From a706da600df4aaa7781abbe99b1381179e4f2f50 Mon Sep 17 00:00:00 2001
From: TZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Date: Fri, 1 Sep 2017 15:19:39 +0100
Subject: [PATCH] JAL-2629 fix hmmbuild validation failing if no AlignFrames
 present

---
 src/jalview/gui/Preferences.java |    8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 7c0ac95..ed86eab 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -697,12 +697,14 @@ public class Preferences extends GPreferences
             Boolean.toString(hmmerFunctioning));
     AlignFrame[] frames = Desktop.getAlignFrames();
     boolean hmmerStatus = hmmerFunctioning && hmmerInstalled ? true : false;
-    for (AlignFrame frame : frames)
+    if (frames != null && frames.length > 0)
     {
-      frame.updateHMMERStatus(hmmerStatus);
+      for (AlignFrame frame : frames)
+      {
+        frame.updateHMMERStatus(hmmerStatus);
+      }
     }
     
-    
     trimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
     if (Cache.getDefault("USE_UNIPROT", false))
     {
-- 
1.7.10.2