X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FUniprot.java;h=6b09eb6ebc6f5700528243dd850ae872202a9770;hb=11e8324f332f5648ba0f13b902621dc7a20137e4;hp=6ddd82812080fbd754fa200846ff11d1bcf949f8;hpb=e957648a02a9e25795a92a4f39a5e3c1e7adb230;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 6ddd828..6b09eb6 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;
@@ -31,13 +32,13 @@ 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.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;
 
@@ -52,6 +53,8 @@ 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 = "|";
 
   /*
@@ -67,6 +70,11 @@ public class Uniprot extends DbSourceProxyImpl
     super();
   }
 
+  private String getDomain()
+  {
+    return Cache.getDefault("UNIPROT_DOMAIN", DEFAULT_UNIPROT_DOMAIN);
+  }
+
   /*
    * (non-Javadoc)
    * 
@@ -162,16 +170,21 @@ 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 = getDomain() + "/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));
@@ -183,8 +196,10 @@ public class Uniprot extends DbSourceProxyImpl
       return al;
     } catch (Exception e)
     {
-      stopQuery();
       throw (e);
+    } finally
+    {
+      stopQuery();
     }
   }
 
@@ -197,12 +212,12 @@ public class Uniprot extends DbSourceProxyImpl
   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,
@@ -212,7 +227,7 @@ 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();
@@ -249,8 +264,8 @@ 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);
 
         }
@@ -263,8 +278,8 @@ public class Uniprot extends DbSourceProxyImpl
       for (UniprotFeature uf : entry.getFeature())
       {
         SequenceFeature copy = new SequenceFeature(uf.getType(),
-                uf.getDescription(), uf.getStatus(), uf.getBegin(),
-                uf.getEnd(), "Uniprot");
+                uf.getDescription(), uf.getBegin(), uf.getEnd(), "Uniprot");
+        copy.setStatus(uf.getStatus());
         sequence.addSequenceFeature(copy);
       }
     }
@@ -303,23 +318,18 @@ 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();