JAL-2964 tree@linkToAllViews attribute added to project schema

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index fdc2847..ffa8301 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -52,7 +52,6 @@ import jalview.schemabinding.version2.Annotation;
 import jalview.schemabinding.version2.AnnotationColours;
 import jalview.schemabinding.version2.AnnotationElement;
 import jalview.schemabinding.version2.CalcIdParam;
-import jalview.schemabinding.version2.Colour;
 import jalview.schemabinding.version2.CompoundMatcher;
 import jalview.schemabinding.version2.DBRef;
 import jalview.schemabinding.version2.Features;
@@ -1124,6 +1123,7 @@ public class Jalview2XML
               tree.setXpos(tp.getX());
               tree.setYpos(tp.getY());
               tree.setId(makeHashCode(tp, null));
+              tree.setLinkToAllViews(tp.treeCanvas.applyToAllViews);
               jms.addTree(tree);
             }
           }
@@ -1450,9 +1450,10 @@ public class Jalview2XML
         }
         else
         {
-          ArrayList<int[]> hiddenRegions = hidden.getHiddenColumnsCopy();
-          for (int[] region : hiddenRegions)
+          Iterator<int[]> hiddenRegions = hidden.iterator();
+          while (hiddenRegions.hasNext())
           {
+            int[] region = hiddenRegions.next();
             HiddenColumns hc = new HiddenColumns();
             hc.setStart(region[0]);
             hc.setEnd(region[1]);
@@ -3795,6 +3796,7 @@ public class Jalview2XML
         tp.showDistances(tree.getShowDistances());
 
         tp.treeCanvas.threshold = tree.getThreshold();
+        tp.treeCanvas.applyToAllViews = tree.isLinkToAllViews();
 
         if (tree.getCurrentTree())
         {