X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDasSequenceFeatureFetcher.java;h=f76a42e39435a763d77d2a6ab47ff74fc292115d;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=e22aa12a944bc5eac86575d278f93abc2f7608a0;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index e22aa12..f76a42e 100644
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -205,8 +205,10 @@ public class DasSequenceFeatureFetcher
         reply = JOptionPane
                 .showInternalConfirmDialog(
                         Desktop.desktop,
-                        MessageManager.getString("info.you_want_jalview_to_find_uniprot_accessions"),
-                        MessageManager.getString("label.find_uniprot_accession_ids"),
+                        MessageManager
+                                .getString("info.you_want_jalview_to_find_uniprot_accessions"),
+                        MessageManager
+                                .getString("label.find_uniprot_accession_ids"),
                         JOptionPane.YES_NO_OPTION,
                         JOptionPane.QUESTION_MESSAGE);
       }
@@ -264,7 +266,9 @@ public class DasSequenceFeatureFetcher
     startTime = System.currentTimeMillis();
     if (af != null)
     {
-      af.setProgressBar(MessageManager.getString("status.fetching_das_sequence_features"), startTime);
+      af.setProgressBar(MessageManager
+              .getString("status.fetching_das_sequence_features"),
+              startTime);
     }
     if (sourceRegistry == null)
     {
@@ -378,8 +382,7 @@ public class DasSequenceFeatureFetcher
                         source));
         for (String id : idl)
         {
-          List<String> qid = Arrays.asList(new String[]
-          { id });
+          List<String> qid = Arrays.asList(new String[] { id });
           try
           {
             DasGFFAdapter dga = featuresc.fetchData(source, qid);
@@ -537,7 +540,9 @@ public class DasSequenceFeatureFetcher
 
     if (af != null)
     {
-      af.setProgressBar(MessageManager.getString("status.no_das_sources_active"), startTime);
+      af.setProgressBar(
+              MessageManager.getString("status.no_das_sources_active"),
+              startTime);
     }
     if (getFeatSettings() != null)
     {
@@ -567,7 +572,9 @@ public class DasSequenceFeatureFetcher
   {
     if (af != null)
     {
-      af.setProgressBar(MessageManager.getString("status.das_feature_fetching_cancelled"), startTime);
+      af.setProgressBar(MessageManager
+              .getString("status.das_feature_fetching_cancelled"),
+              startTime);
     }
     cancelled = true;
   }
@@ -582,12 +589,13 @@ public class DasSequenceFeatureFetcher
     if (!cancelled && af != null)
     {
       // only update the progress bar if we've completed the fetch normally
-      af.setProgressBar(MessageManager.getString("status.das_feature_fetching_complete"), startTime);
+      af.setProgressBar(MessageManager
+              .getString("status.das_feature_fetching_complete"), startTime);
     }
 
     if (af != null && af.featureSettings != null)
     {
-      af.featureSettings.setTableData();
+      af.featureSettings.discoverAllFeatureData();
     }
 
     if (getFeatSettings() != null)
@@ -630,8 +638,7 @@ public class DasSequenceFeatureFetcher
       return null;
     }
     DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
-            seq.getDBRef(), new String[]
-            {
+            seq.getDBRef(), new String[] {
             // jalview.datamodel.DBRefSource.PDB,
             jalview.datamodel.DBRefSource.UNIPROT,
             // jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord
@@ -710,8 +717,7 @@ public class DasSequenceFeatureFetcher
       }
     }
 
-    return new Object[]
-    { ids, qstring };
+    return new Object[] { ids, qstring };
   }
 
   /**