JAL-2629 fix for NPE caused by incorrect initiation of HMM annotation

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index b07e125..f3a4a1c 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -29,8 +29,6 @@ import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Profile;
-import jalview.datamodel.Profiles;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
@@ -428,6 +426,7 @@ public class FileLoader implements Runnable
               AlignmentI alignment = viewport.getAlignment();
               SequenceI seq = alignment
                       .getSequenceAt(alignment.getAbsoluteHeight() - 1);
+              seq.setIsHMMConsensusSequence(true);
               alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
               SequenceGroup sg = viewport.getSelectionGroup();
               if (sg != null)
@@ -445,10 +444,6 @@ public class FileLoader implements Runnable
               {
                 alignment.insertSequenceAt(0, seq);
               }
-              viewport.initInformation();
-              viewport.setSequenceInformationHash(
-                      new Profiles(new Profile[1]), 0);
-              viewport.updateInformation(viewport.getAlignPanel());
               viewport.getAlignPanel().adjustAnnotationHeight();
               viewport.updateSequenceIdColours();
               if (viewport.getAlignPanel().alignFrame