Merge branch 'feature/JAL-4386_JAL-4435_trees_from_annotations_on_alignment_2114_upda...

 # Conflicts:
 #	src/jalview/analysis/AAFrequency.java
 #	src/jalview/analysis/AlignmentUtils.java
 #	src/jalview/analysis/PaSiMap.java
 #	src/jalview/analysis/ccAnalysis.java
 #	src/jalview/analysis/scoremodels/ScoreModels.java
 #	src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
 #	src/jalview/api/AlignViewportI.java
 #	src/jalview/datamodel/SequenceGroup.java
 #	src/jalview/gui/PaSiMapPanel.java
 #	src/jalview/gui/PairwiseAlignPanel.java
 #	src/jalview/gui/PopupMenu.java
 #	src/jalview/gui/SliderPanel.java
 #	src/jalview/jbgui/GAlignFrame.java
 #	src/jalview/jbgui/GPaSiMapPanel.java
 #	src/jalview/project/Jalview2XML.java
 #	src/jalview/renderer/AnnotationRenderer.java
 #	src/jalview/renderer/ResidueShader.java
 #	src/jalview/util/Constants.java
 #	src/jalview/viewmodel/AlignmentViewport.java
 #	test/jalview/analysis/AlignmentUtilsTests.java

diff --cc src/jalview/analysis/AAFrequency.java
index 7ff77af,ca619f9..2620c8d
--- 1/src/jalview/analysis/AAFrequency.java
--- 2/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@@ -253,28 -254,34 +254,33 @@@ public class AAFrequenc
          }
  
          char c = sequences[row].getCharAt(column);
 -        List<AlignmentAnnotation> annots = AlignmentUtils
 -                .getAlignmentAnnotationForSource(sequences[row], source);
 -        if (annots != null)
 -        {
 +
 +        List<AlignmentAnnotation> annots = AlignmentUtils.getAlignmentAnnotationForSource(sequences[row], source);
 +        if(annots!=null) {
            seqWithSSCount++;
-           for(AlignmentAnnotation aa:annots) {
-             if(aa!=null) {
+           for (AlignmentAnnotation aa : annots)
+           {
+             if (aa != null)
+             {
                ssCount++;
              }
-             
-             if (sequences[row].getLength() > column && !Comparison.isGap(c) && aa !=null)
+ 
+             if (sequences[row].getLength() > column && !Comparison.isGap(c)
+                     && aa != null)
              {
-               
+ 
                int seqPosition = sequences[row].findPosition(column);
-               
-               char ss = AlignmentUtils.findSSAnnotationForGivenSeqposition(
-                       aa, seqPosition); 
-               if(ss == '*') {
+ 
+               char ss = AlignmentUtils
+                       .findSSAnnotationForGivenSeqposition(aa, seqPosition);
+               if (ss == '*')
+               {
                  continue;
-               }        
-               ssCounts.add(ss);                    
+               }
+               ssCounts.add(ss);
              }
-             else if(Comparison.isGap(c) && aa!=null) {
+             else if (Comparison.isGap(c) && aa != null)
+             {
                ssCounts.addGap();
              }
            }

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

diff --cc src/jalview/gui/AlignFrame.java
Simple merge

diff --cc src/jalview/gui/AnnotationLabels.java
Simple merge

diff --cc src/jalview/gui/CalculationChooser.java
Simple merge

diff --cc src/jalview/gui/PCAPanel.java
Simple merge

diff --cc src/jalview/gui/PopupMenu.java
Simple merge

diff --cc src/jalview/gui/SliderPanel.java
Simple merge

diff --cc src/jalview/jbgui/GAlignFrame.java
Simple merge

diff --cc src/jalview/project/Jalview2XML.java
Simple merge

diff --cc src/jalview/renderer/AnnotationRenderer.java
index b9411c3,58c93a4..cf552ff
--- 1/src/jalview/renderer/AnnotationRenderer.java
--- 2/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@@ -1646,9 -1667,7 +1667,8 @@@ public class AnnotationRendere
              }
              else
              {
 +
                colour = profcolour.findColour(dc[0], column, null);
- 
              }
              g.setColor(colour == Color.white ? Color.lightGray : colour);
  

diff --cc src/jalview/renderer/ResidueShader.java
Simple merge

diff --cc src/jalview/viewmodel/AlignmentViewport.java
index 8308992,80c9957..0c98f23
--- 1/src/jalview/viewmodel/AlignmentViewport.java
--- 2/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@@ -766,9 -765,8 +765,9 @@@ public abstract class AlignmentViewpor
     * results of alignment consensus analysis for visible portion of view
     */
    protected ProfilesI hconsensus = null;
-   
+ 
    protected Map<String, ProfilesI> hSSConsensusProfileMap = null;
 +  
  
    /**
     * results of cDNA complement consensus visible portion of view

diff --cc test/jalview/analysis/AlignmentUtilsTests.java
Simple merge