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wsdbfetch parameter change again (uniprotkb is dbname for uniprot)
author
jprocter
<Jim Procter>
Fri, 19 Dec 2008 15:34:58 +0000
(15:34 +0000)
committer
jprocter
<Jim Procter>
Fri, 19 Dec 2008 15:34:58 +0000
(15:34 +0000)
src/jalview/ws/dbsources/Uniprot.java
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diff --git
a/src/jalview/ws/dbsources/Uniprot.java
b/src/jalview/ws/dbsources/Uniprot.java
index
f7773d8
..
814c534
100644
(file)
--- a/
src/jalview/ws/dbsources/Uniprot.java
+++ b/
src/jalview/ws/dbsources/Uniprot.java
@@
-138,11
+138,13
@@
public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
startQuery();
try
{
startQuery();
try
{
+ queries = queries.toUpperCase().replaceAll("(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)","");
Alignment al = null;
ebi = new EBIFetchClient();
StringBuffer result = new StringBuffer();
// uniprotxml parameter required since december 2007
Alignment al = null;
ebi = new EBIFetchClient();
StringBuffer result = new StringBuffer();
// uniprotxml parameter required since december 2007
- File file = ebi.fetchDataAsFile("uniprot:" + queries, "uniprotxml",
+ // uniprotkb dbname changed introduced december 2008
+ File file = ebi.fetchDataAsFile("uniprotkb:" + queries, "uniprotxml",
null);
Vector entries = getUniprotEntries(file);
null);
Vector entries = getUniprotEntries(file);