X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FXfam.java;h=26291ebf182f75b5526280d545e880db0f85e0f4;hb=4ed4e90803e3a463458410be06b678ff3154937f;hp=b70beffbcdab6c7e6a56ee4d7d86798e4dc76e57;hpb=2bca29574b68d32c16a80b2c1bfa330ed6012f82;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Xfam.java b/src/jalview/ws/dbsources/Xfam.java
index b70beff..26291eb 100644
--- a/src/jalview/ws/dbsources/Xfam.java
+++ b/src/jalview/ws/dbsources/Xfam.java
@@ -20,8 +20,11 @@
  */
 package jalview.ws.dbsources;
 
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
 
@@ -54,20 +57,26 @@ public abstract class Xfam extends DbSourceProxyImpl
     // retrieved.
     startQuery();
     // TODO: trap HTTP 404 exceptions and return null
-    AlignmentI rcds = new FormatAdapter().readFile(getXFAMURL()
-            + queries.trim().toUpperCase() + getXFAMURLSUFFIX(),
-            jalview.io.FormatAdapter.URL,
-            "STH");
+    String xfamUrl = getXFAMURL() + queries.trim().toUpperCase()
+            + getXFAMURLSUFFIX();
+
+    if (Cache.log != null)
+    {
+      Cache.log.debug("XFAM URL for retrieval is: " + xfamUrl);
+    }
+
+    AlignmentI rcds = new FormatAdapter().readFile(xfamUrl,
+            DataSourceType.URL, FileFormat.Stockholm);
+
     for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
     {
       rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(),
-      // getDbSource(),
+              // getDbSource(),
               getDbVersion(), queries.trim().toUpperCase()));
       if (!getDbSource().equals(getXfamSource()))
       { // add the specific ref too
-        rcds.getSequenceAt(s).addDBRef(
-                new DBRefEntry(getDbSource(), getDbVersion(), queries
-                        .trim().toUpperCase()));
+        rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getDbSource(),
+                getDbVersion(), queries.trim().toUpperCase()));
       }
     }
     stopQuery();
@@ -83,6 +92,7 @@ public abstract class Xfam extends DbSourceProxyImpl
     return true;
   }
 
+  /**
    * default suffix to append the retrieval URL for this source.
    * 
    * @return "" for most Xfam sources