JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / ws / dbsources / Xfam.java

diff --git a/src/jalview/ws/dbsources/Xfam.java b/src/jalview/ws/dbsources/Xfam.java
index 6d90415..6cc383d 100644 (file)
--- a/src/jalview/ws/dbsources/Xfam.java
+++ b/src/jalview/ws/dbsources/Xfam.java
@@ -1,24 +1,28 @@
 /*
- * 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;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
+import jalview.io.FormatAdapter;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
 
 /**
@@ -37,10 +41,12 @@ public abstract class Xfam extends DbSourceProxyImpl
 
   protected abstract String getXFAMURL();
 
+  @Override
   public abstract String getDbVersion();
 
   abstract String getXfamSource();
 
+  @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
     // TODO: this is not a perfect implementation. We need to be able to add
@@ -48,9 +54,9 @@ public abstract class Xfam extends DbSourceProxyImpl
     // retrieved.
     startQuery();
     // TODO: trap HTTP 404 exceptions and return null
-    AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()
-            + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
-            "STH");
+    AlignmentI rcds = new FormatAdapter().readFile(getXFAMURL()
+            + queries.trim().toUpperCase() + getXFAMURLSUFFIX(),
+            jalview.io.FormatAdapter.URL, "STH");
     for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
     {
       rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(),
@@ -67,4 +73,23 @@ public abstract class Xfam extends DbSourceProxyImpl
     return rcds;
   }
 
+  /**
+   * Pfam and Rfam provide alignments
+   */
+  @Override
+  public boolean isAlignmentSource()
+  {
+    return true;
+  }
+
+  /**
+   * default suffix to append the retrieval URL for this source.
+   * 
+   * @return "" for most Xfam sources
+   */
+  public String getXFAMURLSUFFIX()
+  {
+    return "";
+  }
+
 }