JAL-2488 remove finalize methods

[jalview.git] / src / jalview / ws / dbsources / Pfam.java

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index e4f2475..0227e35 100644 (file)
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 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.
  * 
@@ -20,10 +20,7 @@
  */
 package jalview.ws.dbsources;
 
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
-import jalview.io.FormatAdapter;
 
 import com.stevesoft.pat.Regex;
 
@@ -109,37 +106,6 @@ abstract public class Pfam extends Xfam
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
-   */
-  @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 FormatAdapter().readFile(getXFAMURL()
-            + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
-            "STH");
-    for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
-    {
-      rcds.getSequenceAt(s).addDBRef(new DBRefEntry(DBRefSource.PFAM,
-      // getDbSource(),
-              getDbVersion(), queries.trim().toUpperCase()));
-      if (!getDbSource().equals(DBRefSource.PFAM))
-      { // add the specific ref too
-        rcds.getSequenceAt(s).addDBRef(
-                new DBRefEntry(getDbSource(), getDbVersion(), queries
-                        .trim().toUpperCase()));
-      }
-    }
-    stopQuery();
-    return rcds;
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
    */
   @Override