Merge branch 'spike/JAL-1950_hmmer3client' into features/mchmmer_merge_JAL-1950

[jalview.git] / src / jalview / gui / AlignViewport.java

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 862c4fb..39ded7f 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -261,7 +261,11 @@ public class AlignViewport extends AlignmentViewport
     setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
 
     AlignmentI al = getAlignment();
-    al.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+
+    if (Cache.getDefault("NORMALISE_GAPS", true))
+    {
+      al.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+    }
 
     // We must set conservation and consensus before setting colour,
     // as Blosum and Clustal require this to be done