Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

[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 11c7e91..56d9fa4 100644 (file)
--- a/src/jalview/io/vamsas/DatastoreItem.java
+++ b/src/jalview/io/vamsas/DatastoreItem.java
@@ -76,8 +76,8 @@ public abstract class DatastoreItem
     }
     if (Cache.log.isDebugEnabled())
     {
-      Cache.log.debug("Returning null VorbaID binding for jalview object "
-              + jvobj);
+      Cache.log.debug(
+              "Returning null VorbaID binding for jalview object " + jvobj);
     }
     return null;
   }
@@ -95,8 +95,8 @@ public abstract class DatastoreItem
     if (id == null)
     {
       id = cdoc.registerObject(vobj);
-      Cache.log
-              .debug("Registering new object and returning null for getvObj2jv");
+      Cache.log.debug(
+              "Registering new object and returning null for getvObj2jv");
       return null;
     }
     if (vobj2jv.containsKey(vobj.getVorbaId()))
@@ -124,7 +124,8 @@ public abstract class DatastoreItem
       {
         Cache.log.error("Failed to get id for "
                 + (vobj.isRegisterable() ? "registerable"
-                        : "unregisterable") + " object " + vobj);
+                        : "unregisterable")
+                + " object " + vobj);
       }
     }
     if (vobj2jv.containsKey(vobj.getVorbaId())
@@ -132,14 +133,18 @@ public abstract class DatastoreItem
     {
       Cache.log.debug(
               "Warning? Overwriting existing vamsas id binding for "
-                      + vobj.getVorbaId(), new Exception(MessageManager.getString("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()))
     {
       Cache.log.debug(
               "Warning? Overwriting existing jalview object binding for "
-                      + jvobj, new Exception(MessageManager.getString("exception.overwriting_jalview_id_binding")));
+                      + jvobj,
+              new Exception(MessageManager.getString(
+                      "exception.overwriting_jalview_id_binding")));
     }
     /*
      * Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id "
@@ -189,7 +194,10 @@ 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 +236,11 @@ 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 +266,11 @@ 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 +443,7 @@ 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 };
   }
 
   /**
@@ -443,9 +456,9 @@ public abstract class DatastoreItem
     jalview.datamodel.Provenance jprov = new jalview.datamodel.Provenance();
     for (int i = 0; i < prov.getEntryCount(); i++)
     {
-      jprov.addEntry(prov.getEntry(i).getUser(), prov.getEntry(i)
-              .getAction(), prov.getEntry(i).getDate(), prov.getEntry(i)
-              .getId());
+      jprov.addEntry(prov.getEntry(i).getUser(),
+              prov.getEntry(i).getAction(), prov.getEntry(i).getDate(),
+              prov.getEntry(i).getId());
     }
 
     return jprov;