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update author list in license for (JAL-826)
[jalview.git]
/
src
/
jalview
/
ws
/
dbsources
/
Pfam.java
diff --git
a/src/jalview/ws/dbsources/Pfam.java
b/src/jalview/ws/dbsources/Pfam.java
index
8ce586a
..
37108ca
100644
(file)
--- a/
src/jalview/ws/dbsources/Pfam.java
+++ b/
src/jalview/ws/dbsources/Pfam.java
@@
-1,6
+1,6
@@
/*
\r
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
\r
/*
\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
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
\r
*
\r
* This file is part of Jalview.
\r
*
\r
*
\r
* This file is part of Jalview.
\r
*
\r
@@
-37,7
+37,7
@@
import jalview.ws.seqfetcher.DbSourceProxyImpl;
* @author JimP
\r
*
\r
*/
\r
* @author JimP
\r
*
\r
*/
\r
-abstract public class Pfam extends DbSourceProxyImpl implements
\r
+abstract public class Pfam extends Xfam implements
\r
DbSourceProxy
\r
{
\r
\r
DbSourceProxy
\r
{
\r
\r
@@
-95,17
+95,19
@@
abstract public class Pfam extends DbSourceProxyImpl implements
*
\r
* @see jalview.ws.DbSourceProxy#getDbVersion()
\r
*/
\r
*
\r
* @see jalview.ws.DbSourceProxy#getDbVersion()
\r
*/
\r
- public String getDbVersion()
\r
+ @Override
\r
+public String getDbVersion()
\r
{
\r
// TODO Auto-generated method stub
\r
return null;
\r
}
\r
\r
{
\r
// TODO Auto-generated method stub
\r
return null;
\r
}
\r
\r
- /**
\r
+ /**Returns base URL for selected Pfam alignment type
\r
*
\r
* @return PFAM URL stub for this DbSource
\r
*/
\r
*
\r
* @return PFAM URL stub for this DbSource
\r
*/
\r
- protected abstract String getPFAMURL();
\r
+ @Override
\r
+protected abstract String getXFAMURL();
\r
\r
/*
\r
* (non-Javadoc)
\r
\r
/*
\r
* (non-Javadoc)
\r
@@
-118,7
+120,7
@@
abstract public class Pfam extends DbSourceProxyImpl implements
// individual references to each sequence in each family alignment that's
\r
// retrieved.
\r
startQuery();
\r
// individual references to each sequence in each family alignment that's
\r
// retrieved.
\r
startQuery();
\r
- AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getPFAMURL()
\r
+ AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()
\r
+ queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
\r
"STH");
\r
for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
\r
+ queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
\r
"STH");
\r
for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
\r
@@
-151,4
+153,9
@@
abstract public class Pfam extends DbSourceProxyImpl implements
/*
\r
* public String getDbName() { return "PFAM"; // getDbSource(); }
\r
*/
\r
/*
\r
* public String getDbName() { return "PFAM"; // getDbSource(); }
\r
*/
\r
+
\r
+
\r
+ public String getXfamSource() { return jalview.datamodel.DBRefSource.PFAM; }
\r
+
\r
+
\r
}
\r
}
\r