JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[jalview.git] / src / jalview / io / vamsas / DatastoreItem.java

diff --git a/src/jalview/io/vamsas/DatastoreItem.java b/src/jalview/io/vamsas/DatastoreItem.java
index f595ff4..215f2d5 100644 (file)
--- a/src/jalview/io/vamsas/DatastoreItem.java
+++ b/src/jalview/io/vamsas/DatastoreItem.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -130,16 +130,22 @@ public abstract class DatastoreItem
     if (vobj2jv.containsKey(vobj.getVorbaId())
             && !(vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
     {
-      Cache.log.debug(
-              "Warning? Overwriting existing vamsas id binding for "
-                      + vobj.getVorbaId(), new Exception(MessageManager.getString("exception.overwriting_vamsas_id_binding")));
+      Cache.log
+              .debug("Warning? Overwriting existing vamsas id binding for "
+                      + vobj.getVorbaId(),
+                      new Exception(
+                              MessageManager
+                                      .getString("exception.overwriting_vamsas_id_binding")));
     }
     else if (jv2vobj.containsKey(jvobj)
             && !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
     {
-      Cache.log.debug(
-              "Warning? Overwriting existing jalview object binding for "
-                      + jvobj, new Exception(MessageManager.getString("exception.overwriting_jalview_id_binding")));
+      Cache.log
+              .debug("Warning? Overwriting existing jalview object binding for "
+                      + jvobj,
+                      new Exception(
+                              MessageManager
+                                      .getString("exception.overwriting_jalview_id_binding")));
     }
     /*
      * Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id "
@@ -189,7 +195,9 @@ public abstract class DatastoreItem
     Object vobject = jv2vobj.remove(oldjvobject);
     if (vobject == null)
     {
-      throw new Error(MessageManager.formatMessage("error.implementation_error_old_jalview_object_not_bound", new String[]{oldjvobject.toString()}));
+      throw new Error(MessageManager.formatMessage(
+              "error.implementation_error_old_jalview_object_not_bound",
+              new String[] { oldjvobject.toString() }));
     }
     if (newjvobject != null)
     {
@@ -228,8 +236,13 @@ public abstract class DatastoreItem
     tojalview = true;
     if (jvobj != null && !(boundType.isAssignableFrom(jvobj.getClass())))
     {
-      throw new Error(MessageManager.formatMessage("error.implementation_error_vamsas_doc_class_should_bind_to_type"
-                       , new String[]{vobj.getClass().toString(),boundType.toString(),jvobj.getClass().toString()}));
+      throw new Error(
+              MessageManager
+                      .formatMessage(
+                              "error.implementation_error_vamsas_doc_class_should_bind_to_type",
+                              new String[] { vobj.getClass().toString(),
+                                  boundType.toString(),
+                                  jvobj.getClass().toString() }));
     }
     dsReg.registerDsObj(this);
   }
@@ -255,8 +268,13 @@ public abstract class DatastoreItem
     vobj = getjv2vObj(jvobj);
     if (vobj != null && !(boundToType.isAssignableFrom(vobj.getClass())))
     {
-        throw new Error(MessageManager.formatMessage("error.implementation_error_vamsas_doc_class_should_bind_to_type"
-                       , new String[]{jvobj2.getClass().toString(),boundToType.toString(),vobj.getClass().toString()}));
+      throw new Error(
+              MessageManager
+                      .formatMessage(
+                              "error.implementation_error_vamsas_doc_class_should_bind_to_type",
+                              new String[] { jvobj2.getClass().toString(),
+                                  boundToType.toString(),
+                                  vobj.getClass().toString() }));
     }
     dsReg.registerDsObj(this);
   }
@@ -429,8 +447,7 @@ public abstract class DatastoreItem
       end = start;
       start = t;
     }
-    return new int[]
-    { start, end, pol < 0 ? 1 : 0 };
+    return new int[] { start, end, pol < 0 ? 1 : 0 };
   }
 
   /**