X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FXfam.java;h=26291ebf182f75b5526280d545e880db0f85e0f4;hb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;hp=d06151bffe805b4bf172a2dbaf3c45ebc7caaa97;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Xfam.java b/src/jalview/ws/dbsources/Xfam.java
index d06151b..26291eb 100644
--- a/src/jalview/ws/dbsources/Xfam.java
+++ b/src/jalview/ws/dbsources/Xfam.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * 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.
  * 
@@ -20,8 +20,12 @@
  */
 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;
 
 /**
@@ -40,10 +44,12 @@ public abstract class Xfam extends DbSourceProxyImpl
 
   protected abstract String getXFAMURL();
 
+  @Override
   public abstract String getDbVersion();
 
   abstract String getXfamSource();
 
+  @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
     // TODO: this is not a perfect implementation. We need to be able to add
@@ -51,23 +57,49 @@ public abstract class Xfam extends DbSourceProxyImpl
     // retrieved.
     startQuery();
     // TODO: trap HTTP 404 exceptions and return null
-    AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()
-            + queries.trim().toUpperCase(), 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();
     return rcds;
   }
 
+  /**
+   * Pfam and Rfam provide alignments
+   */
+  @Override
+  public boolean isAlignmentSource()
+  {
+    return true;
+  }
+
+  /**
+   * default suffix to append the retrieval URL for this source.
+   * 
+   * @return "" for most Xfam sources
+   */
+  public String getXFAMURLSUFFIX()
+  {
+    return "";
+  }
+
 }