X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FUniprot.java;h=7261cba4910eb80a35d3db2141afd487416919ff;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=ab0b10c408ae867a5ab90f0d00b752c23a40f3cd;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index ab0b10c..7261cba 100644
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -1,62 +1,70 @@
/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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
+ * along with Jalview. If not, see .
+ * 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 com.stevesoft.pat.Regex;
-
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
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.datamodel.xdb.uniprot.UniprotEntry;
+import jalview.datamodel.xdb.uniprot.UniprotFeature;
+import jalview.datamodel.xdb.uniprot.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.net.URL;
+import java.util.ArrayList;
+import java.util.Vector;
+
+import org.exolab.castor.mapping.Mapping;
+import org.exolab.castor.xml.Unmarshaller;
+
+import com.stevesoft.pat.Regex;
+
/**
* @author JimP
*
*/
-public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
+public class Uniprot extends DbSourceProxyImpl
{
+ private static final String BAR_DELIMITER = "|";
+
+ /*
+ * Castor mapping loaded from uniprot_mapping.xml
+ */
+ private static Mapping map;
+
+ /**
+ * Constructor
+ */
public Uniprot()
{
super();
- addDbSourceProperty(DBRefSource.SEQDB, DBRefSource.SEQDB);
- addDbSourceProperty(DBRefSource.PROTSEQDB);
- // addDbSourceProperty(DBRefSource.MULTIACC, new Integer(50));
}
/*
@@ -64,9 +72,10 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
*/
+ @Override
public String getAccessionSeparator()
{
- return null; // ";";
+ return null;
}
/*
@@ -74,9 +83,10 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
+ @Override
public Regex getAccessionValidator()
{
- return null;
+ return new Regex("([A-Z]+[0-9]+[A-Z0-9]+|[A-Z0-9]+_[A-Z0-9]+)");
}
/*
@@ -84,6 +94,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getDbSource()
*/
+ @Override
public String getDbSource()
{
return DBRefSource.UNIPROT;
@@ -94,30 +105,41 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getDbVersion()
*/
+ @Override
public String getDbVersion()
{
return "0"; // we really don't know what version we're on.
}
- private EBIFetchClient ebi = null;
-
- public Vector getUniprotEntries(File file)
+ /**
+ * 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
{
- // 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 Mapping(uni.getClass().getClassLoader());
+ 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);
-
- uni = (UniprotFile) unmar.unmarshal(new FileReader(file));
+ if (fileReader != null)
+ {
+ uni = (UniprotFile) unmar.unmarshal(fileReader);
+ }
} catch (Exception e)
{
System.out.println("Error getUniprotEntries() " + e);
@@ -131,66 +153,31 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
*/
+ @Override
public AlignmentI getSequenceRecords(String queries) throws Exception
{
startQuery();
try
{
- Alignment al = null;
- ebi = new EBIFetchClient();
- StringBuffer result = new StringBuffer();
+ queries = queries.toUpperCase().replaceAll(
+ "(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
+ AlignmentI al = null;
+ EBIFetchClient ebi = new EBIFetchClient();
// uniprotxml parameter required since december 2007
- File file = ebi.fetchDataAsFile("uniprot:" + queries, "uniprotxml",
- null);
- Vector entries = getUniprotEntries(file);
+ // uniprotkb dbname changed introduced december 2008
+ File file = ebi.fetchDataAsFile("uniprotkb:" + queries, "uniprotxml",
+ "xml");
+ Vector entries = getUniprotEntries(new FileReader(file));
if (entries != null)
{
- // First, make the new sequences
- Enumeration en = entries.elements();
- while (en.hasMoreElements())
+ ArrayList seqs = new ArrayList();
+ for (UniprotEntry entry : entries)
{
- UniprotEntry entry = (UniprotEntry) en.nextElement();
-
- StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");
- Enumeration en2 = entry.getAccession().elements();
- while (en2.hasMoreElements())
- {
- name.append("|");
- name.append(en2.nextElement());
- }
- en2 = entry.getName().elements();
- while (en2.hasMoreElements())
- {
- name.append("|");
- name.append(en2.nextElement());
- }
-
- if (entry.getProtein() != null
- && entry.getProtein().getName() != null)
- {
- for (int nm = 0, nmSize = entry.getProtein().getName().size(); nm < nmSize; nm++)
- {
- name.append(" " + entry.getProtein().getName().elementAt(nm));
- }
- }
-
- result.append(name + "\n"
- + entry.getUniprotSequence().getContent() + "\n");
-
+ seqs.add(uniprotEntryToSequenceI(entry));
}
+ al = new Alignment(seqs.toArray(new SequenceI[0]));
- // 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;
@@ -202,68 +189,140 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
}
/**
- * add an ordered set of UniprotEntry objects to an ordered set of seuqences.
*
- * @param al -
- * a sequence of n sequences
- * @param entries
- * a seuqence of n uniprot entries to be analysed.
