X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=7b255315a03ed129f9e914938ad1163e8ce4a232;hb=62df38e7204f2903d1b4e5aaef7762acf96f317d;hp=498489d1902f15837bdebb04123fa04720363233;hpb=4f01ddc72d2297c48c57d4f9c25af45b300df154;p=jalview.git

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 498489d..7b25531 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");
@@ -288,8 +292,16 @@ public class SequenceFetcher
         }
 
         sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);
-        sequence[i].getDatasetSequence().setSequenceFeatures(entry.getFeature());
-
+        if (entry.getFeature() != null)
+        {
+          e = entry.getFeature().elements();
+          while (e.hasMoreElements())
+          {
+            SequenceFeature sf = (SequenceFeature) e.nextElement();
+            sf.setFeatureGroup("Uniprot");
+            sequence[i].getDatasetSequence().addSequenceFeature( sf );
+          }
+        }
       }
     }
   }
@@ -338,7 +350,7 @@ public class SequenceFetcher
 
   SequenceI[] parseResult(String result, String title)
   {
-    String format = IdentifyFile.Identify(result, "Paste");
+    String format = new IdentifyFile().Identify(result, "Paste");
     SequenceI[] sequences = null;
 
     if (FormatAdapter.formats.contains(format))
@@ -448,13 +460,18 @@ public class SequenceFetcher
 
   }
 
-  void showErrorMessage(String error)
+  void showErrorMessage(final String error)
   {
     resetDialog();
-    JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                          error, "Error Retrieving Data",
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+    {
+      public void run()
+      {
+        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                              error, "Error Retrieving Data",
                                           JOptionPane.WARNING_MESSAGE);
-    return;
+      }
+    });
   }
 }