/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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.util.Enumeration;
+import java.io.InputStream;
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Locale;
import java.util.Vector;
-import org.exolab.castor.xml.Unmarshaller;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.JAXBException;
+import javax.xml.stream.FactoryConfigurationError;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
import com.stevesoft.pat.Regex;
+import jalview.bin.Cache;
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.ws.ebi.EBIFetchClient;
-import jalview.ws.seqfetcher.DbSourceProxy;
+import jalview.schemes.ResidueProperties;
+import jalview.util.StringUtils;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
+import jalview.xml.binding.uniprot.DbReferenceType;
+import jalview.xml.binding.uniprot.Entry;
+import jalview.xml.binding.uniprot.FeatureType;
+import jalview.xml.binding.uniprot.LocationType;
+import jalview.xml.binding.uniprot.PositionType;
+import jalview.xml.binding.uniprot.PropertyType;
/**
+ * This class queries the Uniprot database for sequence data, unmarshals the
+ * returned XML, and converts it to Jalview Sequence records (including attached
+ * database references and sequence features)
+ *
* @author JimP
*
*/
-public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
+public class Uniprot extends DbSourceProxyImpl
{
+ private static final String DEFAULT_UNIPROT_DOMAIN = "https://www.uniprot.org";
+
+ private static final String BAR_DELIMITER = "|";
+
+ /**
+ * Constructor
+ */
public Uniprot()
{
super();
- addDbSourceProperty(DBRefSource.SEQDB, DBRefSource.SEQDB);
- addDbSourceProperty(DBRefSource.PROTSEQDB);
- // addDbSourceProperty(DBRefSource.MULTIACC, new Integer(50));
+ }
+
+ private String getDomain()
+ {
+ return Cache.getDefault("UNIPROT_DOMAIN", DEFAULT_UNIPROT_DOMAIN);
}
/*
*
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
*/
+ @Override
public String getAccessionSeparator()
{
- return null; // ";";
+ return null;
}
/*
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
+ @Override
public Regex getAccessionValidator()
{
return new Regex("([A-Z]+[0-9]+[A-Z0-9]+|[A-Z0-9]+_[A-Z0-9]+)");
*
* @see jalview.ws.DbSourceProxy#getDbSource()
*/
+ @Override
public String getDbSource()
{
return DBRefSource.UNIPROT;
*
* @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;
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
+ */
+ @Override
+ public AlignmentI getSequenceRecords(String queries) throws Exception
+ {
+ startQuery();
+ try
+ {
+ queries = queries.toUpperCase(Locale.ROOT).replaceAll(
+ "(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
+ AlignmentI al = null;
- private static org.exolab.castor.mapping.Mapping map;
+ String downloadstring = getDomain() + "/uniprot/" + queries + ".xml";
- public Vector getUniprotEntries(File file)
+ URL url = new URL(downloadstring);
+ HttpURLConnection urlconn = (HttpURLConnection) url.openConnection();
+ // anything other than 200 means we don't have data
+ // TODO: JAL-3882 reuse the EnsemblRestClient's fair
+ // use/backoff logic to retry when the server tells us to go away
+ if (urlconn.getResponseCode() == 200)
+ {
+ InputStream istr = urlconn.getInputStream();
+ List<Entry> entries = getUniprotEntries(istr);
+ if (entries != null)
+ {
+ List<SequenceI> seqs = new ArrayList<>();
+ for (Entry entry : entries)
+ {
+ seqs.add(uniprotEntryToSequence(entry));
+ }
+ al = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
+ }
+ }
+ stopQuery();
+ return al;
+
+ } catch (Exception e)
+ {
+ throw (e);
+ } finally
+ {
+ stopQuery();
+ }
+ }
+
+ /**
+ * Converts an Entry object (bound from Uniprot XML) to a Jalview Sequence
+ *
+ * @param entry
+ * @return
+ */
+ SequenceI uniprotEntryToSequence(Entry entry)
{
- UniprotFile uni = new UniprotFile();
- try
