update author list in license for (JAL-826)

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

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 834dd12..37108ca 100644 (file)
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -1,6 +1,6 @@
 /*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
  * \r
  * This file is part of Jalview.\r
  * \r
@@ -37,7 +37,7 @@ import jalview.ws.seqfetcher.DbSourceProxyImpl;
  * @author JimP\r
  * \r
  */\r
-abstract public class Pfam extends DbSourceProxyImpl implements\r
+abstract public class Pfam extends Xfam implements\r
         DbSourceProxy\r
 {\r
 \r
@@ -46,6 +46,7 @@ abstract public class Pfam extends DbSourceProxyImpl implements
     super();\r
     // all extensions of this PFAM source base class are DOMAINDB sources\r
     addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);\r
+    addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);\r
   }\r
 \r
   /*\r
@@ -94,17 +95,19 @@ abstract public class Pfam extends DbSourceProxyImpl implements
    * \r
    * @see jalview.ws.DbSourceProxy#getDbVersion()\r
    */\r
-  public String getDbVersion()\r
+  @Override\r
+public String getDbVersion()\r
   {\r
     // TODO Auto-generated method stub\r
     return null;\r
   }\r
 \r
-  /**\r
+  /**Returns base URL for selected Pfam alignment type\r
    * \r
    * @return PFAM URL stub for this DbSource\r
    */\r
-  protected abstract String getPFAMURL();\r
+  @Override\r
+protected abstract String getXFAMURL();\r
 \r
   /*\r
    * (non-Javadoc)\r
@@ -117,7 +120,7 @@ abstract public class Pfam extends DbSourceProxyImpl implements
     // individual references to each sequence in each family alignment that's\r
     // retrieved.\r
     startQuery();\r
-    AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getPFAMURL()\r
+    AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()\r
             + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,\r
             "STH");\r
     for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)\r
@@ -150,4 +153,9 @@ abstract public class Pfam extends DbSourceProxyImpl implements
   /*\r
    * public String getDbName() { return "PFAM"; // getDbSource(); }\r
    */\r
+  \r
+  \r
+  public String getXfamSource() { return jalview.datamodel.DBRefSource.PFAM; }\r
+  \r
+  \r
 }\r