer.java:49–270

@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$

 * $LastChangedRevision$
 */
public class ExtendedTreeViewer extends DefaultTreeViewer implements StatusProvider {

    public ExtendedTreeViewer() {
       this(null);
    }

    public ExtendedTreeViewer(JFrame frame) {
        super(frame);

        // setTreesPerPage(1);

        setBackground(Color.white);

    }

    public void setPattern(Pattern pattern) {
        if (pattern != null) {
            //           setBranchDecorator(new ParsimonyBranchDecorator(pattern));
        } else {
            setBranchDecorator(null, false);
        }
    }

    public void addTree(Tree tree) {

        Set<String> names = new TreeSet<String>();
        for (Node node : tree.getNodes()) {
            names.addAll(node.getAttributeNames());
        }
        for (Taxon taxon : tree.getTaxa()) {
            names.addAll(taxon.getAttributeNames());
        }
        for (String name : names) {
            if (!name.startsWith("!")) {
                AnnotationDefinition annotation = getAnnotationDefinitions().get(name);

                Set<Attributable> items = new HashSet<Attributable>(tree.getNodes());
                items.addAll(tree.getTaxa());
                
                AnnotationDefinition.Type type = AnnotationDefinition.guessType(name, items);

                if (annotation == null) {
                    annotation = new AnnotationDefinition(name, type);
                    getAnnotationDefinitions().put(name, annotation);
                } else if (type != annotation.getType()){
                    AnnotationDefinition.Type newType = AnnotationDefinition.Type.STRING;
                    if (type == AnnotationDefinition.Type.INTEGER &&
                            annotation.getType() == AnnotationDefinition.Type.REAL) {
                        newType = AnnotationDefinition.Type.REAL;
                    }

                    if (newType != type) {
                        annotation = new AnnotationDefinition(name, newType);
                        getAnnotationDefinitions().put(name, annotation);
                    }

                }
            }