X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FUniprot.java;h=c9beb8e2ae7b9690532e6c5a67c3ea437324bdc3;hb=d914a47dd53f43cdfd27152e6b19415a937e9a3d;hp=26e97376823a2fa5be066a47f7f408a578443deb;hpb=cbab8bdd83078a8253dbd03570d47f51473df3f1;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 26e9737..c9beb8e 100644
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -1,257 +1,368 @@
-/**
- * 
- */
-package jalview.ws.dbsources;
-
-import java.io.File;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import org.exolab.castor.xml.Unmarshaller;
-
-import com.stevesoft.pat.Regex;
-
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.UniprotEntry;
-import jalview.datamodel.UniprotFile;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
-import jalview.ws.DBRefFetcher;
-import jalview.ws.ebi.EBIFetchClient;
-import jalview.ws.seqfetcher.DbSourceProxy;
-import jalview.ws.seqfetcher.DbSourceProxyImpl;
-
-/**
- * @author JimP
- * 
- */
-public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
-{
-  public Uniprot() {
-    super();
-    addDbSourceProperty(DBRefSource.SEQDB, DBRefSource.SEQDB);
-    addDbSourceProperty(DBRefSource.PROTSEQDB);
-//    addDbSourceProperty(DBRefSource.MULTIACC, new Integer(50));
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
-   */
-  public String getAccessionSeparator()
-  {
-    return null; // ";";
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#getAccessionValidator()
-   */
-  public Regex getAccessionValidator()
-  {
-    return null;
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#getDbSource()
-   */
-  public String getDbSource()
-  {
-    return DBRefSource.UNIPROT;
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#getDbVersion()
-   */
-  public String getDbVersion()
-  {
-    return "0"; // we really don't know what version we're on.
-  }
-
-  private EBIFetchClient ebi = null;
-
-  public Vector getUniprotEntries(File file)
-  {
-    UniprotFile uni = new UniprotFile();
-    try
-    {
-      // 1. Load the mapping information from the file
-      org.exolab.castor.mapping.Mapping map = new org.exolab.castor.mapping.Mapping(uni.getClass().getClassLoader());
-      java.net.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);
-
-      uni = (UniprotFile) unmar.unmarshal(new FileReader(file));
-    }
-    catch (Exception e)
-    {
-      System.out.println("Error getUniprotEntries() " + e);
-    }
-
-    return uni.getUniprotEntries();
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
-   */
-  public AlignmentI getSequenceRecords(String queries) throws Exception
-  {
-    startQuery();
-    try
-    {
-      Alignment al=null;
-      ebi = new EBIFetchClient();
-      StringBuffer result=new StringBuffer();
-      // uniprotxml parameter required since december 2007
-      File file = ebi.fetchDataAsFile("uniprot:" + queries, "uniprotxml", null);
-      Vector entries = getUniprotEntries(file);
-
-      if (entries != null)
-      {
-        // First, make the new sequences
-        Enumeration en = entries.elements();
-        while (en.hasMoreElements())
-        {
-          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())
-          {
-            name.append("|");
-            name.append(en2.nextElement());
-          }
-
-          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));
-              }
-          }
-
-          result.append(name + "\n"
-                  + entry.getUniprotSequence().getContent() + "\n");
-
-        }
-
-        // Then read in the features and apply them to the dataset
-        al = parseResult(result.toString());
-        if (al!=null)
-        {
-          // Decorate the alignment with database entries.
-          addUniprotXrefs(al, entries);
-        } else {
-          results = result;
-        }
-      }
-      stopQuery();
-      return al;
-    } catch (Exception e)
-    {
-      stopQuery();
-      throw(e);
-    }
-  }
-
-  /**
-   * add an ordered set of UniprotEntry objects to an ordered set of seuqences.
-   * 
-   * @param al -
-   *          a sequence of n sequences
-   * @param entries
-   *          a seuqence of n uniprot entries to be analysed.
