/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.UniprotEntry;
import jalview.datamodel.UniprotFile;
import jalview.ws.ebi.EBIFetchClient;
import jalview.ws.seqfetcher.DbSourceProxy;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
import java.io.File;
import java.io.FileReader;
import java.io.Reader;
import java.util.Vector;
import org.exolab.castor.xml.Unmarshaller;
import com.stevesoft.pat.Regex;
/**
* @author JimP
*
*/
public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
{
private static final String BAR_DELIMITER = "|";
private static final String NEWLINE = "\n";
private static org.exolab.castor.mapping.Mapping map;
/**
* Constructor
*/
public Uniprot()
{
super();
addDbSourceProperty(DBRefSource.SEQDB, DBRefSource.SEQDB);
addDbSourceProperty(DBRefSource.PROTSEQDB);
// addDbSourceProperty(DBRefSource.MULTIACC, new Integer(50));
}
/*
* (non-Javadoc)
*
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
*/
public String getAccessionSeparator()
{
return null; // ";";
}
/*
* (non-Javadoc)
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
public Regex getAccessionValidator()
{
return new Regex("([A-Z]+[0-9]+[A-Z0-9]+|[A-Z0-9]+_[A-Z0-9]+)");
}
/*
* (non-Javadoc)
*
* @see jalview.ws.DbSourceProxy#getDbSource()
*/
public String getDbSource()
{
return DBRefSource.UNIPROT;
}
/*
* (non-Javadoc)
*
* @see jalview.ws.DbSourceProxy#getDbVersion()
*/
public String getDbVersion()
{
return "0"; // we really don't know what version we're on.
}
/**
* Reads a file containing the reply to the EBI Fetch Uniprot data query,
* unmarshals it to a UniprotFile object, and returns the list of UniprotEntry
* data models (mapped from <entry> elements)
*
* @param fileReader
* @return
*/
public Vector getUniprotEntries(Reader fileReader)
{
UniprotFile uni = new UniprotFile();
try
{
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 (fileReader != null)
{
uni = (UniprotFile) unmar.unmarshal(fileReader);
}
} catch (Exception e)
{
System.out.println("Error getUniprotEntries() " + e);
}
return uni.getUniprotEntries();
}
/*
* (non-Javadoc)
*
* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
*/
public AlignmentI getSequenceRecords(String queries) throws Exception
{
startQuery();
try
{
queries = queries.toUpperCase().replaceAll(
"(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
AlignmentI al = null;
EBIFetchClient ebi = new EBIFetchClient();
// uniprotxml parameter required since december 2007
// uniprotkb dbname changed introduced december 2008
File file = ebi.fetchDataAsFile("uniprotkb:" + queries, "uniprotxml",
null);
Vector entries = getUniprotEntries(new FileReader(file));
if (entries != null)
{
/*
* If Castor binding included sequence@length, we could guesstimate the
* size of buffer to hold the alignment
*/
StringBuffer result = new StringBuffer(128);
// First, make the new sequences
for (UniprotEntry entry : entries)
{
StringBuilder name = constructSequenceFastaHeader(entry);
result.append(name).append(NEWLINE)
.append(entry.getUniprotSequence().getContent())
.append(NEWLINE);
}
// Then read in the features and apply them to the dataset
al = parseResult(result.toString());
if (al != null)
{
// Decorate the alignment with database entries.
addUniprotXrefs(al, entries);
}
else
{
results = result;
}
}
stopQuery();
return al;
} catch (Exception e)
{
stopQuery();
throw (e);
}
}
/**
* Construct a Fasta-format sequence header by concatenating the source,
* accession id(s) and name(s), delimited by '|', plus any protein names, now
* with space rather than bar delimiter
*
* @param entry
* @return
*/
public static StringBuilder constructSequenceFastaHeader(
UniprotEntry entry)
{
StringBuilder name = new StringBuilder(32);
name.append(">UniProt/Swiss-Prot");
for (String accessionId : entry.getAccession())
{
name.append(BAR_DELIMITER);
name.append(accessionId);
}
for (String n : entry.getName())
{
name.append(BAR_DELIMITER);
name.append(n);
}
if (entry.getProtein() != null && entry.getProtein().getName() != null)
{
for (String nm : entry.getProtein().getName())
{
name.append(" ").append(nm);
}
}
return name;
}
/**
* add an ordered set of UniprotEntry objects to an ordered set of seuqences.
*
* @param al
* - a sequence of n sequences
* @param entries
* a list of n uniprot entries to be analysed.
*/
public void addUniprotXrefs(AlignmentI al, Vector entries)
{
final String dbVersion = getDbVersion();
for (int i = 0; i < entries.size(); i++)
{
UniprotEntry entry = entries.elementAt(i);
Vector onlyPdbEntries = new Vector();
Vector dbxrefs = new Vector();
for (PDBEntry pdb : entry.getDbReference())
{
DBRefEntry dbr = new DBRefEntry();
dbr.setSource(pdb.getType());
dbr.setAccessionId(pdb.getId());
dbr.setVersion(DBRefSource.UNIPROT + ":" + dbVersion);
dbxrefs.addElement(dbr);
if ("PDB".equals(pdb.getType()))
{
onlyPdbEntries.addElement(pdb);
}
}
SequenceI sq = al.getSequenceAt(i);
while (sq.getDatasetSequence() != null)
{
sq = sq.getDatasetSequence();
}
for (String accessionId : entry.getAccession())
{
/*
* add as uniprot whether retrieved from uniprot or uniprot_name
*/
sq.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
accessionId));
}
for (DBRefEntry dbRef : dbxrefs)
{
sq.addDBRef(dbRef);
}
sq.setPDBId(onlyPdbEntries);
if (entry.getFeature() != null)
{
for (SequenceFeature sf : entry.getFeature())
{
sf.setFeatureGroup("Uniprot");
sq.addSequenceFeature(sf);
}
}
}
}
/*
* (non-Javadoc)
*
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
*/
public boolean isValidReference(String accession)
{
// TODO: make the following a standard validator
return (accession == null || accession.length() < 2) ? false
: getAccessionValidator().search(accession);
}
/**
* return LDHA_CHICK uniprot entry
*/
public String getTestQuery()
{
return "P00340";
}
public String getDbName()
{
return "Uniprot"; // getDbSource();
}
@Override
public int getTier()
{
return 0;
}
}