-/**\r
- * \r
- */\r
-package jalview.ws.dbsources;\r
-\r
-import java.io.File;\r
-import java.io.IOException;\r
-import java.util.Enumeration;\r
-import java.util.Hashtable;\r
-import java.util.Vector;\r
-\r
-import com.stevesoft.pat.Regex;\r
-\r
-import jalview.datamodel.Alignment;\r
-import jalview.datamodel.AlignmentI;\r
-import jalview.datamodel.DBRefEntry;\r
-import jalview.datamodel.DBRefSource;\r
-import jalview.datamodel.PDBEntry;\r
-import jalview.datamodel.SequenceFeature;\r
-import jalview.datamodel.SequenceI;\r
-import jalview.datamodel.UniprotEntry;\r
-import jalview.io.FormatAdapter;\r
-import jalview.io.IdentifyFile;\r
-import jalview.ws.DBRefFetcher;\r
-import jalview.ws.DbSourceProxy;\r
-import jalview.ws.DbSourceProxyImpl;\r
-import jalview.ws.EBIFetchClient;\r
-\r
-/**\r
- * @author JimP\r
- * \r
- */\r
-public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy\r
-{\r
- public Uniprot() {\r
- super();\r
- addDbSourceProperty(DBRefSource.SEQDB, DBRefSource.SEQDB);\r
- addDbSourceProperty(DBRefSource.PROTSEQDB);\r
- addDbSourceProperty(DBRefSource.MULTIACC);\r
- }\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see jalview.ws.DbSourceProxy#getAccessionSeparator()\r
- */\r
- public String getAccessionSeparator()\r
- {\r
- return ";";\r
- }\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see jalview.ws.DbSourceProxy#getAccessionValidator()\r
- */\r
- public Regex getAccessionValidator()\r
- {\r
- return null;\r
- }\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see jalview.ws.DbSourceProxy#getDbSource()\r
- */\r
- public String getDbSource()\r
- {\r
- return DBRefSource.UNIPROT;\r
- }\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see jalview.ws.DbSourceProxy#getDbVersion()\r
- */\r
- public String getDbVersion()\r
- {\r
- return "0"; // we really don't know what version we're on.\r
- }\r
-\r
- private EBIFetchClient ebi = null;\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])\r
- */\r
- public AlignmentI getSequenceRecords(String queries) throws Exception\r
- {\r
- startQuery();\r
- try\r
- {\r
- Alignment al=null;\r
- ebi = new EBIFetchClient();\r
- StringBuffer result=new StringBuffer();\r
- File file = ebi.fetchDataAsFile("uniprot:" + queries, "xml", null);\r
- DBRefFetcher dbref = new DBRefFetcher();\r
- Vector entries = dbref.getUniprotEntries(file);\r
-\r
- if (entries != null)\r
- {\r
- // First, make the new sequences\r
- Enumeration en = entries.elements();\r
- while (en.hasMoreElements())\r
- {\r
- UniprotEntry entry = (UniprotEntry) en.nextElement();\r
-\r
- StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");\r
- Enumeration en2 = entry.getAccession().elements();\r
- while (en2.hasMoreElements())\r
- {\r
- name.append("|");\r
- name.append(en2.nextElement());\r
- }\r
- en2 = entry.getName().elements();\r
- while (en2.hasMoreElements())\r
- {\r
- name.append("|");\r
- name.append(en2.nextElement());\r
- }\r
-\r
- if (entry.getProtein() != null)\r
- {\r
- name.append(" " + entry.getProtein().getName().elementAt(0));\r
- }\r
-\r
- result.append(name + "\n"\r
- + entry.getUniprotSequence().getContent() + "\n");\r
-\r
- }\r
-\r
- // Then read in the features and apply them to the dataset\r
- al = parseResult(result.toString());\r
- if (al!=null)\r
- {\r
- // Decorate the alignment with database entries.\r
- addUniprotXrefs(al, entries);\r
- } else {\r
- results = result;\r
- }\r
- }\r
- stopQuery();\r
- return al;\r
- } catch (Exception e)\r
- {\r
- stopQuery();\r
- throw(e);\r
- }\r
- }\r
-\r
- /**\r
- * add an ordered set of UniprotEntry objects to an ordered set of seuqences.\r
- * \r
- * @param al -\r
- * a sequence of n sequences\r
- * @param entries\r
- * a seuqence of n uniprot entries to be analysed.\r
- */\r
- public void addUniprotXrefs(Alignment al, Vector entries)\r
- {\r
- for (int i = 0; i < entries.size(); i++)\r
- {\r
- UniprotEntry entry = (UniprotEntry) entries.elementAt(i);\r
- Enumeration e = entry.getDbReference().elements();\r
- Vector onlyPdbEntries = new Vector();\r
- while (e.hasMoreElements())\r
- {\r
- PDBEntry pdb = (PDBEntry) e.nextElement();\r
- if (!pdb.getType().equals("PDB"))\r
- {\r
- continue;\r
- }\r
-\r
- onlyPdbEntries.addElement(pdb);\r
- }\r
- SequenceI sq = al.getSequenceAt(i);\r
- while (sq.getDatasetSequence()!=null)\r
- {\r
- sq = sq.getDatasetSequence();\r
- }\r
-\r
- Enumeration en2 = entry.getAccession().elements();\r
- while (en2.hasMoreElements())\r
- {\r
- sq.addDBRef(\r
- new DBRefEntry(getDbSource(), getDbVersion(), en2.nextElement()\r
- .toString()));\r
- }\r
- sq.setPDBId(onlyPdbEntries);\r
- if (entry.getFeature() != null)\r
- {\r
- e = entry.getFeature().elements();\r
- while (e.hasMoreElements())\r
- {\r
- SequenceFeature sf = (SequenceFeature) e.nextElement();\r
- sf.setFeatureGroup("Uniprot");\r
- sq.addSequenceFeature(sf);\r
- }\r
- }\r
