X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FUniprot.java;h=73775cf07b247c8f5eadf7fc2b61f592c0550997;hb=8ec36c3e36ff5beb0db07345babe8c8426d0426b;hp=81b4caff9ed04f9ae167d98faa0f8bcd7094b948;hpb=af2dbf10bbcc54d9b9e4d398e9283b3c4a758e06;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 81b4caf..73775cf 100644
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -28,15 +28,16 @@ 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.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.Vector;
 
@@ -161,16 +162,21 @@ 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<UniprotEntry> entries = getUniprotEntries(new FileReader(file));
+
+      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<SequenceI>();
+        ArrayList<SequenceI> seqs = new ArrayList<>();
         for (UniprotEntry entry : entries)
         {
           seqs.add(uniprotEntryToSequenceI(entry));
@@ -182,8 +188,10 @@ public class Uniprot extends DbSourceProxyImpl
       return al;
     } catch (Exception e)
     {
-      stopQuery();
       throw (e);
+    } finally
+    {
+      stopQuery();
     }
   }
 
@@ -193,14 +201,15 @@ 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<DBRefEntry> dbRefs = new ArrayList<DBRefEntry>();
+    ArrayList<DBRefEntry> dbRefs = new ArrayList<>();
     for (String accessionId : entry.getAccession())
     {
       DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
@@ -210,7 +219,7 @@ public class Uniprot extends DbSourceProxyImpl
       dbRefs.add(dbRef);
     }
 
-    Vector<PDBEntry> onlyPdbEntries = new Vector<PDBEntry>();
+    Vector<PDBEntry> onlyPdbEntries = new Vector<>();
     for (PDBEntry pdb : entry.getDbReference())
     {
       DBRefEntry dbr = new DBRefEntry();
@@ -222,18 +231,54 @@ public class Uniprot extends DbSourceProxyImpl
       {
         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 (SequenceFeature sf : entry.getFeature())
+      for (UniprotFeature uf : entry.getFeature())
       {
-        sf.setFeatureGroup("Uniprot");
-        sequence.addSequenceFeature(sf);
+        SequenceFeature copy = new SequenceFeature(uf.getType(),
+                uf.getDescription(), uf.getBegin(), uf.getEnd(), "Uniprot");
+        copy.setStatus(uf.getStatus());
+        sequence.addSequenceFeature(copy);
       }
     }
-    sequence.setDBRefs(dbRefs.toArray(new DBRefEntry[0]));
+    for (DBRefEntry dbr : dbRefs)
+    {
+      sequence.addDBRef(dbr);
+    }
     return sequence;
   }
 
@@ -265,23 +310,18 @@ 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();