X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;fp=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=4f8897adb70bebaf0bcacdd5932462fad7858312;hb=d2f616a89def59116b4a4f8d80251138d2c1da3d;hp=14096cfb72f2f3493af31d02eaaad928c765d47f;hpb=2bb7601808ced07567ddccd02ec1c2a9ad5cc7ab;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 14096cf..4f8897a 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -2320,10 +2320,14 @@ public class AlignmentUtils
       int phase = 0;
       try
       {
-        phase = Integer.parseInt(sf.getPhase());
+    	String s = sf.getPhase();
+    	if (s != null) 
+    	{
+    		phase = Integer.parseInt(s);
+    	}
       } catch (NumberFormatException e)
       {
-        // ignore
+        // SwingJS -- need to avoid these.
       }
       /*
        * phase > 0 on first codon means 5' incomplete - skip to the start