fixed Jalview project archive bug where alignment view is not written to Jar that...

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 5c08fb0..97dfefd 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -228,16 +228,10 @@ public class Jalview2XML
               fileName = fileName + ".xml";
             }
 
-            JarEntry entry = new JarEntry(fileName);
-            jout.putNextEntry(entry);
-            out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8"));
-            SaveState(apanel, fileName,
-                    jout, out);
+            SaveState(apanel, fileName, jout);
           }
         }
       }
-      try { out.flush(); } catch (Exception foo) {};
-      jout.closeEntry();
       try { jout.flush(); } catch (Exception foo) {};
       jout.close();
     } catch (Exception ex)
@@ -265,13 +259,7 @@ public class Jalview2XML
         {
           jfileName = jfileName + ".xml";
         }
-        JarEntry entry = new JarEntry(jfileName);
-        jout.putNextEntry(entry);
-        PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
-        "UTF-8"));
-        SaveState(apanel, jfileName, jout, out);
-        try { out.flush(); } catch (Exception foo) {};
-        jout.closeEntry();
+        SaveState(apanel, jfileName, jout);
       }
 
       try { jout.flush(); } catch (Exception foo) {};
@@ -285,16 +273,16 @@ public class Jalview2XML
   }
 
   /**
-   * DOCUMENT ME!
+   * create a JalviewModel from an algnment view and marshall it
+   * to a JarOutputStream
    *
-   * @param af DOCUMENT ME!
-   * @param timeStamp DOCUMENT ME!
-   * @param fileName DOCUMENT ME!
-   * @param jout DOCUMENT ME!
-   * @param out DOCUMENT ME!
+   * @param ap panel to create jalview model for
+   * @param fileName name of alignment panel written to output stream
+   * @param jout jar output stream
+   * @param out jar entry name
    */
   public JalviewModel SaveState(AlignmentPanel ap, String fileName,
-          JarOutputStream jout, PrintWriter out)
+          JarOutputStream jout)
   {
     initSeqRefs();
     
@@ -986,18 +974,24 @@ public class Jalview2XML
     object.setJalviewModelSequence(jms);
     object.getVamsasModel().addSequenceSet(vamsasSet);
 
-    if (out != null)
+    if (jout!=null && fileName!=null)
     {
       //We may not want to write the object to disk,
       //eg we can copy the alignViewport to a new view object
       //using save and then load
       try
       {
-        org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(out);
+        JarEntry entry = new JarEntry(fileName);
+        jout.putNextEntry(entry);
+        PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
+        "UTF-8"));
+        org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(pout);
         marshaller.marshal(object);
-        out.flush();
+        pout.flush();
+        jout.closeEntry();
       } catch (Exception ex)
       {
+        // TODO: raise error in GUI if marshalling failed.
         ex.printStackTrace();
       }
     }
@@ -1287,6 +1281,9 @@ public class Jalview2XML
               + ex + "\n");
     } catch (Exception ex)
     {
+      System.err.println("Parsing as Jalview Version 2 file failed.");
+      ex.printStackTrace(System.err);
+      
       //Is Version 1 Jar file?
       try {
         af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(file);
@@ -2471,8 +2468,8 @@ public class Jalview2XML
   public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
           boolean keepSeqRefs)
   {
-    jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
-            null, null);
+    jalview.schemabinding.version2.JalviewModel jm = 
+       SaveState(ap, null, null);
 
     if (!keepSeqRefs)
     {