X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=dcb3f44c8879f05b8a6cf56a4cc198a7db4e61bc;hb=2732a03c243a8d57c559e8e33c0e36bcd5d57624;hp=77396c9649c359548052d70ab1c19ac5259f4326;hpb=75cbd01f57e64f0b2946e8b54005dadf139546ee;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 77396c9..dcb3f44 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -61,6 +61,7 @@ public class AlignFrame
   Stack redoList = new Stack();
   private int treeCount = 0;
 
+
   /**
    * Creates a new AlignFrame object.
    *
@@ -161,6 +162,16 @@ public class AlignFrame
 
   }
 
+
+  /*
+   Added so Castor Mapping file can obtain Jalview Version
+  */
+  public String getVersion()
+  {
+    return  jalview.bin.Cache.getProperty("VERSION");
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -1872,7 +1883,7 @@ public class AlignFrame
   {
     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
                                    HistoryItem.SORT));
-    AlignmentSorter.sortByID(viewport.getAlignment());
+    AlignmentSorter.sortByID(viewport.getAlignment(), viewport.showDBPrefix);
     alignPanel.repaint();
   }
 
@@ -2372,7 +2383,7 @@ public class AlignFrame
             {
               SequenceI[] msa = gatherSequencesForAlignment();
               new jalview.ws.MsaWSClient(sh, title, msa,
-                  false, true);
+                  false, true, viewport.getAlignment().getDataset());
 
             }
 
@@ -2389,7 +2400,7 @@ public class AlignFrame
               {
                 SequenceI[] msa = gatherSequencesForAlignment();
                 new jalview.ws.MsaWSClient(sh, title, msa,
-                    true, true);
+                    true, true, viewport.getAlignment().getDataset());
 
               }
 
@@ -2464,8 +2475,8 @@ public class AlignFrame
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
-      vs.store(chooser.getSelectedFile().getAbsolutePath()
-          );
+      //vs.store(chooser.getSelectedFile().getAbsolutePath()   );
+      vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
     }
   }