+ * @param entry
+ * UniprotEntry
+ * @return SequenceI instance created from the UniprotEntry instance
*/
- public void addUniprotXrefs(Alignment al, Vector entries)
+ public SequenceI uniprotEntryToSequenceI(UniprotEntry entry)
{
- for (int i = 0; i < entries.size(); i++)
+ String id = getUniprotEntryId(entry);
+ SequenceI sequence = new Sequence(id, entry.getUniprotSequence()
+ .getContent());
+ sequence.setDescription(getUniprotEntryDescription(entry));
+
+ final String dbVersion = getDbVersion();
+ ArrayList dbRefs = new ArrayList();
+ for (String accessionId : entry.getAccession())
+ {
+ DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
+ accessionId);
+
+ // mark dbRef as a primary reference for this sequence
+ dbRefs.add(dbRef);
+ }
+
+ Vector onlyPdbEntries = new Vector();
+ for (PDBEntry pdb : entry.getDbReference())
{
- UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
- Enumeration e = entry.getDbReference().elements();
- Vector onlyPdbEntries = new Vector();
- Vector dbxrefs = new Vector();
- while (e.hasMoreElements())
+ DBRefEntry dbr = new DBRefEntry();
+ dbr.setSource(pdb.getType());
+ dbr.setAccessionId(pdb.getId());
+ dbr.setVersion(DBRefSource.UNIPROT + ":" + dbVersion);
+ dbRefs.add(dbr);
+ if ("PDB".equals(pdb.getType()))
+ {
+ onlyPdbEntries.addElement(pdb);
+ }
+ if ("EMBL".equals(pdb.getType()))
{
- PDBEntry pdb = (PDBEntry) e.nextElement();
- DBRefEntry dbr = new DBRefEntry();
- dbr.setSource(pdb.getType());
- dbr.setAccessionId(pdb.getId());
- dbr.setVersion(DBRefSource.UNIPROT + ":" + getDbVersion());
- dbxrefs.addElement(dbr);
- if (!pdb.getType().equals("PDB"))
+ // look for a CDS reference and add it, too.
+ String cdsId = (String) pdb.getProperty("protein sequence ID");
+ if (cdsId != null && cdsId.trim().length() > 0)
{
- continue;
+ // remove version
+ String[] vrs = cdsId.split("\\.");
+ dbr = new DBRefEntry(DBRefSource.EMBLCDS, vrs.length > 1 ? vrs[1]
+ : DBRefSource.UNIPROT + ":" + dbVersion, vrs[0]);
+ dbRefs.add(dbr);
}
-
- onlyPdbEntries.addElement(pdb);
}
- SequenceI sq = al.getSequenceAt(i);
- while (sq.getDatasetSequence() != null)
+ if ("Ensembl".equals(pdb.getType()))
{
- sq = sq.getDatasetSequence();
+ /*UniprotXML
+ *
+ *
+ *
+ *
+ *
+ */
+ String cdsId = (String) pdb.getProperty("protein sequence ID");
+ if (cdsId != null && cdsId.trim().length() > 0)
+ {
+ dbr = new DBRefEntry(DBRefSource.ENSEMBL, DBRefSource.UNIPROT
+ + ":" + dbVersion, cdsId.trim());
+ dbRefs.add(dbr);
+
+ }
}
+ }
- Enumeration en2 = entry.getAccession().elements();
- while (en2.hasMoreElements())
+ sequence.setPDBId(onlyPdbEntries);
+ if (entry.getFeature() != null)
+ {
+ for (UniprotFeature uf : entry.getFeature())
{
- // we always add as uniprot if we retrieved from uniprot or uniprot name
- sq.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, getDbVersion(), en2
- .nextElement().toString()));
+ SequenceFeature copy = new SequenceFeature(uf.getType(),
+ uf.getDescription(), uf.getBegin(), uf.getEnd(), "Uniprot");
+ copy.setStatus(uf.getStatus());
+ sequence.addSequenceFeature(copy);
}
- en2 = dbxrefs.elements();
- while (en2.hasMoreElements())
- {
- // we always add as uniprot if we retrieved from uniprot or uniprot name
- sq.addDBRef((DBRefEntry) en2.nextElement());
+ }
+ for (DBRefEntry dbr : dbRefs)
+ {
+ sequence.addDBRef(dbr);
+ }
+ return sequence;
+ }
- }
- sq.setPDBId(onlyPdbEntries);
- if (entry.getFeature() != null)
+ /**
+ *
+ * @param entry
+ * UniportEntry
+ * @return protein name(s) delimited by a white space character
+ */
+ public static String getUniprotEntryDescription(UniprotEntry entry)
+ {
+ StringBuilder desc = new StringBuilder(32);
+ if (entry.getProtein() != null && entry.getProtein().getName() != null)
+ {
+ boolean first = true;
+ for (String nm : entry.getProtein().getName())
{
- e = entry.getFeature().elements();
- while (e.hasMoreElements())
+ if (!first)
{
- SequenceFeature sf = (SequenceFeature) e.nextElement();
- sf.setFeatureGroup("Uniprot");
- sq.addSequenceFeature(sf);
+ desc.append(" ");
}
+ first = false;
+ desc.append(nm);
}
}
+ return desc.toString();
+ }
+
+ /**
+ *
+ * @param entry
+ * UniportEntry
+ * @return The accession id(s) and name(s) delimited by '|'.
+ */
+ public static String getUniprotEntryId(UniprotEntry entry)
+ {
+ StringBuilder name = new StringBuilder(32);
+ // name.append("UniProt/Swiss-Prot");
+ // use 'canonicalised' name for optimal id matching
+ name.append(DBRefSource.UNIPROT);
+ for (String accessionId : entry.getAccession())
+ {
+ name.append(BAR_DELIMITER);
+ name.append(accessionId);
+ }
+ for (String n : entry.getName())
+ {
+ name.append(BAR_DELIMITER);
+ name.append(n);
+ }
+ return name.toString();
}
/*
@@ -271,21 +330,32 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
*/
+ @Override
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 LDHA_CHICK uniprot entry
*/
+ @Override
public String getTestQuery()
{
return "P00340";
}
+ @Override
public String getDbName()
{
return "Uniprot"; // getDbSource();
}
+
+ @Override
+ public int getTier()
+ {
+ return 0;
+ }
}