JAL-3615 used gzip endpoints for Pfam and Rfam

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

diff --git a/src/jalview/ws/dbsources/PfamFull.java b/src/jalview/ws/dbsources/PfamFull.java
index 3d3ab53..d71892b 100644 (file)
--- a/src/jalview/ws/dbsources/PfamFull.java
+++ b/src/jalview/ws/dbsources/PfamFull.java
@@ -1,43 +1,74 @@
-/**\r
- * \r
- */\r
-package jalview.ws.dbsources;\r
-\r
-import jalview.ws.seqfetcher.DbSourceProxy;\r
-\r
-/**\r
- * flyweight class specifying retrieval of Full family alignments from PFAM\r
- *\r
- */\r
-public class PfamFull extends Pfam implements DbSourceProxy\r
-{\r
-  public PfamFull()\r
-  {\r
-    super();\r
-  }\r
-\r
-  /* (non-Javadoc)\r
-   * @see jalview.ws.dbsources.Pfam#getPFAMURL()\r
-   */\r
-  protected String getPFAMURL()\r
-  {\r
-    return "http://pfam.sanger.ac.uk/family/alignment/download/format?alnType=full&format=stockholm&order=t&case=l&gaps=default&entry=";\r
-  }\r
-\r
-  /* (non-Javadoc)\r
-   * @see jalview.ws.seqfetcher.DbSourceProxy#getDbName()\r
-   */\r
-  public String getDbName()\r
-  {\r
-    return "PFAM (Full)";\r
-  }\r
-  public String getDbSource()\r
-  {\r
-    return getDbName(); // so we have unique DbSource string.\r
-  }\r
-  public String getTestQuery()\r
-  {\r
-    return "PF00535"; // TODO: Pick a better full alignment to retrieve.\r
-  }\r
-\r
-}\r
+/*
+ * 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 Full family alignments from PFAM
+ * 
+ */
+public class PfamFull extends Pfam
+{
+  public PfamFull()
+  {
+    super();
+  }
+
+  @Override
+  public String getURLSuffix()
+  {
+    return "/alignment/full" + GZIPPED;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.seqfetcher.DbSourceProxy#getDbName()
+   */
+  @Override
+  public String getDbName()
+  {
+    return "PFAM (Full)";
+  }
+
+  @Override
+  public String getDbSource()
+  {
+    return getDbName(); // so we have unique DbSource string.
+  }
+
+  @Override
+  public String getTestQuery()
+  {
+    return "PF03760";
+  }
+
+  @Override
+  public String getDbVersion()
+  {
+    return null;
+  }
+
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
+}