X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FXfam.java;h=9340f659ef5e125b01546a2e61b04938ab6a0861;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;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..9340f65 100644
--- a/src/jalview/ws/dbsources/Xfam.java
+++ b/src/jalview/ws/dbsources/Xfam.java
@@ -20,8 +20,13 @@
  */
 package jalview.ws.dbsources;
 
+import java.util.Locale;
+
+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;
 
@@ -33,13 +38,17 @@ import jalview.ws.seqfetcher.DbSourceProxyImpl;
  */
 public abstract class Xfam extends DbSourceProxyImpl
 {
-
   public Xfam()
   {
     super();
   }
 
-  protected abstract String getXFAMURL();
+  /**
+   * the base URL for this Xfam-like service
+   * 
+   * @return
+   */
+  protected abstract String getURLPrefix();
 
   @Override
   public abstract String getDbVersion();
@@ -54,26 +63,37 @@ 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 = getURL(queries);
+
+    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(),
-              getDbVersion(), queries.trim().toUpperCase()));
+              // getDbSource(),
+              getDbVersion(), queries.trim().toUpperCase(Locale.ROOT)));
       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(Locale.ROOT)));
       }
     }
     stopQuery();
     return rcds;
   }
 
+  String getURL(String queries)
+  {
+    return getURLPrefix() + "/family/" + queries.trim().toUpperCase(Locale.ROOT)
+            + getURLSuffix();
+  }
+
   /**
    * Pfam and Rfam provide alignments
    */
@@ -83,11 +103,12 @@ public abstract class Xfam extends DbSourceProxyImpl
     return true;
   }
 
+  /**
    * default suffix to append the retrieval URL for this source.
    * 
    * @return "" for most Xfam sources
    */
-  public String getXFAMURLSUFFIX()
+  public String getURLSuffix()
   {
     return "";
   }