Merge branch 'features/JAL-1767pcaInProject' into bug/JAL-3171_maintain_datasets_acro...

diff --cc resources/lang/Messages.properties
Simple merge

diff --cc resources/lang/Messages_es.properties
Simple merge

diff --cc schemas/jalview.xsd
Simple merge

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

diff --cc src/jalview/gui/Jalview2XML.java
index 5cd8f9a,689261c..42760f3
--- 1/src/jalview/gui/Jalview2XML.java
--- 2/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@@ -3784,12 -3967,10 +3988,11 @@@ public class Jalview2XM
            tp.setTitle(tree.getTitle());
            tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(),
                    tree.getWidth(), tree.getHeight()));
 -          tp.av = av;
 -          tp.treeCanvas.av = av; // af.viewport;
 -          tp.treeCanvas.ap = ap; // af.alignPanel;
 -
 +          tp.setViewport(av); // af.viewport; // TODO: verify 'associate with all
 +          // views'
 +          // works still
 +          tp.getTreeCanvas().setViewport(av); // af.viewport;
 +          tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
- 
          }
          if (tp == null)
          {
@@@ -3816,7 -3997,8 +4019,8 @@@
          tp.showBootstrap(tree.getShowBootstrap());
          tp.showDistances(tree.getShowDistances());
  
 -        tp.treeCanvas.threshold = tree.getThreshold();
 +        tp.getTreeCanvas().setThreshold(tree.getThreshold());
+         tp.treeCanvas.applyToAllViews = tree.isLinkToAllViews();
  
          if (tree.getCurrentTree())
          {

diff --cc src/jalview/gui/PCAPanel.java
index c1e935a,5ff0881..da1dffe
--- 1/src/jalview/gui/PCAPanel.java
--- 2/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@@ -604,12 -494,12 +494,12 @@@ public class PCAPanel extends GPCAPane
  
      JRadioButtonMenuItem item;
      ButtonGroup buttonGroup = new ButtonGroup();
-     int i, iSize = aps.length;
-     final PCAPanel thisPCAPanel = this;
-     for (i = 0; i < iSize; i++)
+     int iSize = aps.length;
+ 
+     for (int i = 0; i < iSize; i++)
      {
 -      final AlignmentPanel panel = aps[i];
 -      item = new JRadioButtonMenuItem(panel.av.viewName, panel.av == rc.av);
 +      final AlignmentPanel ap = aps[i];
 +      item = new JRadioButtonMenuItem(ap.av.getViewName(), ap.av == rc.av);
        buttonGroup.add(item);
        item.addActionListener(new ActionListener()
        {

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

diff --cc test/jalview/io/Jalview2xmlTests.java
Simple merge