+ String id = getUniprotEntryId(entry);
+ /*
+ * Sequence should not include any whitespace, but JAXB leaves these in
+ */
+ String seqString = entry.getSequence().getValue().replaceAll("\\s*",
+ "");
+
+ SequenceI sequence = new Sequence(id, seqString);
+ sequence.setDescription(getUniprotEntryDescription(entry));
+ final String uniprotRecordVersion = "" + entry.getVersion();
+ /*
+ * add a 'self' DBRefEntry for each accession
+ */
+ final String dbVersion = getDbVersion();
+ List<DBRefEntry> dbRefs = new ArrayList<>();
+ boolean canonical = true;
+ for (String accessionId : entry.getAccession())
+ {
+ DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT,
+ uniprotRecordVersion, accessionId, null, canonical);
+ canonical = false;
+ dbRefs.add(dbRef);
+ }
+
+ /*
+ * add a DBRefEntry for each dbReference element in the XML;
+ * also add a PDBEntry if type="PDB";
+ * also add an EMBLCDS dbref if protein sequence id is given
+ * also add an Ensembl dbref " " " " " "
+ */
+ Vector<PDBEntry> pdbRefs = new Vector<>();
+ for (DbReferenceType dbref : entry.getDbReference())
{
- if (map == null)
+ String type = dbref.getType();
+ DBRefEntry dbr = new DBRefEntry(type,
+ DBRefSource.UNIPROT + ":" + dbVersion, dbref.getId());
+ dbRefs.add(dbr);
+ if ("PDB".equals(type))
{
- // 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);
+ pdbRefs.add(new PDBEntry(dbr));
+ }
+ if ("EMBL".equals(type))
+ {
+ /*
+ * e.g. Uniprot accession Q9BXM7 has
+ * <dbReference type="EMBL" id="M19359">
+ * <property type="protein sequence ID" value="AAA40981.1"/>
+ * <property type="molecule type" value="Genomic_DNA"/>
+ * </dbReference>
+ */
+ String cdsId = getProperty(dbref.getProperty(),
+ "protein sequence ID");
+ if (cdsId != null && cdsId.trim().length() > 0)
+ {
+ // remove version
+ String[] vrs = cdsId.split("\\.");
+ String version = vrs.length > 1 ? vrs[1]
+ : DBRefSource.UNIPROT + ":" + uniprotRecordVersion;
+ dbr = new DBRefEntry(DBRefSource.EMBLCDS, version, vrs[0]);
+ // TODO: process VARIANT features to allow EMBLCDS record's product to
+ // match Uniprot
+ dbr.setCanonical(true);
+ dbRefs.add(dbr);
+ }
+ }
+ if (type != null
+ && type.toLowerCase(Locale.ROOT).startsWith("ensembl"))
+ {
+ // remove version
+ String[] vrs = dbref.getId().split("\\.");
+ String version = vrs.length > 1 ? vrs[1]
+ : DBRefSource.UNIPROT + ":" + uniprotRecordVersion;
+ dbr.setAccessionId(vrs[0]);
+ dbr.setVersion(version);
+ /*
+ * e.g. Uniprot accession Q9BXM7 has
+ * <dbReference type="Ensembl" id="ENST00000321556">
+ * <molecule id="Q9BXM7-1"/>
+ * <property type="protein sequence ID" value="ENSP00000364204"/>
+ * <property type="gene ID" value="ENSG00000158828"/>
+ * </dbReference>
+ */
+ String cdsId = getProperty(dbref.getProperty(),
+ "protein sequence ID");
+ if (cdsId != null && cdsId.trim().length() > 0)
+ {
+ // remove version
+ String[] cdsVrs = cdsId.split("\\.");
+ String cdsVersion = cdsVrs.length > 1 ? cdsVrs[1]
+ : DBRefSource.UNIPROT + ":" + uniprotRecordVersion;
+ dbr = new DBRefEntry(DBRefSource.ENSEMBL,
+ DBRefSource.UNIPROT + ":" + cdsVersion, cdsVrs[0]);
+ dbRefs.add(dbr);
+ }
}
+ }
- // 2. Unmarshal the data
- Unmarshaller unmar = new Unmarshaller(uni);
- unmar.setIgnoreExtraElements(true);
- unmar.setMapping(map);
- if (file != null)
+ /*
+ * create features; they have either begin and end, or position, in XML
+ */
+ sequence.setPDBId(pdbRefs);
+ if (entry.getFeature() != null)
+ {
+ for (FeatureType uf : entry.getFeature())
{
- uni = (UniprotFile) unmar.unmarshal(new FileReader(file));
+ LocationType location = uf.getLocation();
+ int start = 0;
+ int end = 0;
+ if (location.getPosition() != null)
+ {
+ start = location.getPosition().getPosition().intValue();
+ end = start;
+ }
+ else
+ {
+ start = location.getBegin().getPosition().intValue();
+ end = location.getEnd().getPosition().intValue();
+ }
