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

 Conflicts:
	src/jalview/gui/AlignViewport.java

diff --cc src/jalview/datamodel/AlignmentAnnotation.java
Simple merge

diff --cc src/jalview/gui/AlignViewport.java
index 862c4fb,15c0971..39ded7f
--- 1/src/jalview/gui/AlignViewport.java
--- 2/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@@ -260,14 -254,16 +260,18 @@@ public class AlignViewport extends Alig
  
      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))
+     {
 -      alignment.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(
 -              0));
++      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
 -    if (hconsensus == null && !isDataset)
 +    if (consensusProfiles == null && !isDataset)
      {
 -      if (!alignment.isNucleotide())
 +      if (!al.isNucleotide())
        {
          showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
          showQuality = Cache.getDefault("SHOW_QUALITY", true);