+ private AlignmentViewPanel viewpanel;
+
+ public static String FILE = "File";
+
+ public static String URL = "URL";
+
+ public static String PASTE = "Paste";
+
+ public static String CLASSLOADER = "ClassLoader";
+
+ /**
+ * add jalview-derived non-secondary structure annotation from PDB structure
+ */
+ boolean annotFromStructure = false;
+
+ /**
+ * add secondary structure from PDB data with built-in algorithms
+ */
+ boolean localSecondaryStruct = false;
+
+ /**
+ * process PDB data with web services
+ */
+ boolean serviceSecondaryStruct = false;
+
+ private AlignFile alignFile = null;
+
+ String inFile;
+
+ /**
+ * character used to write newlines
+ */
+ protected String newline = System.getProperty("line.separator");
+
+ private AlignExportSettingI exportSettings;
+