-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 ($$Version-Rel$$)
+ * 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;
+ }
+}