JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/ws/dbsources/PfamSeed.java b/src/jalview/ws/dbsources/PfamSeed.java
index 5cde798..027db80 100644 (file)
--- a/src/jalview/ws/dbsources/PfamSeed.java
+++ b/src/jalview/ws/dbsources/PfamSeed.java
@@ -1,66 +1,73 @@
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- * \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- * \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
- * GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
- */\r
-package jalview.ws.dbsources;\r
-\r
-import jalview.ws.seqfetcher.DbSourceProxy;\r
-\r
-/**\r
- * flyweight class specifying retrieval of Seed alignments from PFAM\r
- * \r
- * @author JimP\r
- * \r
- */\r
-public class PfamSeed extends Pfam implements DbSourceProxy\r
-{\r
-  public PfamSeed()\r
-  {\r
-    super();\r
-  }\r
-\r
-  /*\r
-   * (non-Javadoc)\r
-   * \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=seed&format=stockholm&order=t&case=l&gaps=default&entry=";\r
-  }\r
-\r
-  /*\r
-   * (non-Javadoc)\r
-   * \r
-   * @see jalview.ws.seqfetcher.DbSourceProxy#getDbName()\r
-   */\r
-  public String getDbName()\r
-  {\r
-    return "PFAM (Seed)";\r
-  }\r
-\r
-  public String getDbSource()\r
-  {\r
-    return jalview.datamodel.DBRefSource.PFAM; // archetype source\r
-  }\r
-\r
-  public String getTestQuery()\r
-  {\r
-    return "PF03760";\r
-  }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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;
+
+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 getXFAMURL()
+  {
+    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";
+  }
+
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
+}