X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=2fc526bcb5073bd472a09ed7c3f3bec95168604d;hb=132fa48b35a4821ca0d8e241ba27989e573e61e5;hp=adf44477c8cddd71fceb91740456c88d40bf4b0a;hpb=4d64932654de3f6ffe07db11d18f2d21f558c6e6;p=jalview.git

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index adf4447..2fc526b 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -338,10 +338,8 @@ 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.");
                 }
               }
             }
@@ -2248,7 +2246,7 @@ public class VamsasAppDatastore
           Float val = null;
           try
           {
-            val = new Float(props[p].getContent());
+            val = Float.valueOf(props[p].getContent());
           } catch (Exception e)
           {
             Cache.log.warn("Failed to parse threshold property");
@@ -2537,7 +2535,7 @@ public class VamsasAppDatastore
           int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);
           for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)
           {
-            posList.add(new Integer(p));
+            posList.add(Integer.valueOf(p));
           }
         }
       }
@@ -2548,7 +2546,7 @@ public class VamsasAppDatastore
         for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
         {
           pos = dseta.getPos(p).getI();
-          posList.add(new Integer(pos));
+          posList.add(Integer.valueOf(pos));
         }
       }
     }