+ SequenceFeature sf = new SequenceFeature(uf.getType(),
+ getDescription(uf), start, end, "Uniprot");
+ sf.setStatus(uf.getStatus());
+ sequence.addSequenceFeature(sf);
}
- } catch (Exception e)
+ }
+ for (DBRefEntry dbr : dbRefs)
{
- System.out.println("Error getUniprotEntries() " + e);
+ sequence.addDBRef(dbr);
}
-
- return uni.getUniprotEntries();
+ return sequence;
}
- /*
- * (non-Javadoc)
+ /**
+ * A helper method that builds a sequence feature description
*
- * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
+ * @param feature
+ * @return
*/
- public AlignmentI getSequenceRecords(String queries) throws Exception
+ static String getDescription(FeatureType feature)
{
- startQuery();
- try
+ String orig = feature.getOriginal();
+ List<String> variants = feature.getVariation();
+ StringBuilder sb = new StringBuilder();
+
+ /*
+ * append variant in standard format if present
+ * e.g. p.Arg59Lys
+ * multiple variants are split over lines using <br>
+ */
+ boolean asHtml = false;
+ if (orig != null && !orig.isEmpty() && variants != null
+ && !variants.isEmpty())
{
- 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
- // uniprotkb dbname changed introduced december 2008
- File file = ebi.fetchDataAsFile("uniprotkb:" + queries, "uniprotxml",
- null);
- Vector entries = getUniprotEntries(file);
-
- if (entries != null)
+ int p = 0;
+ for (String var : variants)
{
- // First, make the new sequences
- Enumeration en = entries.elements();
- while (en.hasMoreElements())
+ // TODO proper HGVS nomenclature for delins structural variations
+ // http://varnomen.hgvs.org/recommendations/protein/variant/delins/
+ // for now we are pragmatic - any orig/variant sequence longer than
+ // three characters is shown with single-character notation rather than
+ // three-letter notation
+ sb.append("p.");
+ if (orig.length() < 4)
{
- 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())
+ for (int c = 0, clen = orig.length(); c < clen; c++)
{
- name.append("|");
- name.append(en2.nextElement());
+ char origchar = orig.charAt(c);
+ String orig3 = ResidueProperties.aa2Triplet.get("" + origchar);
+ sb.append(orig3 == null ? origchar
+ : StringUtils.toSentenceCase(orig3));
}
+ }
+ else
+ {
+ sb.append(orig);
+ }
- 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));
- }
- }
+ LocationType location = feature.getLocation();
+ PositionType start = location.getPosition() == null
+ ? location.getBegin()
+ : location.getPosition();
+ sb.append(Integer.toString(start.getPosition().intValue()));
- result.append(name + "\n"
- + entry.getUniprotSequence().getContent() + "\n");
+ if (var.length() < 4)
+ {
+ for (int c = 0, clen = var.length(); c < clen; c++)
+ {
+ char varchar = var.charAt(c);
+ String var3 = ResidueProperties.aa2Triplet.get("" + varchar);
+ sb.append(var3 != null ? StringUtils.toSentenceCase(var3)
+ : "" + varchar);
+ }
}
-
- // Then read in the features and apply them to the dataset
- al = parseResult(result.toString());
- if (al != null)
+ else
+ {
+ sb.append(var);
+ }
+ if (++p != variants.size())
{
- // Decorate the alignment with database entries.
- addUniprotXrefs(al, entries);
+ sb.append("<br/> ");
+ asHtml = true;
}
else
{
- results = result;
+ sb.append(" ");
}
}
- stopQuery();
- return al;
- } catch (Exception e)
+ }
+ String description = feature.getDescription();
+ if (description != null)
{
- stopQuery();
- throw (e);
+ sb.append(description);
+ }
+ if (asHtml)
+ {
+ sb.insert(0, "<html>");
+ sb.append("</html>");
}
+
+ return sb.toString();
}
/**
- * add an ordered set of UniprotEntry objects to an ordered set of seuqences.
+ * A helper method that searches the list of properties for one with the given
+ * key, and if found returns the property value, else returns null
*
- * @param al
- * - a sequence of n sequences
- * @param entries
- * a seuqence of n uniprot entries to be analysed.
