git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge branch 'develop' into features/JAL-1793VCF
[jalview.git]
/
src
/
jalview
/
ws
/
dbsources
/
PfamFull.java
diff --git
a/src/jalview/ws/dbsources/PfamFull.java
b/src/jalview/ws/dbsources/PfamFull.java
index
a07c90e
..
ec9fcbb
100644
(file)
--- a/
src/jalview/ws/dbsources/PfamFull.java
+++ b/
src/jalview/ws/dbsources/PfamFull.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,13
+20,11
@@
*/
package jalview.ws.dbsources;
*/
package jalview.ws.dbsources;
-import jalview.ws.seqfetcher.DbSourceProxy;
-
/**
* flyweight class specifying retrieval of Full family alignments from PFAM
*
*/
/**
* flyweight class specifying retrieval of Full family alignments from PFAM
*
*/
-public class PfamFull extends Pfam implements DbSourceProxy
+public class PfamFull extends Pfam
{
public PfamFull()
{
{
public PfamFull()
{
@@
-38,9
+36,17
@@
public class PfamFull extends Pfam implements DbSourceProxy
*
* @see jalview.ws.dbsources.Pfam#getPFAMURL()
*/
*
* @see jalview.ws.dbsources.Pfam#getPFAMURL()
*/
+ @Override
protected String getXFAMURL()
{
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";
}
/*
}
/*
@@
-48,21
+54,25
@@
public class PfamFull extends Pfam implements DbSourceProxy
*
* @see jalview.ws.seqfetcher.DbSourceProxy#getDbName()
*/
*
* @see jalview.ws.seqfetcher.DbSourceProxy#getDbName()
*/
+ @Override
public String getDbName()
{
return "PFAM (Full)";
}
public String getDbName()
{
return "PFAM (Full)";
}
+ @Override
public String getDbSource()
{
return getDbName(); // so we have unique DbSource string.
}
public String getDbSource()
{
return getDbName(); // so we have unique DbSource string.
}
+ @Override
public String getTestQuery()
{
return "PF03760";
}
public String getTestQuery()
{
return "PF03760";
}
+ @Override
public String getDbVersion()
{
return null;
public String getDbVersion()
{
return null;