Merge branch 'develop' into features/JAL-2446NCList

[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 2ce15af..c868576 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.
  * 
@@ -28,8 +28,9 @@ 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.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;
 
@@ -165,8 +166,9 @@ public class Uniprot extends DbSourceProxyImpl
       // 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));
+              "xml");
+      Vector<UniprotEntry> entries = getUniprotEntries(
+              new FileReader(file));
 
       if (entries != null)
       {
@@ -196,8 +198,8 @@ 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();
@@ -226,8 +228,7 @@ public class Uniprot extends DbSourceProxyImpl
       if ("EMBL".equals(pdb.getType()))
       {
         // look for a CDS reference and add it, too.
-        String cdsId = (String) pdb.getProperty()
-                .get("protein sequence ID");
+        String cdsId = (String) pdb.getProperty("protein sequence ID");
         if (cdsId != null && cdsId.trim().length() > 0)
         {
           // remove version
@@ -246,26 +247,26 @@ public class Uniprot extends DbSourceProxyImpl
         * <property type="gene ID" value="ENSG00000158828"/>
         * </dbReference> 
          */
-        String cdsId = (String) pdb.getProperty()
-                .get("protein sequence ID");
+        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)