Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons

[jalview.git] / src / jalview / gui / SequenceFetcher.java

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index dab42b5..caecbba 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -803,8 +803,15 @@ public class SequenceFetcher extends JPanel implements Runnable
   {
     return "Retrieved from " + database.getSelectedItem();
   }
-
-  AlignmentI parseResult(AlignmentI al, String title,
+  /**
+   * constructs an alignment frame given the data and metadata
+   * @param al
+   * @param title
+   * @param currentFileFormat
+   * @param preferredFeatureColours
+   * @return the alignment 
+   */
+  public AlignmentI parseResult(AlignmentI al, String title,
           FileFormatI currentFileFormat,
           FeatureSettingsModelI preferredFeatureColours)
   {
@@ -837,10 +844,7 @@ public class SequenceFetcher extends JPanel implements Runnable
           }
         }
 
-        if (preferredFeatureColours != null)
-        {
-          af.getViewport().applyFeaturesStyle(preferredFeatureColours);
-        }
+        af.getViewport().applyFeaturesStyle(preferredFeatureColours);
         if (Cache.getDefault("HIDE_INTRONS", true))
         {
           af.hideFeatureColumns(SequenceOntologyI.EXON, false);