X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPfamFull.java;h=ec9fcbb482a623c36b965719e40c09f82e445319;hb=06de78be50c3934158fa1d35ec92ad86b54e959f;hp=75d4559c7cac4632a4b308471a9c3fc9c12e19a2;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/ws/dbsources/PfamFull.java b/src/jalview/ws/dbsources/PfamFull.java
index 75d4559..ec9fcbb 100644
--- a/src/jalview/ws/dbsources/PfamFull.java
+++ b/src/jalview/ws/dbsources/PfamFull.java
@@ -1,29 +1,30 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * 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 .
+ * 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;
-import jalview.ws.seqfetcher.DbSourceProxy;
-
/**
* flyweight class specifying retrieval of Full family alignments from PFAM
*
*/
-public class PfamFull extends Pfam implements DbSourceProxy
+public class PfamFull extends Pfam
{
public PfamFull()
{
@@ -35,9 +36,17 @@ public class PfamFull extends Pfam implements DbSourceProxy
*
* @see jalview.ws.dbsources.Pfam#getPFAMURL()
*/
+ @Override
protected String getXFAMURL()
{
- return "http://pfam.sanger.ac.uk/family/alignment/download/format?alnType=full&format=stockholm&order=t&case=l&gaps=default&entry=";
+ return "http://pfam.xfam.org/family/";
+
+ }
+
+ @Override
+ public String getXFAMURLSUFFIX()
+ {
+ return "/alignment/full";
}
/*
@@ -45,24 +54,33 @@ public class PfamFull extends Pfam implements DbSourceProxy
*
* @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;
+ }
}