X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FXfam.java;h=36d98915a11341da8e5059603d6cc78b0c55fb5d;hb=1128674a17df402a2219d278ab332c291cb93443;hp=3554f0177faf6efc15f549db7b1342f2a950e918;hpb=230fac58c5afe1843bf7177834fe1bd1d7e6f9d5;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Xfam.java b/src/jalview/ws/dbsources/Xfam.java
index 3554f01..36d9891 100644
--- a/src/jalview/ws/dbsources/Xfam.java
+++ b/src/jalview/ws/dbsources/Xfam.java
@@ -20,6 +20,9 @@
  */
 package jalview.ws.dbsources;
 
+import java.util.Locale;
+
+import jalview.bin.Console;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.io.DataSourceType;
@@ -35,13 +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();
@@ -56,25 +63,34 @@ 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(),
+    String xfamUrl = getURL(queries);
+
+    Console.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
    */
@@ -89,7 +105,7 @@ public abstract class Xfam extends DbSourceProxyImpl
    * 
    * @return "" for most Xfam sources
    */
-  public String getXFAMURLSUFFIX()
+  public String getURLSuffix()
   {
     return "";
   }