X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FUniprot.java;h=86282c7a5b151bf041b51f7beb1ccaba6bf1096b;hb=7e82e1fed011077e5cd4cc40ac8ad3519d7c47a8;hp=c86857606edc7e6d619afd1b1ee73633311fed5a;hpb=be762d8d9c71a7aa3121e845c45911c7192b7827;p=jalview.git diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java index c868576..86282c7 100644 --- a/src/jalview/ws/dbsources/Uniprot.java +++ b/src/jalview/ws/dbsources/Uniprot.java @@ -20,6 +20,7 @@ */ package jalview.ws.dbsources; +import jalview.bin.Cache; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefEntry; @@ -28,36 +29,45 @@ import jalview.datamodel.PDBEntry; 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.ws.ebi.EBIFetchClient; +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.File; -import java.io.FileReader; -import java.io.Reader; +import java.io.InputStream; 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 * */ public class Uniprot extends DbSourceProxyImpl { - private static final String BAR_DELIMITER = "|"; + private static final String DEFAULT_UNIPROT_DOMAIN = "https://www.uniprot.org"; - /* - * Castor mapping loaded from uniprot_mapping.xml - */ - private static Mapping map; + private static final String BAR_DELIMITER = "|"; /** * Constructor @@ -67,6 +77,11 @@ public class Uniprot extends DbSourceProxyImpl super(); } + private String getDomain() + { + return Cache.getDefault("UNIPROT_DOMAIN", DEFAULT_UNIPROT_DOMAIN); + } + /* * (non-Javadoc) * @@ -111,43 +126,6 @@ public class Uniprot extends DbSourceProxyImpl 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 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) * @@ -162,111 +140,154 @@ public class Uniprot extends DbSourceProxyImpl 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", - "xml"); - Vector entries = getUniprotEntries( - new FileReader(file)); + String downloadstring = getDomain() + "/uniprot/" + queries + + ".xml"; + + URL url = new URL(downloadstring); + URLConnection urlconn = url.openConnection(); + InputStream istr = urlconn.getInputStream(); + List entries = getUniprotEntries(istr); if (entries != null) { - ArrayList seqs = new ArrayList(); - for (UniprotEntry entry : entries) + List 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) { - stopQuery(); throw (e); + } finally + { + stopQuery(); } } /** + * 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 dbRefs = new ArrayList(); + List 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()) + /* + * 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 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 + * + * + * + * + */ + 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 * - * - * - * - * + * + * + * + * */ - 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(), - uf.getDescription(), 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) @@ -277,50 +298,156 @@ public class Uniprot extends DbSourceProxyImpl } /** + * A helper method that builds a sequence feature description * - * @param entry - * UniportEntry - * @return protein name(s) delimited by a white space character + * @param feature + * @return */ - public static String getUniprotEntryDescription(UniprotEntry entry) + static String getDescription(FeatureType feature) { - StringBuilder desc = new StringBuilder(32); - if (entry.getProtein() != null && entry.getProtein().getName() != null) + String orig = feature.getOriginal(); + List 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
+ */ + boolean asHtml = false; + if (orig != null && !orig.isEmpty() && variants != null + && !variants.isEmpty()) { - boolean first = true; - for (String nm : entry.getProtein().getName()) + int p = 0; + for (String var : variants) { - if (!first) + // 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) { - desc.append(" "); + for (int c = 0, clen = orig.length(); c < clen; c++) + { + char origchar = orig.charAt(c); + String orig3 = ResidueProperties.aa2Triplet.get("" + origchar); + sb.append(orig3 == null ? origchar + : StringUtils.toSentenceCase(orig3)); + } + } + else + { + sb.append(orig); + } + + LocationType location = feature.getLocation(); + PositionType start = location.getPosition() == null + ? location.getBegin() + : location.getPosition(); + sb.append(Integer.toString(start.getPosition().intValue())); + + 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); + } + } + else + { + sb.append(var); + } + if (++p != variants.size()) + { + sb.append("
  "); + asHtml = true; + } + else + { + sb.append(" "); + } + } + } + String description = feature.getDescription(); + if (description != null) + { + sb.append(description); + } + if (asHtml) + { + sb.insert(0, ""); + sb.append(""); + } + + return sb.toString(); + } + + /** + * 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 properties + * @param key + * @return + */ + static String getProperty(List properties, String key) + { + String value = null; + if (properties != null) + { + for (PropertyType prop : properties) + { + if (key.equals(prop.getType())) + { + value = prop.getValue(); + break; } - first = false; - desc.append(nm); } } - return desc.toString(); + return value; } /** - * + * Extracts xml element entry/protein/recommendedName/fullName + * * @param entry - * UniportEntry - * @return The accession id(s) and name(s) delimited by '|'. + * @return */ - public static String getUniprotEntryId(UniprotEntry entry) + static String getUniprotEntryDescription(Entry 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()) + String desc = ""; + if (entry.getProtein() != null + && entry.getProtein().getRecommendedName() != null) { - name.append(BAR_DELIMITER); - name.append(accessionId); + // 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 + * @return + */ + static String getUniprotEntryId(Entry entry) + { + StringBuilder name = new StringBuilder(32); for (String n : entry.getName()) { - name.append(BAR_DELIMITER); + if (name.length() > 0) + { + name.append(BAR_DELIMITER); + } name.append(n); } return name.toString(); @@ -359,4 +486,35 @@ public class Uniprot extends DbSourceProxyImpl { 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 getUniprotEntries(InputStream is) + { + List 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; + } }