import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.datamodel.xdb.uniprot.UniprotEntry;
-import jalview.datamodel.xdb.uniprot.UniprotFeature;
-import jalview.datamodel.xdb.uniprot.UniprotFile;
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;
import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.Reader;
import java.net.URL;
import java.net.URLConnection;
import java.util.ArrayList;
import java.util.List;
import java.util.Vector;
-import org.exolab.castor.mapping.Mapping;
-import org.exolab.castor.xml.Unmarshaller;
+import javax.xml.bind.JAXBContext;
+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;
/**
+ * 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
*
*/
private static final String BAR_DELIMITER = "|";
- /*
- * Castor mapping loaded from uniprot_mapping.xml
- */
- private static Mapping map;
-
/**
* Constructor
*/
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<UniprotEntry> getUniprotEntries(Reader fileReader)
- {
- UniprotFile uni = new UniprotFile();
- try
- {
- 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);
- if (fileReader != null)
- {
- uni = (UniprotFile) unmar.unmarshal(fileReader);
- }
- } catch (Exception e)
- {
- System.out.println("Error getUniprotEntries() " + e);
- }
-
- return uni.getUniprotEntries();
- }
-
/*
* (non-Javadoc)
*
String downloadstring = getDomain() + "/uniprot/" + queries
+ ".xml";
- URL url = null;
- URLConnection urlconn = null;
- url = new URL(downloadstring);
- urlconn = url.openConnection();
+ URL url = new URL(downloadstring);
+ URLConnection urlconn = url.openConnection();
InputStream istr = urlconn.getInputStream();
- Vector<UniprotEntry> entries = getUniprotEntries(
- new InputStreamReader(istr, "UTF-8"));
-
+ List<Entry> entries = getUniprotEntries(istr);
if (entries != null)
{
- ArrayList<SequenceI> seqs = new ArrayList<>();
- for (UniprotEntry entry : entries)
+ List<SequenceI> seqs = new ArrayList<>();
+ for (Entry entry : entries)
{
- seqs.add(uniprotEntryToSequenceI(entry));
+ seqs.add(uniprotEntryToSequence(entry));
}
- al = new Alignment(seqs.toArray(new SequenceI[0]));
-
+ al = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
}
+
stopQuery();
return al;
} catch (Exception e)
}
/**
+ * Converts an Entry object (bound from Uniprot XML) to a Jalview Sequence
*
* @param entry
- * UniprotEntry
- * @return SequenceI instance created from the UniprotEntry instance
+ * @return
*/
- public SequenceI uniprotEntryToSequenceI(UniprotEntry entry)
+ SequenceI uniprotEntryToSequence(Entry entry)
{
String id = getUniprotEntryId(entry);
+ String seqString = entry.getSequence().getValue();
+
+ /*
+ * for backwards compatibility with Castor processing,
+ * remove any internal spaces
+ */
+ if (seqString.indexOf(' ') > -1)
+ {
+ seqString = seqString.replace(" ", "");
+ }
SequenceI sequence = new Sequence(id,
- entry.getUniprotSequence().getContent());
+ seqString);
sequence.setDescription(getUniprotEntryDescription(entry));
+ /*
+ * add a 'self' DBRefEntry for each accession
+ */
final String dbVersion = getDbVersion();
- ArrayList<DBRefEntry> dbRefs = new ArrayList<>();
+ List<DBRefEntry> 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<PDBEntry> onlyPdbEntries = new Vector<>();
- for (PDBEntry pdb : entry.getDbReference())
+ /*
+ * 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())
{
- DBRefEntry dbr = new DBRefEntry();
- dbr.setSource(pdb.getType());
- dbr.setAccessionId(pdb.getId());
- dbr.setVersion(DBRefSource.UNIPROT + ":" + dbVersion);
+ String type = dbref.getType();
+ DBRefEntry dbr = new DBRefEntry(type,
+ DBRefSource.UNIPROT + ":" + dbVersion, dbref.getId());
dbRefs.add(dbr);
- if ("PDB".equals(pdb.getType()))
+ if ("PDB".equals(type))
{
- onlyPdbEntries.addElement(pdb);
+ pdbRefs.add(new PDBEntry(dbr));
}
- if ("EMBL".equals(pdb.getType()))
+ if ("EMBL".equals(type))
{
- // look for a CDS reference and add it, too.