-   */
-  public void addUniprotXrefs(Alignment al, Vector entries)
-  {
-    for (int i = 0; i < entries.size(); i++)
-    {
-      UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
-      Enumeration e = entry.getDbReference().elements();
-      Vector onlyPdbEntries = new Vector();
-      while (e.hasMoreElements())
-      {
-        PDBEntry pdb = (PDBEntry) e.nextElement();
-        if (!pdb.getType().equals("PDB"))
-        {
-          continue;
-        }
-
-        onlyPdbEntries.addElement(pdb);
-      }
-      SequenceI sq = al.getSequenceAt(i);
-      while (sq.getDatasetSequence()!=null)
-      {
-        sq = sq.getDatasetSequence();
-      }
-
-      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()));
-      }
-      sq.setPDBId(onlyPdbEntries);
-      if (entry.getFeature() != null)
-      {
-        e = entry.getFeature().elements();
-        while (e.hasMoreElements())
-        {
-          SequenceFeature sf = (SequenceFeature) e.nextElement();
-          sf.setFeatureGroup("Uniprot");
-          sq.addSequenceFeature(sf);
-        }
-      }
-    }
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
-   */
-  public boolean isValidReference(String accession)
-  {
-    return true;
-  }
-  /**
-   * return LDHA_CHICK uniprot entry
-   */
-  public String getTestQuery()
-  {
-    return "P00340";
-  }
-  public String getDbName()
-  {
-    return getDbSource();
-  }
-}
+/*
+ * 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.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.xdb.uniprot.UniprotEntry;
+import jalview.datamodel.xdb.uniprot.UniprotFeature;
+import jalview.datamodel.xdb.uniprot.UniprotFile;
+import jalview.ws.seqfetcher.DbSourceProxyImpl;
+
+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.Vector;
+
+import org.exolab.castor.mapping.Mapping;
+import org.exolab.castor.xml.Unmarshaller;
+
+import com.stevesoft.pat.Regex;
+
+/**
+ * @author JimP
+ * 
+ */
+public class Uniprot extends DbSourceProxyImpl
+{
+  private static final String BAR_DELIMITER = "|";
+
+  /*
+   * Castor mapping loaded from uniprot_mapping.xml
+   */
+  private static Mapping map;
+
+  /**
+   * Constructor
+   */
+  public Uniprot()
+  {
+    super();
+  }
+
+  /*
+   * (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.
+  }
+
+  /**
+   * 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 &lt;entry&gt; 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)
+   * 
+   * @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 = "http://www.uniprot.org/uniprot/" + queries
+              + ".xml";
+      URL url = null;
+      URLConnection urlconn = null;
+
+      url = new URL(downloadstring);
+      urlconn = url.openConnection();
+      InputStream istr = urlconn.getInputStream();
+      Vector<UniprotEntry> entries = getUniprotEntries(
+              new InputStreamReader(istr, "UTF-8"));
+
+      if (entries != null)
+      {
+        ArrayList<SequenceI> seqs = new ArrayList<>();
+        for (UniprotEntry entry : entries)
+        {
+          seqs.add(uniprotEntryToSequenceI(entry));
+        }
+        al = new Alignment(seqs.toArray(new SequenceI[0]));
+
+      }
+      stopQuery();
+      return al;
+    } catch (Exception e)
+    {
+      throw (e);
+    } finally
+    {
+      stopQuery();
+    }
+  }
+
+  /**
+   * 
+   * @param entry
+   *          UniprotEntry
+   * @return SequenceI instance created from the UniprotEntry instance
+   */
+  public SequenceI uniprotEntryToSequenceI(UniprotEntry entry)
+  {
+    String id = getUniprotEntryId(entry);
+    SequenceI sequence = new Sequence(id,
+            entry.getUniprotSequence().getContent());
+    sequence.setDescription(getUniprotEntryDescription(entry));
+
+    final String dbVersion = getDbVersion();
+    ArrayList<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())
+    {
+      DBRefEntry dbr = new DBRefEntry();
+      dbr.setSource(pdb.getType());
+      dbr.setAccessionId(pdb.getId());
+      dbr.setVersion(DBRefSource.UNIPROT + ":" + dbVersion);
+      dbRefs.add(dbr);
+      if ("PDB".equals(pdb.getType()))
+      {
+        onlyPdbEntries.addElement(pdb);
+      }
+      if ("EMBL".equals(pdb.getType()))
+      {
+        // look for a CDS reference and add it, too.
+        String cdsId = (String) pdb.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]);
+          dbRefs.add(dbr);
+        }
+      }
+      if ("Ensembl".equals(pdb.getType()))
+      {
+        /*UniprotXML
+         * <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 = (String) pdb.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);
+    if (entry.getFeature() != null)
+    {
+      for (UniprotFeature uf : entry.getFeature())
+      {
+        SequenceFeature copy = new SequenceFeature(uf.getType(),
+                uf.getDescription(), uf.getBegin(), uf.getEnd(), "Uniprot");
+        copy.setStatus(uf.getStatus());
+        sequence.addSequenceFeature(copy);
+      }
+    }
+    for (DBRefEntry dbr : dbRefs)
+    {
+      sequence.addDBRef(dbr);
+    }
+    return sequence;
+  }
+
+  /**
+   * 
+   * @param entry
+   *          UniportEntry
+   * @return protein name(s) delimited by a white space character
+   */
+  public static String getUniprotEntryDescription(UniprotEntry entry)
+  {
+    StringBuilder desc = new StringBuilder(32);
+    if (entry.getProtein() != null && entry.getProtein().getName() != null)
+    {
+      boolean first = true;
+      for (String nm : entry.getProtein().getName())
+      {
+        if (!first)
+        {
+          desc.append(" ");
+        }
+        first = false;
+        desc.append(nm);
+      }
+    }
+    return desc.toString();
+  }
+
+  /**
+   *
+   * @param entry
+   *          UniportEntry
+   * @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);
+      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;
+  }
+}