From 6fd5f99f753ae1ce8c09b22fff11de2b6cdb3954 Mon Sep 17 00:00:00 2001
From: TZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Date: Thu, 24 Aug 2017 14:13:30 +0100
Subject: [PATCH] JAL-2629 fix for NPE caused by incorrect initiation of HMM
 annotation

---
 src/jalview/hmmer/HMMERCommands.java         |    1 -
 src/jalview/io/FileLoader.java               |    7 +------
 src/jalview/viewmodel/AlignmentViewport.java |    5 +++++
 3 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/src/jalview/hmmer/HMMERCommands.java b/src/jalview/hmmer/HMMERCommands.java
index 913eee8..6b81b65 100644
--- a/src/jalview/hmmer/HMMERCommands.java
+++ b/src/jalview/hmmer/HMMERCommands.java
@@ -173,7 +173,6 @@ public class HMMERCommands
     af.alignPanel.adjustAnnotationHeight();
     af.getViewport().updateSequenceIdColours();
     af.buildSortByAnnotationScoresMenu();
-    af.getViewport().initInformation();
   }
 
   /**
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index b07e125..f3a4a1c 100755
--- 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
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index a4b494a..eeea831 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -779,6 +779,10 @@ public abstract class AlignmentViewport
   @Override
   public void setSequenceInformationHash(ProfilesI info, int index)
   {
+    if (hinformation.size() < index + 1)
+    {
+      return;
+    }
     hinformation.set(index, info);
   }
 
@@ -1997,6 +2001,7 @@ public abstract class AlignmentViewport
     {
       updateStrucConsensus(ap);
     }
+    initInformation();
     updateInformation(ap);
 
     List<SequenceI> hmmSequences;
-- 
1.7.10.2