- String cdsId = (String) pdb.getProperty("protein sequence ID");
+ /*
+ * 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("\\.");
- dbr = new DBRefEntry(DBRefSource.EMBLCDS, vrs.length > 1 ? vrs[1]
- : DBRefSource.UNIPROT + ":" + dbVersion, vrs[0]);
+ String version = vrs.length > 1 ? vrs[1]
+ : DBRefSource.UNIPROT + ":" + dbVersion;
+ dbr = new DBRefEntry(DBRefSource.EMBLCDS, version, vrs[0]);
dbRefs.add(dbr);
}
}
- if ("Ensembl".equals(pdb.getType()))
+ if ("Ensembl".equals(type))
{
- /*UniprotXML
+ /*
+ * 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>
+ * <molecule id="Q9BXM7-1"/>
+ * <property type="protein sequence ID" value="ENSP00000364204"/>
+ * <property type="gene ID" value="ENSG00000158828"/>
+ * </dbReference>
*/
- String cdsId = (String) pdb.getProperty("protein sequence ID");
+ String cdsId = getProperty(dbref.getProperty(),
+ "protein sequence ID");
if (cdsId != null && cdsId.trim().length() > 0)
{
dbr = new DBRefEntry(DBRefSource.ENSEMBL,
DBRefSource.UNIPROT + ":" + dbVersion, cdsId.trim());
dbRefs.add(dbr);
-
}
}
}
- sequence.setPDBId(onlyPdbEntries);
+ /*
+ * create features; they have either begin and end, or position, in XML
+ */
+ sequence.setPDBId(pdbRefs);
if (entry.getFeature() != null)
{
- for (UniprotFeature uf : entry.getFeature())
+ for (FeatureType uf : entry.getFeature())
{
- SequenceFeature copy = new SequenceFeature(uf.getType(),
- getDescription(uf), uf.getBegin(), uf.getEnd(), "Uniprot");
- copy.setStatus(uf.getStatus());
- sequence.addSequenceFeature(copy);
+ 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);
}
}
for (DBRefEntry dbr : dbRefs)
}
/**
- * Constructs a feature description from the description and (optionally)
- * original and variant fields of the Uniprot XML feature
+ * A helper method that builds a sequence feature description
*
- * @param uf
+ * @param feature
* @return
*/
- protected static String getDescription(UniprotFeature uf)
+ static String getDescription(FeatureType feature)
{
- String orig = uf.getOriginal();
- List<String> variants = uf.getVariation();
+ String orig = feature.getOriginal();
+ List<String> variants = feature.getVariation();
StringBuilder sb = new StringBuilder();
/*
sb.append(orig);
}
- sb.append(Integer.toString(uf.getPosition()));
+ LocationType location = feature.getLocation();
+ PositionType start = location.getPosition() == null
+ ? location.getBegin()
+ : location.getPosition();
+ sb.append(Integer.toString(start.getPosition().intValue()));
if (var.length() < 4)
{
}
}
}
- String description = uf.getDescription();
+ String description = feature.getDescription();
if (description != null)
{
sb.append(description);
}
/**
+ * 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 entry
- * UniportEntry
- * @return protein name(s) delimited by a white space character
+ * @param properties
+ * @param key
+ * @return
*/
- public static String getUniprotEntryDescription(UniprotEntry entry)
+ static String getProperty(List<PropertyType> properties, String key)
{
- StringBuilder desc = new StringBuilder(32);
- if (entry.getProtein() != null && entry.getProtein().getName() != null)
+ String value = null;
+ if (properties != null)
{
- boolean first = true;
- for (String nm : entry.getProtein().getName())
+ for (PropertyType prop : properties)
{
- if (!first)
+ if (key.equals(prop.getType()))
{
- desc.append(" ");
+ value = prop.getValue();
+ break;
}
- first = false;
- desc.append(nm);
}
}
- return desc.toString();
+ return value;
+ }
+
+ /**
+ * 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;
}
/**
- *
+ * Constructs a sequence id by concatenating all entry/name elements with '|'
+ * separator
+ *
* @param entry
- * UniprotEntry
- * @return The accession id(s) and name(s) delimited by '|'.
+ * @return
*/
- public static String getUniprotEntryId(UniprotEntry entry)
+ static String getUniprotEntryId(Entry entry)
{
StringBuilder name = new StringBuilder(32);
for (String n : entry.getName())
{
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();
+ jalview.xml.binding.uniprot.Uniprot uniprot = (jalview.xml.binding.uniprot.Uniprot) um.unmarshal(streamReader);
+ if (uniprot != null && !uniprot.getEntry().isEmpty())
+ {
+ entries = uniprot.getEntry();
+ }
+ } catch (JAXBException | XMLStreamException
+ | FactoryConfigurationError e)
+ {
+ e.printStackTrace();
+ }
+ return entries;
+ }
}
git://source.jalview.org / jalview.git / blobdiff