JAL-3608 formatting save only

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 8c9d391..a0a8815 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,27 +20,6 @@
  */
 package jalview.bin;
 
-import jalview.ext.so.SequenceOntology;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.PromptUserConfig;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.BioJsHTMLOutput;
-import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FileFormatException;
-import jalview.io.FileFormatI;
-import jalview.io.FileLoader;
-import jalview.io.HtmlSvgOutput;
-import jalview.io.IdentifyFile;
-import jalview.io.NewickFile;
-import jalview.io.gff.SequenceOntologyFactory;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.jws2.Jws2Discoverer;
-
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -68,6 +47,26 @@ import com.threerings.getdown.util.LaunchUtil;
 
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
+import jalview.ext.so.SequenceOntology;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.PromptUserConfig;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.BioJsHTMLOutput;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
+import jalview.io.FileLoader;
+import jalview.io.HtmlSvgOutput;
+import jalview.io.IdentifyFile;
+import jalview.io.NewickFile;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.jws2.Jws2Discoverer;
 
 /**
  * Main class for Jalview Application <br>
@@ -183,7 +182,7 @@ public class Jalview
    * main class for Jalview application
    * 
    * @param args
-   *               open <em>filename</em>
+   *          open <em>filename</em>
    */
   public static void main(String[] args)
   {
@@ -198,22 +197,24 @@ public class Jalview
   {
     System.setSecurityManager(null);
     System.out
-            .println("Java version: "
-                    + System.getProperty("java.version"));
+            .println("Java version: " + System.getProperty("java.version"));
     System.out.println("Java Home: " + System.getProperty("java.home"));
     System.out.println(System.getProperty("os.arch") + " "
             + System.getProperty("os.name") + " "
             + System.getProperty("os.version"));
     String val = System.getProperty("sys.install4jVersion");
-    if (val != null) {
-    System.out.println("Install4j version: " + val);
+    if (val != null)
+    {
+      System.out.println("Install4j version: " + val);
     }
     val = System.getProperty("installer_template_version");
-    if (val != null) {
+    if (val != null)
+    {
       System.out.println("Install4j template version: " + val);
     }
     val = System.getProperty("launcher_version");
-    if (val != null) {
+    if (val != null)
+    {
       System.out.println("Launcher version: " + val);
     }
 
@@ -836,10 +837,10 @@ public class Jalview
    * Locate the given string as a file and pass it to the groovy interpreter.
    * 
    * @param groovyscript
-   *                         the script to execute
+   *          the script to execute
    * @param jalviewContext
-   *                         the Jalview Desktop object passed in to the groovy
-   *                         binding as the 'Jalview' object.
+   *          the Jalview Desktop object passed in to the groovy binding as the
+   *          'Jalview' object.
    */
   private void executeGroovyScript(String groovyscript, AlignFrame af)
   {
@@ -968,8 +969,8 @@ public class Jalview
   }
 
   /**
-   * Quit method delegates to Desktop.quit - unless running in headless mode when
-   * it just ends the JVM
+   * Quit method delegates to Desktop.quit - unless running in headless mode
+   * when it just ends the JVM
    */
   public void quit()
   {