From c922c120c74560d83649e89c2cf1a6346941c50b Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 9 Jun 2009 15:14:59 +0000
Subject: [PATCH] fix null pointer when new view created on alignment with
 existing sequence mappings (cDNA list is null)

---
 src/jalview/io/VamsasAppDatastore.java |   12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index fe971d9..886f515 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -2048,7 +2048,7 @@ public class VamsasAppDatastore
             {
               Cache.log.warn("ignoring additional "
                       + (ae[aa].getValueCount() - 1)
-                      + "values in annotation element.");
+                      + " values in annotation element.");
             }
             val = ae[aa].getValue(0);
           }
@@ -2646,7 +2646,13 @@ public class VamsasAppDatastore
         Cache.log.warn("Creating new dataset for an alignment.");
         jal.setDataset(null);
       }
-      dataset = (DataSet) getjv2vObj(jal.getDataset());
+      dataset = (DataSet) ((Alignment) getjv2vObj(viewport.getSequenceSetId())).getV_parent(); //   jal.getDataset());
+      if (dataset==null)
+      {
+        dataset = (DataSet) getjv2vObj(jal.getDataset());
+        Cache.log.error("Can't find the correct dataset for the alignment in this view. Creating new one.");
+
+      }
       // Store any sequence mappings.
       if (av.getAlignment().getCodonFrames() != null
               && av.getAlignment().getCodonFrames().length > 0)
@@ -2655,7 +2661,7 @@ public class VamsasAppDatastore
                 .getCodonFrames();
         for (int cf = 0; cf < cframes.length; cf++)
         {
-          if (cframes[cf].getdnaSeqs().length > 0)
+          if (cframes[cf].getdnaSeqs()!=null && cframes[cf].getdnaSeqs().length > 0)
           {
             jalview.datamodel.SequenceI[] dmps = cframes[cf].getdnaSeqs();
             jalview.datamodel.Mapping[] mps = cframes[cf].getProtMappings();
-- 
1.7.10.2