X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPfamSeed.java;h=9f07e5dfc4b8e4c0fed819e0d9b00d29ff526957;hb=fda3adcb9abc603b03188404f532a5bc8097dd55;hp=885e18a323ae15b40a60c1da4663ed434111fcde;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/ws/dbsources/PfamSeed.java b/src/jalview/ws/dbsources/PfamSeed.java
index 885e18a..9f07e5d 100644
--- a/src/jalview/ws/dbsources/PfamSeed.java
+++ b/src/jalview/ws/dbsources/PfamSeed.java
@@ -1,65 +1,80 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- * 
- * 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.
- * 
- * 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/>.
- */
-package jalview.ws.dbsources;
-
-import jalview.ws.seqfetcher.DbSourceProxy;
-
-/**
- * flyweight class specifying retrieval of Seed alignments from PFAM
- * 
- * @author JimP
- * 
- */
-public class PfamSeed extends Pfam implements DbSourceProxy
-{
-  public PfamSeed()
-  {
-    super();
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.dbsources.Pfam#getPFAMURL()
-   */
-  protected String getPFAMURL()
-  {
-    return "http://pfam.sanger.ac.uk/family/alignment/download/format?alnType=seed&format=stockholm&order=t&case=l&gaps=default&entry=";
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.seqfetcher.DbSourceProxy#getDbName()
-   */
-  public String getDbName()
-  {
-    return "PFAM (Seed)";
-  }
-
-  public String getDbSource()
-  {
-    return jalview.datamodel.DBRefSource.PFAM; // archetype source
-  }
-
-  public String getTestQuery()
-  {
-    return "PF03760";
-  }
-
-}
+/*
+ * 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.dbsources;
+
+/**
+ * flyweight class specifying retrieval of Seed alignments from PFAM
+ * 
+ * @author JimP
+ * 
+ */
+public class PfamSeed extends Pfam
+{
+  public PfamSeed()
+  {
+    super();
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.dbsources.Pfam#getPFAMURL()
+   */
+  @Override
+  protected String getXFAMURL()
+  {
+    return "http://pfam.xfam.org/family/";
+  }
+
+  @Override
+  public String getXFAMURLSUFFIX()
+  {
+    return "/alignment/seed";
+  }
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.seqfetcher.DbSourceProxy#getDbName()
+   */
+  @Override
+  public String getDbName()
+  {
+    return "PFAM (Seed)";
+  }
+
+  @Override
+  public String getDbSource()
+  {
+    return jalview.datamodel.DBRefSource.PFAM; // archetype source
+  }
+
+  @Override
+  public String getTestQuery()
+  {
+    return "PF03760";
+  }
+
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
+}