- }\r
- }\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)\r
- */\r
- public boolean isValidReference(String accession)\r
- {\r
- return true;\r
- }\r
- /**\r
- * return LDHA_CHICK uniprot entry\r
- */\r
- public String getTestQuery()\r
- {\r
- return "P00340";\r
- }\r
-}\r
+/*
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.dbsources;
+
+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.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.net.URL;
+import java.net.URLConnection;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Vector;
+
+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 DEFAULT_UNIPROT_DOMAIN = "https://www.uniprot.org";
+
+ private static final String BAR_DELIMITER = "|";
+
+ /**
+ * Constructor
+ */
+ public Uniprot()
+ {
+ super();
+ }
+
+ private String getDomain()
+ {
+ return Cache.getDefault("UNIPROT_DOMAIN", DEFAULT_UNIPROT_DOMAIN);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
+ */
+ @Override
+ public String getAccessionSeparator()
+ {
+ return null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @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]+)");
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbSource()
+ */
+ @Override
+ public String getDbSource()
+ {
+ return DBRefSource.UNIPROT;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbVersion()
+ */
+ @Override
+ public String getDbVersion()
+ {
+ return "0"; // we really don't know what version we're on.
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
+ */
+ @Override
+ public AlignmentI getSequenceRecords(String queries) throws Exception
+ {
+ startQuery();
+ try
+ {
+ queries = queries.toUpperCase().replaceAll(
+ "(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
+ AlignmentI al = null;
+
+ String downloadstring = getDomain() + "/uniprot/" + queries
+ + ".xml";
+
+ URL url = new URL(downloadstring);
+ URLConnection urlconn = url.openConnection();
+ 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)
+ {
+ 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,
+ seqString);
+ sequence.setDescription(getUniprotEntryDescription(entry));
+
+ /*
+ * add a 'self' DBRefEntry for each accession
+ */
+ final String dbVersion = getDbVersion();
+ List<DBRefEntry> dbRefs = new ArrayList<>();
+ for (String accessionId : entry.getAccession())
+ {
+ DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
+ accessionId);
+ 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())
+ {
+ String type = dbref.getType();
+ DBRefEntry dbr = new DBRefEntry(type,
+ DBRefSource.UNIPROT + ":" + dbVersion, dbref.getId());
+ dbRefs.add(dbr);
+ if ("PDB".equals(type))
+ {
+ 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 + ":" + dbVersion;
+ dbr = new DBRefEntry(DBRefSource.EMBLCDS, version, vrs[0]);
+ dbRefs.add(dbr);
+ }
+ }
+ if ("Ensembl".equals(type))
+ {
+ /*
+ * 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)
+ {
+ dbr = new DBRefEntry(DBRefSource.ENSEMBL,
+ DBRefSource.UNIPROT + ":" + dbVersion, cdsId.trim());
+ dbRefs.add(dbr);
+ }
+ }
+ }
+
+ /*
+ * create features; they have either begin and end, or position, in XML
+ */
+ sequence.setPDBId(pdbRefs);
+ if (entry.getFeature() != null)
+ {
+ for (FeatureType uf : entry.getFeature())
+ {
+ 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)
+ {
+ sequence.addDBRef(dbr);
+ }
+ return sequence;
+ }
+
+ /**
+ * A helper method that builds a sequence feature description
+ *
+ * @param feature
+ * @return
+ */
+ static String getDescription(FeatureType feature)
+ {
+ 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())
+ {
+ int p = 0;
+ for (String var : variants)
+ {
+ // 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)
+ {
+ 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("<br/> ");
+ asHtml = true;
+ }
+ else
+ {
+ sb.append(" ");
+ }
+ }
+ }
+ String description = feature.getDescription();
+ if (description != null)
+ {
+ sb.append(description);
+ }
+ if (asHtml)
+ {
+ sb.insert(0, "<html>");
+ sb.append("</html>");
+ }
+
+ 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<PropertyType> properties, String key)
+ {
+ String value = null;
+ if (properties != null)
+ {
+ for (PropertyType prop : properties)
+ {
+ if (key.equals(prop.getType()))
+ {
+ value = prop.getValue();
+ break;
+ }
+ }
+ }
+ 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
+ * @return
+ */
+ static String getUniprotEntryId(Entry entry)
+ {
+ StringBuilder name = new StringBuilder(32);
+ for (String n : entry.getName())
+ {
+ if (name.length() > 0)
+ {
+ name.append(BAR_DELIMITER);
+ }
+ name.append(n);
+ }
+ return name.toString();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
+ */
+ @Override
+ public boolean isValidReference(String accession)
+ {
+ // 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;
+ }
+
+ /**
+ * 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