X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FUniprot.java;h=167758f8815a60e57614971edbbd5964135fdc55;hb=e9aa1cee679000405c5549829ee08e1c08b2ffd5;hp=f29a555c4c74c9c3f81f01a2a63b9cd55a5fedcf;hpb=25ae256a88bf092f45a78b649a48f41e6fd5d70b;p=jalview.git
diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index f29a555..167758f 100644
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -1,5 +1,19 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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.
*
+ * 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 .
*/
package jalview.ws.dbsources;
@@ -36,11 +50,12 @@ import jalview.ws.seqfetcher.DbSourceProxyImpl;
*/
public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
{
- public Uniprot() {
+ public Uniprot()
+ {
super();
addDbSourceProperty(DBRefSource.SEQDB, DBRefSource.SEQDB);
addDbSourceProperty(DBRefSource.PROTSEQDB);
-// addDbSourceProperty(DBRefSource.MULTIACC, new Integer(50));
+ // addDbSourceProperty(DBRefSource.MULTIACC, new Integer(50));
}
/*
@@ -60,7 +75,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
*/
public Regex getAccessionValidator()
{
- return null;
+ return new Regex("([A-Z]+[0-9]+[A-Z0-9]+|[A-Z0-9]+_[A-Z0-9]+)");
}
/*
@@ -91,7 +106,8 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
try
{
// 1. Load the mapping information from the file
- org.exolab.castor.mapping.Mapping map = new org.exolab.castor.mapping.Mapping(uni.getClass().getClassLoader());
+ org.exolab.castor.mapping.Mapping map = new org.exolab.castor.mapping.Mapping(
+ uni.getClass().getClassLoader());
java.net.URL url = getClass().getResource("/uniprot_mapping.xml");
map.loadMapping(url);
@@ -99,10 +115,11 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
Unmarshaller unmar = new Unmarshaller(uni);
unmar.setIgnoreExtraElements(true);
unmar.setMapping(map);
-
- uni = (UniprotFile) unmar.unmarshal(new FileReader(file));
- }
- catch (Exception e)
+ if (file != null)
+ {
+ uni = (UniprotFile) unmar.unmarshal(new FileReader(file));
+ }
+ } catch (Exception e)
{
System.out.println("Error getUniprotEntries() " + e);
}
@@ -120,11 +137,15 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
startQuery();
try
{
- Alignment al=null;
+ queries = queries.toUpperCase().replaceAll(
+ "(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
+ Alignment al = null;
ebi = new EBIFetchClient();
- StringBuffer result=new StringBuffer();
+ StringBuffer result = new StringBuffer();
// uniprotxml parameter required since december 2007
- File file = ebi.fetchDataAsFile("uniprot:" + queries, "uniprotxml", null);
+ // uniprotkb dbname changed introduced december 2008
+ File file = ebi.fetchDataAsFile("uniprotkb:" + queries, "uniprotxml",
+ null);
Vector entries = getUniprotEntries(file);
if (entries != null)
@@ -149,12 +170,13 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
name.append(en2.nextElement());
}
- if (entry.getProtein()!=null && entry.getProtein().getName()!=null)
+ if (entry.getProtein() != null
+ && entry.getProtein().getName() != null)
{
- for (int nm=0,nmSize=entry.getProtein().getName().size(); nm