X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2Fdas%2Fdatamodel%2FDasSequenceSource.java;h=32e4f3e0f7e31c3ae2e0709de0fb87278cd4f255;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=7bb643699f39d8f5c98cfac6e00ef6d7bec3e6c6;hpb=1fe15a0bb2006a51a24f4757c89337d99db4ad26;p=jalview.git

diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
index 7bb6436..32e4f3e 100644
--- a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
@@ -1,22 +1,36 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * 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.
+ * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws.dbsources.das.datamodel;
 
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.ws.seqfetcher.DbSourceProxy;
+import jalview.ws.seqfetcher.DbSourceProxyImpl;
+
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
@@ -36,15 +50,6 @@ import org.biodas.jdas.schema.sources.VERSION;
 
 import com.stevesoft.pat.Regex;
 
-import jalview.ws.dbsources.das.api.jalviewSourceI;
-import jalview.ws.seqfetcher.*;
-import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-
 /**
  * an instance of this class is created for each unique DAS Sequence source (ie
  * one capable of handling the 'sequence' for a particular MapMaster)
@@ -70,9 +75,10 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
   protected MultipleConnectionPropertyProviderI connprops = null;
 
   /**
-   * DAS sources are tier 1 - if we have a direct DB connection then we should prefer it
+   * DAS sources are tier 1 - if we have a direct DB connection then we should
+   * prefer it
    */
-  private int tier=1;
+  private int tier = 1;
 
   /**
    * create a new DbSource proxy for a DAS 1 source
@@ -96,9 +102,11 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
     if (!(jsrc = new JalviewSource(source, connprops, false))
             .isSequenceSource())
     {
-      throw new Exception("Source " + source.getTitle()
-              + " does not support the sequence command.");
+      throw new Exception(MessageManager.formatMessage(
+              "exception.das_source_doesnt_support_sequence_command",
+              new String[] { source.getTitle() }));
     }
+    this.tier = 1 + ((jsrc.isLocal() || jsrc.isReferenceSource()) ? 0 : 1);
     this.source = source;
     this.dbname = dbname;
     this.dbrefname = dbrefname.toUpperCase();
@@ -167,8 +175,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
                   connprops.getConnectionPropertyProviderFor(sr));
           for (String q : toks)
           {
-            List<String> qset = Arrays.asList(new String[]
-            { q });
+            List<String> qset = Arrays.asList(new String[] { q });
             try
             {
               DasSequenceAdapter s = sq.fetchData(sr, qset);