+ order[i] = fr.getOrder(data[i][0].toString());
+ if (order[i] < 0)
+ {
+ order[i] = fr.setOrder(data[i][0].toString(), i / order.length);
+ }
+ if (i > 1)
+ {
+ sort = sort || order[i - 1] > order[i];
+ }
+ }
+ if (sort)
+ {
+ jalview.util.QuickSort.sort(order, data);
+ }
+ }
+
+ /**
+ * Offers a file chooser dialog, and then loads the feature colours and
+ * filters from file in XML format and unmarshals to Jalview feature settings
+ */
+ void load()
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser("fc",
+ SEQUENCE_FEATURE_COLOURS);
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(
+ MessageManager.getString("label.load_feature_colours"));
+ chooser.setToolTipText(MessageManager.getString("action.load"));
+ chooser.setResponseHandler(0, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ File file = chooser.getSelectedFile();
+ load(file);
+ }
+ });
+ chooser.showOpenDialog(this);
+ }
+
+ /**
+ * Loads feature colours and filters from XML stored in the given file
+ *
+ * @param file
+ */
+ void load(File file)
+ {
+ try
+ {
+ InputStreamReader in = new InputStreamReader(
+ new FileInputStream(file), "UTF-8");
+
+ JAXBContext jc = JAXBContext
+ .newInstance("jalview.xml.binding.jalview");
+ javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+ XMLStreamReader streamReader = XMLInputFactory.newInstance()
+ .createXMLStreamReader(in);
+ JAXBElement<JalviewUserColours> jbe = um.unmarshal(streamReader,
+ JalviewUserColours.class);
+ JalviewUserColours jucs = jbe.getValue();
+
+ // JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
+
+ /*
+ * load feature colours
+ */
+ for (int i = jucs.getColour().size() - 1; i >= 0; i--)
+ {
+ Colour newcol = jucs.getColour().get(i);
+ FeatureColourI colour = jalview.project.Jalview2XML
+ .parseColour(newcol);
+ fr.setColour(newcol.getName(), colour);
+ fr.setOrder(newcol.getName(), i / (float) jucs.getColour().size());
+ }
+
+ /*
+ * load feature filters; loaded filters will replace any that are
+ * currently defined, other defined filters are left unchanged
+ */
+ for (int i = 0; i < jucs.getFilter().size(); i++)
+ {
+ Filter filterModel = jucs.getFilter().get(i);
+ String featureType = filterModel.getFeatureType();
+ FeatureMatcherSetI filter = jalview.project.Jalview2XML
+ .parseFilter(featureType, filterModel.getMatcherSet());
+ if (!filter.isEmpty())
+ {
+ fr.setFeatureFilter(featureType, filter);
+ }
+ }
+
+ /*
+ * update feature settings table
+ */
+ if (table != null)
+ {
+ resetTable(null);
+ Object[][] data = ((FeatureTableModel) table.getModel()).getData();
+ ensureOrder(data);
+ updateFeatureRenderer(data, false);
+ table.repaint();
+ }
+ } catch (Exception ex)
+ {
+ System.out.println("Error loading User Colour File\n" + ex);
+ }
+ }
+
+ /**
+ * Offers a file chooser dialog, and then saves the current feature colours
+ * and any filters to the selected file in XML format
+ */
+ void save()
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser("fc",
+ SEQUENCE_FEATURE_COLOURS);
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(
+ MessageManager.getString("label.save_feature_colours"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
+ int option = chooser.showSaveDialog(this);
+ if (option == JalviewFileChooser.APPROVE_OPTION)
+ {
+ File file = chooser.getSelectedFile();
+ save(file);