JAL-1620 version bump and release notes

[jalview.git] / src / jalview / io / VamsasAppDatastore.java

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index 72a5d3b..2ec7fde 100644 (file)
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
  * This file is part of Jalview.
- *
+ * 
  * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
@@ -30,6 +33,8 @@ import jalview.io.vamsas.Datasetsequence;
 import jalview.io.vamsas.DatastoreItem;
 import jalview.io.vamsas.DatastoreRegistry;
 import jalview.io.vamsas.Rangetype;
+import jalview.util.MessageManager;
+
 import java.io.IOException;
 import java.util.Enumeration;
 import java.util.HashMap;
@@ -219,8 +224,7 @@ public class VamsasAppDatastore
     {
       Cache.log.debug(
               "Warning? Overwriting existing vamsas id binding for "
-                      + vobj.getVorbaId(), new Exception(
-                      "Overwriting vamsas id binding."));
+                      + vobj.getVorbaId(), new Exception(MessageManager.getString("exception.overwriting_vamsas_id_binding")));
     }
     else if (jv2vobj.containsKey(jvobj)
             && !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
@@ -307,8 +311,7 @@ public class VamsasAppDatastore
                 if (vbound.getV_parent() != null
                         && dataset != vbound.getV_parent())
                 {
-                  throw new Error(
-                          "IMPLEMENTATION ERROR: Cannot map an alignment of sequences from different datasets into a single alignment in the vamsas document.");
+                  throw new Error(MessageManager.getString("error.implementation_error_cannot_map_alignment_sequences"));
                   // This occurs because the dataset for the alignment we are
                   // trying to
                 }
@@ -1470,9 +1473,7 @@ public class VamsasAppDatastore
     {
       // NOTE: this happens if user deletes object in one session then updates
       // from another client
-      throw new Error(
-              "IMPLEMENTATION ERROR: old jalview object is not bound ! ("
-                      + oldjvobject + ")");
+      throw new Error(MessageManager.formatMessage("error.implementation_error_old_jalview_object_not_bound", new String[]{oldjvobject.toString()}));
     }
     if (newjvobject != null)
     {
@@ -2414,8 +2415,7 @@ public class VamsasAppDatastore
       int[] se = null;
       if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
       {
-        throw new Error(
-                "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+        throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
       }
       if (dseta.getSegCount() > 0)
       {
@@ -2473,8 +2473,7 @@ public class VamsasAppDatastore
       int[] se = null;
       if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
       {
-        throw new Error(
-                "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+          throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
       }
       if (dseta.getSegCount() > 0)
       {
@@ -2730,8 +2729,7 @@ public class VamsasAppDatastore
       }
     } catch (Exception e)
     {
-      throw new Exception("Couldn't store sequence mappings for " + title,
-              e);
+      throw new Exception(MessageManager.formatMessage("exception.couldnt_store_sequence_mappings", new String[]{title}),e);
     }
   }