Merge branch 'bug/JAL-2791selectVisibleFeatures' into

features/JAL-1793VCF

Conflicts:
	src/jalview/controller/AlignViewController.java

diff --combined 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
@@@ -216,8 -216,9 +216,9 @@@ public class AlignViewController implem
  
    /**
     * Sets a bit in the BitSet for each column (base 0) in the sequence
-    * collection which includes the specified feature type. Returns the number of
-    * sequences which have the feature in the selected range.
+    * collection which includes a visible feature of the specified feature type.
+    * Returns the number of sequences which have the feature visible in the
+    * selected range.
     * 
     * @param featureType
     * @param sqcol
@@@ -227,8 -228,8 +228,8 @@@
    int findColumnsWithFeature(String featureType,
            SequenceCollectionI sqcol, BitSet bs)
    {
-     FeatureRendererModel fr = (FeatureRendererModel) alignPanel
-             .getFeatureRenderer();
+     FeatureRendererModel fr = alignPanel == null ? null
+             : (FeatureRendererModel) alignPanel.getFeatureRenderer();
      List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
  
      final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
@@@ -243,20 -244,22 +244,22 @@@
          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());