X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPfam.java;h=37108ca07c1d55047b9dcc057473ffb67d70e02a;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=d5b65052b6c92bf9287e1651c287b2603e099cc2;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index d5b6505..37108ca 100644
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -37,7 +37,7 @@ import jalview.ws.seqfetcher.DbSourceProxyImpl;
  * @author JimP
  * 
  */
-abstract public class Pfam extends DbSourceProxyImpl implements
+abstract public class Pfam extends Xfam implements
         DbSourceProxy
 {
 
@@ -46,6 +46,7 @@ abstract public class Pfam extends DbSourceProxyImpl implements
     super();
     // all extensions of this PFAM source base class are DOMAINDB sources
     addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
+    addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);
   }
 
   /*
@@ -94,17 +95,19 @@ abstract public class Pfam extends DbSourceProxyImpl implements
    * 
    * @see jalview.ws.DbSourceProxy#getDbVersion()
    */
-  public String getDbVersion()
+  @Override
+public String getDbVersion()
   {
     // TODO Auto-generated method stub
     return null;
   }
 
-  /**
+  /**Returns base URL for selected Pfam alignment type
    * 
    * @return PFAM URL stub for this DbSource
    */
-  protected abstract String getPFAMURL();
+  @Override
+protected abstract String getXFAMURL();
 
   /*
    * (non-Javadoc)
@@ -117,7 +120,7 @@ abstract public class Pfam extends DbSourceProxyImpl implements
     // individual references to each sequence in each family alignment that's
     // retrieved.
     startQuery();
-    AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getPFAMURL()
+    AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()
             + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
             "STH");
     for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
@@ -150,4 +153,9 @@ abstract public class Pfam extends DbSourceProxyImpl implements
   /*
    * public String getDbName() { return "PFAM"; // getDbSource(); }
    */
+  
+  
+  public String getXfamSource() { return jalview.datamodel.DBRefSource.PFAM; }
+  
+  
 }