X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=7375d438c12c979247fabdf26a8e60f571f17582;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=c60fd88c84cf12b8061adf9a8685227ade343d4d;hpb=e82c0bb610425c3829037bec88b6c03509d07e36;p=jalview.git

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index c60fd88..7375d43 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -35,8 +35,10 @@ import jalview.io.vamsas.DatastoreRegistry;
 import jalview.io.vamsas.Rangetype;
 import jalview.project.Jalview2XML;
 import jalview.util.MessageManager;
+import jalview.util.jarInputStreamProvider;
 import jalview.viewmodel.AlignmentViewport;
 
+import java.io.File;
 import java.io.IOException;
 import java.util.Enumeration;
 import java.util.HashMap;
@@ -338,10 +340,8 @@ public class VamsasAppDatastore
                 if (vbound.getV_parent() != null
                         && dataset != vbound.getV_parent())
                 {
-                  throw new Error(MessageManager.getString(
-                          "error.implementation_error_cannot_map_alignment_sequences"));
-                  // This occurs because the dataset for the alignment we are
-                  // trying to
+                  throw new Error(
+                          "IMPLEMENTATION ERROR: Cannot map an alignment of sequences from different datasets into a single alignment in the vamsas document.");
                 }
               }
             }
@@ -1320,7 +1320,7 @@ public class VamsasAppDatastore
             // and
             // mapValuesToString
             fromxml.setSkipList(skipList);
-            jalview.util.jarInputStreamProvider jprovider = new jalview.util.jarInputStreamProvider()
+            jarInputStreamProvider jprovider = new jarInputStreamProvider()
             {
 
               @Override
@@ -1338,6 +1338,12 @@ public class VamsasAppDatastore
                         "Returning client input stream for Jalview from Vamsas Document.");
                 return new JarInputStream(cappdata.getClientInputStream());
               }
+
+              @Override
+              public File getFile()
+              {
+                return null;
+              }
             };
             if (dojvsync)
             {
@@ -1368,7 +1374,7 @@ public class VamsasAppDatastore
           fromxml.setSkipList(skipList);
           fromxml.setObjectMappingTables(mapKeysToString(vobj2jv),
                   mapValuesToString(jv2vobj));
-          jalview.util.jarInputStreamProvider jarstream = new jalview.util.jarInputStreamProvider()
+          jarInputStreamProvider jarstream = new jarInputStreamProvider()
           {
 
             @Override
@@ -1386,6 +1392,12 @@ public class VamsasAppDatastore
                       "Returning user input stream for Jalview from Vamsas Document.");
               return new JarInputStream(cappdata.getUserInputStream());
             }
+
+            @Override
+            public File getFile()
+            {
+              return null;
+            }
           };
           if (dojvsync)
           {