Jalview 2.8 Source Header

[jalview.git] / src / jalview / ws / dbsources / das / datamodel / DasSourceRegistry.java

diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
index 3ed597e..e7f51f2 100644 (file)
--- a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
@@ -1,5 +1,19 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 
+ * 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 
+ * 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/>.
  */
 package jalview.ws.dbsources.das.datamodel;
 
@@ -70,6 +84,14 @@ public class DasSourceRegistry implements DasSourceRegistryI,
               DEFAULT_REGISTRY);
       registry = DEFAULT_REGISTRY;
     }
+    if (registry.lastIndexOf("sources.xml") == registry.length() - 11)
+    {
+      // no trailing sources.xml document for registry in JDAS
+      jalview.bin.Cache.setProperty(
+              jalview.bin.Cache.DAS_REGISTRY_URL,
+              registry = registry.substring(0,
+                      registry.lastIndexOf("sources.xml")));
+    }
     return registry;
   }
 
@@ -92,7 +114,8 @@ public class DasSourceRegistry implements DasSourceRegistryI,
    * @param registryURL
    *          return sources from registryURL
    */
-  private static List<jalviewSourceI> getDASSources(String registryURL, MultipleConnectionPropertyProviderI registry)
+  private static List<jalviewSourceI> getDASSources(String registryURL,
+          MultipleConnectionPropertyProviderI registry)
   {
     try
     {
@@ -104,21 +127,26 @@ public class DasSourceRegistry implements DasSourceRegistryI,
 
       List<SOURCE> dassources = sources.getSOURCE();
       ArrayList<jalviewSourceI> dsrc = new ArrayList<jalviewSourceI>();
-      HashMap<String,Integer> latests=new HashMap<String, Integer>();
+      HashMap<String, Integer> latests = new HashMap<String, Integer>();
       Integer latest;
       for (SOURCE src : dassources)
       {
-        JalviewSource jsrc=new JalviewSource(src, registry, false);
-        latest=latests.get(jsrc.getSourceURL());
-        if (latest!=null)
+        JalviewSource jsrc = new JalviewSource(src, registry, false);
+        latest = latests.get(jsrc.getSourceURL());
+        if (latest != null)
         {
           if (jsrc.isNewerThan(dsrc.get(latest.intValue())))
           {
             dsrc.set(latest.intValue(), jsrc);
-          } else {
-            System.out.println("Debug: Ingored older source "+jsrc.getTitle());
           }
-        } else {
+          else
+          {
+            System.out.println("Debug: Ignored older source "
+                    + jsrc.getTitle());
+          }
+        }
+        else
+        {
           latests.put(jsrc.getSourceURL(), Integer.valueOf(dsrc.size()));
           dsrc.add(jsrc);
         }
@@ -147,7 +175,7 @@ public class DasSourceRegistry implements DasSourceRegistryI,
     }
     return appendLocalSources();
   }
-  
+
   /**
    * generate Sources from the local das source list
    *