/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
import java.io.File;
import java.io.FileReader;
-import java.io.IOException;
import java.util.Enumeration;
-import java.util.Hashtable;
import java.util.Vector;
import org.exolab.castor.xml.Unmarshaller;
import jalview.datamodel.SequenceI;
import jalview.datamodel.UniprotEntry;
import jalview.datamodel.UniprotFile;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
-import jalview.ws.DBRefFetcher;
import jalview.ws.ebi.EBIFetchClient;
import jalview.ws.seqfetcher.DbSourceProxy;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
*/
public Regex getAccessionValidator()
{
- return null;
+ return new Regex("([A-Z]+[0-9]+[A-Z0-9]+|[A-Z0-9]+_[A-Z0-9]+)");
}
/*
private EBIFetchClient ebi = null;
+ private static org.exolab.castor.mapping.Mapping map;
+
public Vector getUniprotEntries(File file)
{
UniprotFile uni = new UniprotFile();
try
{
- // 1. Load the mapping information from the file
- 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);
+ if (map == null)
+ {
+ // 1. Load the mapping information from the file
+ map = new org.exolab.castor.mapping.Mapping(uni.getClass()
+ .getClassLoader());
+ java.net.URL url = getClass().getResource("/uniprot_mapping.xml");
+ map.loadMapping(url);
+ }
// 2. Unmarshal the data
Unmarshaller unmar = new Unmarshaller(uni);
unmar.setIgnoreExtraElements(true);
unmar.setMapping(map);
- if (file!=null)
+ if (file != null)
{
uni = (UniprotFile) unmar.unmarshal(new FileReader(file));
}
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);
/**
* add an ordered set of UniprotEntry objects to an ordered set of seuqences.
*
- * @param al -
- * a sequence of n sequences
+ * @param al
+ * - a sequence of n sequences
* @param entries
- * a seuqence of n uniprot entries to be analysed.
+ * a seuqence of n uniprot entries to be analysed.
*/
public void addUniprotXrefs(Alignment al, Vector entries)
{
*/
public boolean isValidReference(String accession)
{
- return true;
+ // TODO: make the following a standard validator
+ return (accession == null || accession.length() < 2) ? false
+ : getAccessionValidator().search(accession);
}
/**
{
return "Uniprot"; // getDbSource();
}
+
+ @Override
+ public int getTier()
+ {
+ return 0;
+ }
}