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
+ *
+ * Neighbour Joining Using BLOSUM62
+ *
+ * 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(Locale.ROOT));
+
+ /*
+ * short score model name (long description can be too long)
+ */
+ String smn = scoreModelName;
+
+ /*
+ * put them together as Using
+ */
+ final String ttl = MessageManager.formatMessage("label.calc_title",
+ treecalcnm, smn);
+ return ttl;
+ }
+
+ /**
+ * Builds an EPS image and writes it to the specified file.
+ *
+ * @param outFile
+ * @param textOption
+ * true for Text character rendering, false for Lineart
+ */
+ protected void writeEpsFile(File outFile, boolean textOption)
+ {
+ try
+ {
+ int width = treeCanvas.getWidth();
+ int height = treeCanvas.getHeight();
+
+ FileOutputStream out = new FileOutputStream(
+ outFile);
+ EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
+ height);
+ pg.setAccurateTextMode(!textOption);
+ treeCanvas.draw(pg, width, height);
+
+ pg.flush();
+ pg.close();
+ } catch (Exception ex)
+ {
+ System.err.println("Error writing tree as EPS");
+ ex.printStackTrace();
+ }
+ }
+
+ public AlignViewport getViewport()
+ {
+ return av;
+ }
+
+ public void setViewport(AlignViewport av)
+ {
+ this.av = av;
+ }
+
+ public TreeCanvas getTreeCanvas()
+ {
+ return treeCanvas;
+ }
+}