X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FRangetype.java;h=9c94ddd3f74791f9fdba8e0a04706e01164066f0;hb=faf491e024f9835435f5dd6c20a033250dd9297d;hp=ee4fa8306092c72a4db5d85cd237ffdf41531d27;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/io/vamsas/Rangetype.java b/src/jalview/io/vamsas/Rangetype.java
index ee4fa83..9c94ddd 100644
--- a/src/jalview/io/vamsas/Rangetype.java
+++ b/src/jalview/io/vamsas/Rangetype.java
@@ -20,6 +20,7 @@
  */
 package jalview.io.vamsas;
 
+import jalview.bin.Console;
 import jalview.io.VamsasAppDatastore;
 import jalview.util.MessageManager;
 
@@ -148,7 +149,7 @@ public abstract class Rangetype extends DatastoreItem
           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));
           }
         }
       }
@@ -159,7 +160,7 @@ public abstract class Rangetype extends DatastoreItem
         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));
         }
       }
     }
@@ -193,8 +194,8 @@ public abstract class Rangetype extends DatastoreItem
         for (int s = 0, sSize = range.getSegCount(); s < sSize; s++)
         {
           se = getSegRange(range.getSeg(s), false);
-          posList.addElement(new Integer(se[0]));
-          posList.addElement(new Integer(se[1]));
+          posList.addElement(Integer.valueOf(se[0]));
+          posList.addElement(Integer.valueOf(se[1]));
         }
       }
       else if (range.getPosCount() > 0)
@@ -204,8 +205,8 @@ public abstract class Rangetype extends DatastoreItem
         for (int p = 0, pSize = range.getPosCount(); p < pSize; p++)
         {
           pos = range.getPos(p).getI();
-          posList.add(new Integer(pos));
-          posList.add(new Integer(pos));
+          posList.add(Integer.valueOf(pos));
+          posList.add(Integer.valueOf(pos));
         }
       }
     }
@@ -271,10 +272,9 @@ public abstract class Rangetype extends DatastoreItem
   {
     if (!map.getLocal().hasUnit() || map.getMapped().hasUnit())
     {
-      jalview.bin.Cache.log
-              .warn("using default mapping length of 1:1 for map "
-                      + (map.isRegistered() ? map.getVorbaId().toString()
-                              : ("<no Id registered> " + map.toString())));
+      Console.warn("using default mapping length of 1:1 for map "
+              + (map.isRegistered() ? map.getVorbaId().toString()
+                      : ("<no Id registered> " + map.toString())));
     }
     return parsemapType(map, 1, 1);
   }
@@ -305,8 +305,8 @@ public abstract class Rangetype extends DatastoreItem
   {
     if (ml == null)
     {
-      throw new Error(MessageManager
-              .getString("error.implementation_error_maplist_is_null"));
+      throw new Error(
+              "Implementation error. MapList is null for initMapType.");
     }
     maprange.setLocal(new Local());
     maprange.setMapped(new Mapped());