Merge branch 'develop' into spike/JAL-1950_hmmer3client

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 53d118b..9e794a8 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -259,9 +259,11 @@ public class AlignViewport extends AlignmentViewport implements
 
     setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
 
-    alignment
-            .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
-
+    if (Cache.getDefault("NORMALISE_GAPS", true))
+    {
+      alignment.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
     if (hconsensus == null && !isDataset)