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

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

diff --git a/src/jalview/ws/dbsources/Rfam.java b/src/jalview/ws/dbsources/Rfam.java
index 76f8b10..97f73d0 100644 (file)
--- a/src/jalview/ws/dbsources/Rfam.java
+++ b/src/jalview/ws/dbsources/Rfam.java
@@ -1,41 +1,40 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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 com.stevesoft.pat.Regex;
+import jalview.datamodel.DBRefSource;
 
-import jalview.ws.seqfetcher.DbSourceProxy;
+import com.stevesoft.pat.Regex;
 
 /**
  * Contains methods for fetching sequences from Rfam database
  * 
  * @author Lauren Michelle Lui
  */
-abstract public class Rfam extends Xfam implements DbSourceProxy
+abstract public class Rfam extends Xfam
 {
 
   public Rfam()
   {
     super();
-    // all extensions of this RFAM source base class are DOMAINDB sources
-    addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
-    addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);
   }
 
   /*
@@ -44,6 +43,7 @@ abstract public class Rfam extends Xfam implements DbSourceProxy
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator() Left here for
    * consistency with Pfam class
    */
+  @Override
   public String getAccessionSeparator()
   {
     // TODO Auto-generated method stub
@@ -55,6 +55,7 @@ abstract public class Rfam extends Xfam implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getAccessionValidator() * Left here for
    */
+  @Override
   public Regex getAccessionValidator()
   {
     // TODO Auto-generated method stub
@@ -98,6 +99,7 @@ abstract public class Rfam extends Xfam implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
    */
+  @Override
   public boolean isValidReference(String accession)
   {
     return accession.indexOf("RF") == 0;
@@ -108,9 +110,10 @@ abstract public class Rfam extends Xfam implements DbSourceProxy
    * 
    * @see jalview.ws.dbsources.Xfam#getXfamSource()
    */
+  @Override
   public String getXfamSource()
   {
-    return jalview.datamodel.DBRefSource.RFAM;
+    return DBRefSource.RFAM;
   }
 
 }