From: jprocter <Jim Procter>
Date: Fri, 19 Dec 2008 15:34:58 +0000 (+0000)
Subject: wsdbfetch parameter change again (uniprotkb is dbname for uniprot)
X-Git-Tag: Release_2_5~369
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9f982f18f80a75d1be6f6c002c8ba81ff8a00a0a;p=jalview.git

wsdbfetch parameter change again (uniprotkb is dbname for uniprot)
---

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index f7773d8..814c534 100644
--- 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
     {
+      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
-      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);