+ // convert description of sort order to enum name for save
+ SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
+ .forDescription(sortAnnBy.getSelectedItem().toString());
+ if (annSortOrder != null)
+ {
+ Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
+ annSortOrder.name());
+ }
+
+ final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
+ Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
+ Boolean.valueOf(showAutocalcFirst).toString());
+
+ /*
+ * Save Colours settings
+ */
+ Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
+ .getSelectedItem().toString());
+ Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
+ minColour.getBackground());
+ Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
+ maxColour.getBackground());
+
+ /*
+ * Save Structure settings
+ */
+ Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
+ Boolean.toString(addTempFactor.isSelected()));
+ Cache.applicationProperties.setProperty(ADD_SS_ANN,
+ Boolean.toString(addSecondaryStructure.isSelected()));
+ Cache.applicationProperties.setProperty(USE_RNAVIEW,
+ Boolean.toString(useRnaView.isSelected()));
+ Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
+ Boolean.toString(structFromPdb.isSelected()));
+ Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
+ .getSelectedItem().toString());
+ Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
+
+ /*
+ * Save Output settings
+ */