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 63cbfbd..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
@@ -279,6 +283,10 @@ public class AlignViewport extends AlignmentViewport
       showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
       normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
               false);
+      // for now, use consensus options for Information till it gets its own
+      setShowHMMSequenceLogo(showSequenceLogo);
+      setNormaliseHMMSequenceLogo(normaliseSequenceLogo);
+      setShowInformationHistogram(showConsensusHistogram);
       showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
       showConsensus = Cache.getDefault("SHOW_IDENTITY", true);