X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPfamSeed.java;h=33c39b139ac67f49dfdb4146c1ca6c758662f1f0;hb=06de78be50c3934158fa1d35ec92ad86b54e959f;hp=8004678c5dee4793725c4eb3817332e47330fa66;hpb=323a457c9d0643be2406b6661246e8e988c0d0f6;p=jalview.git
diff --git a/src/jalview/ws/dbsources/PfamSeed.java b/src/jalview/ws/dbsources/PfamSeed.java
index 8004678..33c39b1 100644
--- a/src/jalview/ws/dbsources/PfamSeed.java
+++ b/src/jalview/ws/dbsources/PfamSeed.java
@@ -1,65 +1,81 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * 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 .
- */
-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";
- }
-
-}
+/*
+ * 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 .
+ * 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;
+ }
+}