+
+ /**
+ * change node labels to the annotation referred to by labelClass TODO:
+ * promote to a datamodel modification that can be undone TODO: make argument
+ * one case of a generic transformation function ie { undoStep = apply(Tree,
+ * TransformFunction)};
+ *
+ * @param labelClass
+ */
+ public void changeNames(final String labelClass)
+ {
+ tree.applyToNodes(new NodeTransformI()
+ {
+
+ @Override
+ public void transform(BinaryNode node)
+ {
+ if (node instanceof SequenceNode
+ && !((SequenceNode) node).isPlaceholder()
+ && !((SequenceNode) node).isDummy())
+ {
+ String newname = null;
+ SequenceI sq = (SequenceI) ((SequenceNode) node).element();
+ if (sq != null)
+ {
+ // search dbrefs, features and annotation
+ DBRefEntry[] refs = jalview.util.DBRefUtils
+ .selectRefs(sq.getDBRefs(), new String[]
+ { labelClass.toUpperCase() });
+ if (refs != null)
+ {
+ for (int i = 0; i < refs.length; i++)
+ {
+ if (newname == null)
+ {
+ newname = new String(refs[i].getAccessionId());
+ }
+ else
+ {
+ newname = newname + "; " + refs[i].getAccessionId();
+ }
+ }
+ }
+ if (newname == null)
+ {
+ List<SequenceFeature> features = sq.getFeatures()
+ .getPositionalFeatures(labelClass);
+ for (SequenceFeature feature : features)
+ {
+ if (newname == null)
+ {
+ newname = feature.getDescription();
+ }
+ else
+ {
+ newname = newname + "; " + feature.getDescription();
+ }
+ }
+ }
+ }
+ if (newname != null)
+ {
+ // String oldname = ((SequenceNode) node).getName();
+ // TODO : save oldname in the undo object for this modification.
+ ((SequenceNode) node).setName(newname);
+ }
+ }
+ }
+ });
+ }
+
+ /**
+ * Formats a localised title for the tree panel, like
+ * <p>
+ * Neighbour Joining Using BLOSUM62
+ * <p>
+ * For a tree loaded from file, just uses the file name
+ *
+ * @return
+ */
+ public String getPanelTitle()
+ {
+ if (treeTitle != null)
+ {
+ return treeTitle;
+ }
+
+ /*
+ * i18n description of Neighbour Joining or Average Distance method
+ */
+ String treecalcnm = MessageManager
+ .getString("label.tree_calc_" + treeType.toLowerCase());
+
+ /*
+ * short score model name (long description can be too long)
+ */
+ String smn = scoreModelName;
+
+ /*
+ * put them together as <method> Using <model>
+ */
+ final String ttl = MessageManager.formatMessage("label.calc_title",
+ treecalcnm, smn);
+ return ttl;
+ }
+
+ public AlignViewport getViewport()
+ {
+ return av;
+ }
+
+ public void setViewport(AlignViewport av)
+ {
+ this.av = av;
+ }
+
+ public TreeCanvas getTreeCanvas()
+ {
+ return treeCanvas;
+ }