X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=fc8f042fcdce14a099f219c02b3101b12d5f107a;hb=e651bfd6da43bae19e157d6fdf1efbb484acda76;hp=2e2456b8812510c1a39318744ab2b3db681fd38c;hpb=366b11bb8e79ff5bb1a9e6c50b648c3d4101862c;p=jalview.git

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 2e2456b..fc8f042 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -239,6 +239,7 @@ public class SequenceFetcher
   {
     EBIFetchClient ebi = new EBIFetchClient();
     File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
+   // File file = new File("H:/jalview/classes/fer1.xml");
     SequenceFeatureFetcher sff = new SequenceFeatureFetcher();
     Vector entries = sff.getUniprotEntries(file);
 
@@ -249,7 +250,8 @@ public class SequenceFetcher
       while (en.hasMoreElements())
       {
         UniprotEntry entry = (UniprotEntry) en.nextElement();
-        StringBuffer name = new StringBuffer(">Uniprot/Swiss-Prot");
+
+        StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");
         Enumeration en2 = entry.getAccession().elements();
         while (en2.hasMoreElements())
         {
@@ -263,8 +265,10 @@ public class SequenceFetcher
           name.append(en2.nextElement());
         }
 
-        if (entry.getProteinName() != null)
-          name.append(" " + entry.getProteinName().elementAt(0));
+        if (entry.getProtein() != null)
+        {
+           name.append(" " + entry.getProtein().getName().elementAt(0));
+        }
 
         result.append(name + "\n" + entry.getUniprotSequence().getContent() +
                       "\n");
@@ -288,10 +292,15 @@ public class SequenceFetcher
         }
 
         sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);
-        e = entry.getFeature().elements();
-        while(e.hasMoreElements())
+        if (entry.getFeature() != null)
         {
-          sequence[i].getDatasetSequence().addSequenceFeature((SequenceFeature)e.nextElement());
+          e = entry.getFeature().elements();
+          while (e.hasMoreElements())
+          {
+            SequenceFeature sf = (SequenceFeature) e.nextElement();
+            sf.setFeatureGroup("Uniprot");
+            sequence[i].getDatasetSequence().addSequenceFeature( sf );
+          }
         }
       }
     }