JAL-3148 SequenceRenderer, ResidueColourFinder overloads and

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index fdc2847..39755f9 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -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]);
@@ -1731,8 +1732,8 @@ public class Jalview2XML
           state.setHeight(viewFrame.getHeight());
           final String viewId = viewFrame.getViewId();
           state.setViewId(viewId);
-          state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
-          state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
+          state.setAlignwithAlignPanel(viewFrame.isUsedForAligment(ap));
+          state.setColourwithAlignPanel(viewFrame.isUsedForColourBy(ap));
           state.setColourByJmol(viewFrame.isColouredByViewer());
           state.setType(viewFrame.getViewerType().toString());
           pdb.addStructureState(state);