createColourFromName if not specified

[jalview.git] / src / jalview / io / SequenceFeatureFetcher.java

diff --git a/src/jalview/io/SequenceFeatureFetcher.java b/src/jalview/io/SequenceFeatureFetcher.java
index 61b25f9..edbf862 100755 (executable)
--- a/src/jalview/io/SequenceFeatureFetcher.java
+++ b/src/jalview/io/SequenceFeatureFetcher.java
@@ -65,16 +65,19 @@ public class SequenceFeatureFetcher implements Runnable
       map.loadMapping(url);\r
 \r
       // 2. Unmarshal the data\r
-      Unmarshaller unmar = new Unmarshaller();\r
+      Unmarshaller unmar = new Unmarshaller(uni);\r
       unmar.setIgnoreExtraElements(true);\r
       unmar.setMapping(map);\r
-      uni = (UniprotFile) unmar.unmarshal(new FileReader(file));\r
+   //   unmar.setDebug(true);\r
 \r
+      uni = (UniprotFile) unmar.unmarshal(new FileReader(file));\r
     }\r
     catch (Exception e)\r
     {\r
       System.out.println("Error getUniprotEntries() "+e);\r
     }\r
+\r
+\r
     return uni.getUniprotEntries();\r
   }\r
 \r
@@ -113,7 +116,8 @@ public class SequenceFeatureFetcher implements Runnable
              seqIndex++, i++)\r
         {\r
           Sequence sequence = (Sequence) sequences.get(seqIndex);\r
-          Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[] { "Uniprot"});\r
+          Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[] {\r
+              jalview.datamodel.DBRefSource.UNIPROT});\r
           if (uprefs!=null)\r
           {\r
             // we know the id for this entry, so don't note its ID in the unknownSequences list\r