Merge remote-tracking branch 'origin/develop' into

features/JAL-2388hiddencolumnschanges

Conflicts:
	src/jalview/appletgui/TreePanel.java
	src/jalview/gui/AnnotationColumnChooser.java
	src/jalview/gui/PCAPanel.java
	src/jalview/gui/TreePanel.java

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

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

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

diff --cc src/jalview/appletgui/PCAPanel.java
index 2ef7d10,2d77c59..5dc57f9
--- 1/src/jalview/appletgui/PCAPanel.java
--- 2/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@@ -20,9 -20,12 +20,12 @@@
   */
  package jalview.appletgui;
  
+ import jalview.analysis.scoremodels.ScoreModels;
+ import jalview.analysis.scoremodels.SimilarityParams;
+ import jalview.api.analysis.ScoreModelI;
  import jalview.datamodel.Alignment;
  import jalview.datamodel.AlignmentView;
 -import jalview.datamodel.ColumnSelection;
 +import jalview.datamodel.HiddenColumns;
  import jalview.datamodel.SeqCigar;
  import jalview.datamodel.SequenceI;
  import jalview.util.MessageManager;

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

diff --cc src/jalview/appletgui/TreePanel.java
index 23b23be,8b1f79c..c7bf6aa
--- 1/src/jalview/appletgui/TreePanel.java
--- 2/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@@ -20,15 -20,17 +20,17 @@@
   */
  package jalview.appletgui;
  
+ import jalview.analysis.AverageDistanceTree;
  import jalview.analysis.NJTree;
+ import jalview.analysis.TreeBuilder;
+ import jalview.analysis.TreeModel;
+ import jalview.analysis.scoremodels.ScoreModels;
+ import jalview.analysis.scoremodels.SimilarityParams;
  import jalview.api.analysis.ScoreModelI;
- import jalview.api.analysis.ViewBasedAnalysisI;
  import jalview.datamodel.Alignment;
- import jalview.datamodel.AlignmentView;
 -import jalview.datamodel.ColumnSelection;
 +import jalview.datamodel.HiddenColumns;
  import jalview.datamodel.SequenceI;
  import jalview.io.NewickFile;
- import jalview.schemes.ResidueProperties;
  import jalview.util.MessageManager;
  
  import java.awt.BorderLayout;
@@@ -171,9 -150,9 +150,9 @@@ public class TreePanel extends EmbmenuF
        } catch (Exception ex)
        {
        }
-       ;
-       Object[] alAndColsel = tree.seqData
+ 
+       Object[] alAndColsel = tree.getOriginalData()
 -              .getAlignmentAndColumnSelection(gc);
 +              .getAlignmentAndHiddenColumns(gc);
  
        if (alAndColsel != null && alAndColsel[0] != null)
        {

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

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

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

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

diff --cc src/jalview/gui/AnnotationColumnChooser.java
index 0fe6462,999d217..dedb8b8
--- 1/src/jalview/gui/AnnotationColumnChooser.java
--- 2/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@@ -21,8 -21,7 +21,7 @@@
  
  package jalview.gui;
  
- import jalview.datamodel.AlignmentAnnotation;
 -import jalview.datamodel.ColumnSelection;
 +import jalview.datamodel.HiddenColumns;
  import jalview.schemes.AnnotationColourGradient;
  import jalview.util.MessageManager;
  import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
@@@ -86,8 -86,12 +86,12 @@@ public class AnnotationColumnChooser ex
  
    private int actionOption = ACTION_OPTION_SELECT;
  
 -  private ColumnSelection oldColumnSelection;
 +  private HiddenColumns oldHiddenColumns;
  
+   protected int MIN_WIDTH = 420;
+ 
+   protected int MIN_HEIGHT = 430;
+ 
    public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
    {
      super(av, ap);

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

diff --cc src/jalview/gui/PCAPanel.java
index 1f68124,e9ba1e7..d8e6b06
--- 1/src/jalview/gui/PCAPanel.java
--- 2/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@@ -23,11 -27,9 +27,9 @@@ import jalview.api.analysis.SimilarityP
  import jalview.datamodel.Alignment;
  import jalview.datamodel.AlignmentI;
  import jalview.datamodel.AlignmentView;
 -import jalview.datamodel.ColumnSelection;
 +import jalview.datamodel.HiddenColumns;
- import jalview.datamodel.SeqCigar;
  import jalview.datamodel.SequenceI;
  import jalview.jbgui.GPCAPanel;
- import jalview.schemes.ResidueProperties;
  import jalview.util.MessageManager;
  import jalview.viewmodel.AlignmentViewport;
  import jalview.viewmodel.PCAModel;

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

diff --cc src/jalview/gui/SeqPanel.java
index 31fe2b6,1432fcb..749b390
--- 1/src/jalview/gui/SeqPanel.java
--- 2/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@@ -2101,14 -2118,16 +2128,20 @@@ public class SeqPanel extends JPanel im
      /*
       * Map column selection
       */
 -    ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
 -            av);
 +    // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
 +    // av);
 +    ColumnSelection cs = new ColumnSelection();
 +    HiddenColumns hs = new HiddenColumns();
 +    MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
      av.setColumnSelection(cs);
 +    av.getAlignment().setHiddenColumns(hs);
  
+     // lastly, update any dependent dialogs
+     if (ap.getCalculationDialog() != null)
+     {
+       ap.getCalculationDialog().validateCalcTypes();
+     }
+ 
      PaintRefresher.Refresh(this, av.getSequenceSetId());
  
      return true;

diff --cc src/jalview/gui/TreePanel.java
index 96d0746,9dd805e..35998eb
--- 1/src/jalview/gui/TreePanel.java
--- 2/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@@ -514,8 -431,9 +431,8 @@@ public class TreePanel extends GTreePan
      } catch (Exception ex)
      {
      }
-     ;
-     Object[] alAndColsel = tree.seqData.getAlignmentAndHiddenColumns(gc);
+ 
 -    Object[] alAndColsel = originalData
 -            .getAlignmentAndColumnSelection(gc);
++    Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
  
      if (alAndColsel != null && alAndColsel[0] != null)
      {

diff --cc src/jalview/structure/StructureSelectionManager.java
Simple merge