X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FUniprot.java;h=274ad3248e81f57142e07e2a956d93d2cbd7377c;hb=11f6e7a63cc627f5dffb0dd382343bd99d15121c;hp=caed598c315885c681801416c75f0f9347a8e4ff;hpb=e838644df5d5a10a16cf0ad7fb23d24dd7d2729a;p=jalview.git diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java index caed598..274ad32 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; @@ -28,16 +29,20 @@ 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.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 java.io.File; -import java.io.FileReader; +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; @@ -51,6 +56,8 @@ import com.stevesoft.pat.Regex; */ public class Uniprot extends DbSourceProxyImpl { + private static final String DEFAULT_UNIPROT_DOMAIN = "https://www.uniprot.org"; + private static final String BAR_DELIMITER = "|"; /* @@ -66,6 +73,11 @@ public class Uniprot extends DbSourceProxyImpl super(); } + private String getDomain() + { + return Cache.getDefault("UNIPROT_DOMAIN", DEFAULT_UNIPROT_DOMAIN); + } + /* * (non-Javadoc) * @@ -161,16 +173,21 @@ 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 = null; + URLConnection urlconn = null; + + url = new URL(downloadstring); + urlconn = url.openConnection(); + InputStream istr = urlconn.getInputStream(); + Vector entries = getUniprotEntries( + new InputStreamReader(istr, "UTF-8")); if (entries != null) { - ArrayList seqs = new ArrayList(); + ArrayList seqs = new ArrayList<>(); for (UniprotEntry entry : entries) { seqs.add(uniprotEntryToSequenceI(entry)); @@ -182,8 +199,10 @@ public class Uniprot extends DbSourceProxyImpl return al; } catch (Exception e) { - stopQuery(); throw (e); + } finally + { + stopQuery(); } } @@ -193,14 +212,15 @@ public class Uniprot extends DbSourceProxyImpl * UniprotEntry * @return SequenceI instance created from the UniprotEntry instance */ - public SequenceI uniprotEntryToSequenceI(UniprotEntry entry){ + public SequenceI uniprotEntryToSequenceI(UniprotEntry entry) + { String id = getUniprotEntryId(entry); - SequenceI sequence = new Sequence(id, entry.getUniprotSequence() - .getContent()); + SequenceI sequence = new Sequence(id, + entry.getUniprotSequence().getContent()); sequence.setDescription(getUniprotEntryDescription(entry)); final String dbVersion = getDbVersion(); - ArrayList dbRefs = new ArrayList(); + ArrayList dbRefs = new ArrayList<>(); for (String accessionId : entry.getAccession()) { DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion, @@ -210,7 +230,7 @@ public class Uniprot extends DbSourceProxyImpl dbRefs.add(dbRef); } - Vector onlyPdbEntries = new Vector(); + Vector onlyPdbEntries = new Vector<>(); for (PDBEntry pdb : entry.getDbReference()) { DBRefEntry dbr = new DBRefEntry(); @@ -247,22 +267,23 @@ public class Uniprot extends DbSourceProxyImpl 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()); + dbr = new DBRefEntry(DBRefSource.ENSEMBL, + DBRefSource.UNIPROT + ":" + dbVersion, cdsId.trim()); dbRefs.add(dbr); } } - } sequence.setPDBId(onlyPdbEntries); if (entry.getFeature() != null) { - for (SequenceFeature sf : entry.getFeature()) + for (UniprotFeature uf : entry.getFeature()) { - sf.setFeatureGroup("Uniprot"); - sequence.addSequenceFeature(sf); + SequenceFeature copy = new SequenceFeature(uf.getType(), + getDescription(uf), uf.getBegin(), uf.getEnd(), "Uniprot"); + copy.setStatus(uf.getStatus()); + sequence.addSequenceFeature(copy); } } for (DBRefEntry dbr : dbRefs) @@ -273,6 +294,68 @@ public class Uniprot extends DbSourceProxyImpl } /** + * Constructs a feature description from the description and (optionally) + * original and variant fields of the Uniprot XML feature + * + * @param uf + * @return + */ + protected static String getDescription(UniprotFeature uf) + { + String orig = uf.getOriginal(); + List variants = uf.getVariation(); + StringBuilder sb = new StringBuilder(); + + /* + * append variant in standard format if present + * e.g. p.Arg59Lys + */ + if (orig != null && !orig.isEmpty() && variants != null + && !variants.isEmpty()) + { + int p = 0; + for (String var : variants) + { + // TODO proper HGVC nomenclature for delins structural variations + sb.append("p."); + 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)); + } + + sb.append(Integer.toString(uf.getPosition())); + + 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); + } + if (++p != variants.size()) + { + sb.append("\n"); + } + else + { + sb.append(" "); + } + } + } + String description = uf.getDescription(); + if (description != null) + { + sb.append(description); + } + + return sb.toString(); + } + + /** * * @param entry * UniportEntry @@ -300,23 +383,18 @@ public class Uniprot extends DbSourceProxyImpl /** * * @param entry - * UniportEntry + * UniprotEntry * @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); + if (name.length() > 0) + { + name.append(BAR_DELIMITER); + } name.append(n); } return name.toString();