Fixed T-Coffee file scores parser to support extended format including residue numbers

[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 3d477a4..9d044bc 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;
 
@@ -7,20 +21,12 @@ import java.net.HttpURLConnection;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.Enumeration;
 import java.util.HashMap;
-import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.List;
-import java.util.Map;
-import java.util.Set;
 import java.util.StringTokenizer;
-import java.util.Vector;
 
-import javax.swing.JOptionPane;
-
-import org.apache.http.auth.InvalidCredentialsException;
 import org.biodas.jdas.client.ConnectionPropertyProviderI;
 import org.biodas.jdas.client.SourcesClient;
 import org.biodas.jdas.client.threads.MultipleConnectionPropertyProviderI;
@@ -73,8 +79,10 @@ public class DasSourceRegistry implements DasSourceRegistryI,
     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")));
+      jalview.bin.Cache.setProperty(
+              jalview.bin.Cache.DAS_REGISTRY_URL,
+              registry = registry.substring(0,
+                      registry.lastIndexOf("sources.xml")));
     }
     return registry;
   }