Merge branch 'bug/JAL-2791selectVisibleFeatures' into

features/JAL-1793VCF

Conflicts:
	src/jalview/controller/AlignViewController.java

diff --cc src/jalview/controller/AlignViewController.java
index cc5a184,7bb295e..8b001b3
--- 1/src/jalview/controller/AlignViewController.java
--- 2/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@@ -243,20 -244,22 +244,22 @@@ public class AlignViewController implem
          List<SequenceFeature> sfs = sq.findFeatures(startColumn,
                  endColumn, featureType);
  
-         if (!sfs.isEmpty())
-         {
-           nseq++;
-         }
- 
+         boolean found = false;
          for (SequenceFeature sf : sfs)
          {
 -          {
 -            if (!visibleFeatures.contains(sf.getType())
 -                    || fr.getColour(sf) == null) // could pull up getColour to
 -                                                 // FeatureRenderer interface
 -            {
 -              continue;
 +          { 
 +            if (!visibleFeatures.contains(sf.getType()) 
 +                    || fr.getColour(sf) == null) // could pull up getColour to FeatureRenderer interface 
 +            { 
 +              continue; 
              }
            }
+           if (!found)
+           {
+             nseq++;
+           }
+           found = true;
++
            int sfStartCol = sq.findIndex(sf.getBegin());
            int sfEndCol = sq.findIndex(sf.getEnd());