+ * @param properties
+ * @param key
+ * @return
*/
- public void addUniprotXrefs(Alignment al, Vector entries)
+ static String getProperty(List<PropertyType> properties, String key)
{
- for (int i = 0; i < entries.size(); i++)
+ String value = null;
+ if (properties != null)
{
- UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
- Enumeration e = entry.getDbReference().elements();
- Vector onlyPdbEntries = new Vector();
- Vector dbxrefs = new Vector();
- while (e.hasMoreElements())
+ for (PropertyType prop : properties)
{
- 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"))
+ if (key.equals(prop.getType()))
{
- continue;
+ value = prop.getValue();
+ break;
}
-
- onlyPdbEntries.addElement(pdb);
- }
- SequenceI sq = al.getSequenceAt(i);
- while (sq.getDatasetSequence() != null)
- {
- sq = sq.getDatasetSequence();
}
+ }
+ return value;
+ }
- Enumeration en2 = entry.getAccession().elements();
- while (en2.hasMoreElements())
- {
- // we always add as uniprot if we retrieved from uniprot or uniprot name
- sq.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, getDbVersion(), en2
- .nextElement().toString()));
- }
- en2 = dbxrefs.elements();
- while (en2.hasMoreElements())
- {
- // we always add as uniprot if we retrieved from uniprot or uniprot name
- sq.addDBRef((DBRefEntry) en2.nextElement());
+ /**
+ * Extracts xml element entry/protein/recommendedName/fullName
+ *
+ * @param entry
+ * @return
+ */
+ static String getUniprotEntryDescription(Entry entry)
+ {
+ String desc = "";
+ if (entry.getProtein() != null
+ && entry.getProtein().getRecommendedName() != null)
+ {
+ // fullName is mandatory if recommendedName is present
+ desc = entry.getProtein().getRecommendedName().getFullName()
+ .getValue();
+ }
+ return desc;
+ }
- }
- sq.setPDBId(onlyPdbEntries);
- if (entry.getFeature() != null)
+ /**
+ * Constructs a sequence id by concatenating all entry/name elements with '|'
+ * separator
+ *
+ * @param entry
+ * @return
+ */
+ static String getUniprotEntryId(Entry entry)
+ {
+ StringBuilder name = new StringBuilder(32);
+ for (String n : entry.getName())
+ {
+ if (name.length() > 0)
{
- e = entry.getFeature().elements();
- while (e.hasMoreElements())
- {
- SequenceFeature sf = (SequenceFeature) e.nextElement();
- sf.setFeatureGroup("Uniprot");
- sq.addSequenceFeature(sf);
- }
+ name.append(BAR_DELIMITER);
}
+ name.append(n);
}
+ return name.toString();
}
/*
*
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
*/
+ @Override
public boolean isValidReference(String accession)
{
// TODO: make the following a standard validator
/**
* return LDHA_CHICK uniprot entry
*/
+ @Override
public String getTestQuery()
{
return "P00340";
}
+ @Override
public String getDbName()
{
return "Uniprot"; // getDbSource();
}
+
+ @Override
+ public int getTier()
+ {
+ return 0;
+ }
+
+ /**
+ * Reads the reply to the EBI Fetch Uniprot data query, unmarshals it to an
+ * Uniprot object, and returns the enclosed Entry objects, or null on any
+ * failure
+ *
+ * @param is
+ * @return
+ */
+ public List<Entry> getUniprotEntries(InputStream is)
+ {
+ List<Entry> entries = null;
+ try
+ {
+ JAXBContext jc = JAXBContext
+ .newInstance("jalview.xml.binding.uniprot");
+ XMLStreamReader streamReader = XMLInputFactory.newInstance()
+ .createXMLStreamReader(is);
+ javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+ JAXBElement<jalview.xml.binding.uniprot.Uniprot> uniprotElement = um
+ .unmarshal(streamReader,
+ jalview.xml.binding.uniprot.Uniprot.class);
+ jalview.xml.binding.uniprot.Uniprot uniprot = uniprotElement
+ .getValue();
+
+ if (uniprot != null && !uniprot.getEntry().isEmpty())
+ {
+ entries = uniprot.getEntry();
+ }
+ } catch (JAXBException | XMLStreamException
+ | FactoryConfigurationError e)
+ {
+ if (e instanceof javax.xml.bind.UnmarshalException
+ && e.getCause() != null
+ && e.getCause() instanceof XMLStreamException
+ && e.getCause().getMessage().contains("[row,col]:[1,1]"))
+ {
+ // trying to parse an empty stream
+ return null;
+ }
+ e.printStackTrace();
+ }
+ return entries;
+ }
}
git://source.jalview.org / jalview.git / blobdiff