bugfix for vamsas demo and IO rearrangement for AMSAFile output

[jalview.git] / src / jalview / gui / VamsasApplication.java

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 5ede8fe..18c2e55 100644 (file)
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -257,6 +257,17 @@ public class VamsasApplication
           vds.storeVAMSAS(af.getViewport(), af.getTitle());
         }
       }
+      //REVERSE ORDER
+      for (int i = frames.length - 1; i > -1; i--)
+      {
+        if (frames[i] instanceof AlignFrame)
+        {
+          AlignFrame af = (AlignFrame) frames[i];
+
+          // add any AlignedCodonFrame mappings on this alignment to any other.
+          vds.storeSequenceMappings(af.getViewport(), af.getTitle());
+        }
+      }
     }
     catch (Exception e)
     {
@@ -376,6 +387,10 @@ public class VamsasApplication
               {
                 return;
               }
+              //if (Cache.log.isDebugEnabled())
+              //{
+              //  Cache.log.debug("Received MouseOverMessage "+mm.getVorbaID()+" "+mm.getPosition());
+              //}
               Object jvobj = vobj2jv.get(mm.getVorbaID());
               if (jvobj != null && jvobj instanceof SequenceI)
               {
@@ -392,12 +407,14 @@ public class VamsasApplication
           int i=-1;
           public void mouseOver(SequenceI seq, int index)
           {
+            if (jv2vobj==null)
+              return;
             if (seq!=last || i!=index)
             {
               VorbaId v = (VorbaId) jv2vobj.get(seq);
               if (v!=null)
               {
-                // Cache.log.debug("Mouse over "+v.getId()+" bound to "+seq+" at "+index);
+                Cache.log.debug("Mouse over "+v.getId()+" bound to "+seq+" at "+index);
                 last = seq;
                 i=index;
                 MouseOverMessage message = new MouseOverMessage(v.getId(), index);