X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAMSAFile.java;h=4f218752392fe0cd9af1df94c971cf2ac6e7c2d2;hb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;hp=12a659db8145c4c9d08ada6da9da411f08c50598;hpb=68a0d4900885cec55096d1f266ee15ef6217f754;p=jalview.git

diff --git a/src/jalview/io/AMSAFile.java b/src/jalview/io/AMSAFile.java
index 12a659d..4f21875 100644
--- a/src/jalview/io/AMSAFile.java
+++ b/src/jalview/io/AMSAFile.java
@@ -47,7 +47,7 @@ public class AMSAFile extends jalview.io.FastaFile
         for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
         {
           aa = al.getAlignmentAnnotation()[i];
-          if (aa.autoCalculated)
+          if (aa.autoCalculated || !aa.visible)
             continue;
 
           out.append(">#_" + aa.label);