Merge remote-tracking branch 'origin/develop' into

features/JAL-2388hiddencolumnschanges

Conflicts:
	src/jalview/gui/AnnotationColumnChooser.java
	src/jalview/io/AnnotationFile.java

diff --cc src/jalview/appletgui/AlignViewport.java
Simple merge

diff --cc src/jalview/appletgui/AnnotationColumnChooser.java
Simple merge

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

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

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

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

diff --cc src/jalview/io/AnnotationFile.java
index 31aeffa,ef903e3..e685627
--- 1/src/jalview/io/AnnotationFile.java
--- 2/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@@ -110,23 -109,24 +110,22 @@@ public class AnnotationFil
     */
    public class ViewDef
    {
-     public String viewname;
+     // TODO this class is not used - remove?
+     public final String viewname;
  
-     public HiddenSequences hidseqs;
+     public final HiddenSequences hidseqs;
  
-     public HiddenColumns hiddencols;
 -    public final ColumnSelection hiddencols;
 -
 -    // public final Vector visibleGroups;
++    public final HiddenColumns hiddencols;
  
-     public Vector visibleGroups;
+     public final Hashtable hiddenRepSeqs;
  
-     public Hashtable hiddenRepSeqs;
- 
-     public ViewDef(String viewname, HiddenSequences hidseqs,
-             HiddenColumns hiddencols, Hashtable hiddenRepSeqs)
+     public ViewDef(String vname, HiddenSequences hseqs,
 -            ColumnSelection hcols, Hashtable hRepSeqs)
++            HiddenColumns hcols, Hashtable hRepSeqs)
      {
-       this.viewname = viewname;
-       this.hidseqs = hidseqs;
-       this.hiddencols = hiddencols;
-       this.hiddenRepSeqs = hiddenRepSeqs;
+       this.viewname = vname;
+       this.hidseqs = hseqs;
+       this.hiddencols = hcols;
+       this.hiddenRepSeqs = hRepSeqs;
      }
    }
  

diff --cc src/jalview/io/JSONFile.java
Simple merge

diff --cc src/jalview/viewmodel/AlignmentViewport.java
Simple merge

diff --cc test/jalview/io/AnnotationFileIOTest.java
Simple merge

diff --cc test/jalview/io/JSONFileTest.java
index 6ccbd5d,acde68d..3b418ec
--- 1/test/jalview/io/JSONFileTest.java
--- 2/test/jalview/io/JSONFileTest.java
+++ b/test/jalview/io/JSONFileTest.java
@@@ -357,9 -359,16 +359,16 @@@ public class JSONFileTes
        JSONFile bioJsonFile = (JSONFile) formatAdapter.getAlignFile();
        AlignFrame alignFrame = new AlignFrame(_alignment,
                bioJsonFile.getHiddenSequences(),
 -              bioJsonFile.getColumnSelection(), AlignFrame.DEFAULT_WIDTH,
 +              bioJsonFile.getHiddenColumns(), AlignFrame.DEFAULT_WIDTH,
                AlignFrame.DEFAULT_HEIGHT);
-       // Change colour scheme to 'None' and perform round trip
+ 
+       /*
+        * Create a group on the alignment;
+        * Change global and group colour scheme to 'None' and perform round trip
+        */
+       SequenceGroup sg = new SequenceGroup();
+       sg.addSequence(_alignment.getSequenceAt(0), false);
+       sg.setColourScheme(null);
        ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
                ResidueColourScheme.NONE, _alignment);
        alignFrame.changeColour(cs);