X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fdbsources%2FXfam.java;h=f0cb14b204a0cf42aa49618d37eef32ebc0e400a;hb=339d1bf247a3b0d000044892bee3d5668a8d9b11;hp=031ef2e1e362912cc752aa0b7795050be8a0df22;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Xfam.java b/src/jalview/ws/dbsources/Xfam.java
index 031ef2e..f0cb14b 100644
--- a/src/jalview/ws/dbsources/Xfam.java
+++ b/src/jalview/ws/dbsources/Xfam.java
@@ -1,24 +1,31 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 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;
 
 /**
@@ -29,41 +36,79 @@ 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();
 
   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
     // individual references to each sequence in each family alignment that's
     // retrieved.
     startQuery();
-    AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()
-            + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
-            "STH");
+    // TODO: trap HTTP 404 exceptions and return null
+    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(),
+              // 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;
   }
 
-}
\ No newline at end of file
+  String getURL(String queries)
+  {
+    return getURLPrefix() + "/family/" + queries.trim().toUpperCase()
+            + getURLSuffix();
+  }
+
+  /**
+   * 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 getURLSuffix()
+  {
+    return "";
+  }
+
+}