X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPfam.java;h=37108ca07c1d55047b9dcc057473ffb67d70e02a;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=91ffbca2d29c4f85539be361f010a656a81673a6;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 91ffbca..37108ca 100644
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, 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 program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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;
 
@@ -38,7 +37,7 @@ import jalview.ws.seqfetcher.DbSourceProxyImpl;
  * @author JimP
  * 
  */
-abstract public class Pfam extends DbSourceProxyImpl implements
+abstract public class Pfam extends Xfam implements
         DbSourceProxy
 {
 
@@ -47,6 +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);
   }
 
   /*
@@ -75,17 +75,17 @@ abstract public class Pfam extends DbSourceProxyImpl implements
    * (non-Javadoc)
    * 
    * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
-   *      this doesn't work - DbSource is key for the hash of DbSourceProxy
-   *      instances - 1:many mapping for DbSource to proxy will be lost. *
-   *      suggest : PFAM is an 'alignment' source - means proxy is higher level
-   *      than a sequence source. return jalview.datamodel.DBRefSource.PFAM; }
+   * this doesn't work - DbSource is key for the hash of DbSourceProxy instances
+   * - 1:many mapping for DbSource to proxy will be lost. * suggest : PFAM is an
+   * 'alignment' source - means proxy is higher level than a sequence source.
+   * return jalview.datamodel.DBRefSource.PFAM; }
    */
 
   /*
    * (non-Javadoc)
    * 
    * @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable
-   *      getDbSourceProperties() {
+   * getDbSourceProperties() {
    * 
    * return null; }
    */
@@ -95,17 +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)
@@ -118,7 +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++)
@@ -151,4 +153,9 @@ abstract public class Pfam extends DbSourceProxyImpl implements
   /*
    * public String getDbName() { return "PFAM"; // getDbSource(); }
    */
+  
+  
+  public String getXfamSource() { return jalview.datamodel.DBRefSource.PFAM; }
+  
+  
 }