+ sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
+ sortAnnBy
+ .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
+ sortAnnBy
+ .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
+ SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
+ .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ sortAnnBy.setSelectedItem(savedSort.toString());
+
+ sortAutocalc.addItem("Autocalculated first");
+ sortAutocalc.addItem("Autocalculated last");
+ final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
+ sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
+ : sortAutocalc.getItemAt(1));
+ startupCheckbox
+ .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
+ startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
+ Cache.getDefault("www.jalview.org", "http://www.jalview.org")
+ + "/examples/exampleFile_2_3.jar"));
+
+ /*
+ * Set Colours tab defaults
+ */
+ protColour.addItem(ResidueColourScheme.NONE);
+ nucColour.addItem(ResidueColourScheme.NONE);
+ for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
+ {
+ String name = cs.getSchemeName();
+ protColour.addItem(name);
+ nucColour.addItem(name);
+ }
+ String oldProp = Cache.getDefault(DEFAULT_COLOUR,
+ ResidueColourScheme.NONE);
+ String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
+ protColour.setSelectedItem(newProp != null ? newProp : oldProp);
+ newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
+ nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
+ minColour.setBackground(
+ Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
+ maxColour.setBackground(
+ Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
+
+ /*
+ * Set overview panel defaults
+ */
+ gapColour.setBackground(
+ Cache.getDefaultColour(GAP_COLOUR,
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
+ hiddenColour.setBackground(
+ Cache.getDefaultColour(HIDDEN_COLOUR,
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
+ useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
+ gapLabel.setEnabled(!useLegacyGap.isSelected());
+ gapColour.setEnabled(!useLegacyGap.isSelected());
+ showHiddenAtStart
+ .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
+
+ /*
+ * Set Structure tab defaults.
+ */
+ final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
+ structFromPdb.setSelected(structSelected);
+ useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
+ useRnaView.setEnabled(structSelected);
+ addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
+ addSecondaryStructure.setEnabled(structSelected);
+ addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
+ addTempFactor.setEnabled(structSelected);
+ structViewer.setSelectedItem(
+ Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
+ chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
+ chimeraPath.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ validateChimeraPath();
+ }
+ });
+
+ if (Cache.getDefault("MAP_WITH_SIFTS", false))
+ {
+ siftsMapping.setSelected(true);
+ }
+ else
+ {
+ nwMapping.setSelected(true);
+ }
+
+ SiftsSettings
+ .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
+
+ /*
+ * Set Connections tab defaults
+ */
+
+ // set up sorting
+ linkUrlTable.setModel(dataModel);
+ final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
+ linkUrlTable.getModel());
+ linkUrlTable.setRowSorter(sorter);
+ List<RowSorter.SortKey> sortKeys = new ArrayList<>();
+
+ UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
+ sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
+ SortOrder.DESCENDING));
+ sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
+ SortOrder.DESCENDING));
+ sortKeys.add(
+ new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
+
+ sorter.setSortKeys(sortKeys);
+ // BH 2018 setSortKeys will do the sort
+ // sorter.sort();
+
+ // set up filtering
+ ActionListener onReset;
+ onReset = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ filterTB.setText("");
+ sorter.setRowFilter(RowFilter.regexFilter(""));
+ }