JAL-2748 formatting

[jalview.git] / src / jalview / ws / dbsources / Uniprot.java

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 1a58479..c9beb8e 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -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();
     }
   }
 
@@ -196,12 +204,12 @@ 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,
@@ -211,7 +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();
@@ -248,22 +256,23 @@ 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(),
+                uf.getDescription(), uf.getBegin(), uf.getEnd(), "Uniprot");
+        copy.setStatus(uf.getStatus());
+        sequence.addSequenceFeature(copy);
       }
     }
     for (DBRefEntry dbr : dbRefs)