From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 9 Dec 2015 16:03:51 +0000 (+0000)
Subject: JAL-1982 hotfix to prevent NPE with applet launch on Jpred4 site
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=f92b601879c3cb6f3f8cf475786dbca82ff8ab23

JAL-1982 hotfix to prevent NPE with applet launch on Jpred4 site
---

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 50fe3a7..d4127ab 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -930,12 +930,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     boolean showForAlignment = showAlignmentAnnotations.getState();
     boolean showForSequences = showSequenceAnnotations.getState();
-    for (AlignmentAnnotation aa : alignPanel.getAlignment()
+    if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
+    {
+      for (AlignmentAnnotation aa : alignPanel.getAlignment()
             .getAlignmentAnnotation())
     {
       boolean visible = (aa.sequenceRef == null ? showForAlignment
               : showForSequences);
       aa.visible = visible;
+      }
     }
     alignPanel.validateAnnotationDimensions(true);
     validate();
@@ -2609,6 +2612,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   }
 
+  @Override
   public void changeColour(ColourSchemeI cs)
   {
 
@@ -3759,6 +3763,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     this.add(statusBar, BorderLayout.SOUTH);
   }
 
+  @Override
   public void setStatus(String string)
   {
     statusBar.setText(string);