X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=0c31a2a007adcac04d169c2dd035da558362d7ee;hb=1d0f5219658cdf6ad5e1a1cbe6e1bb8cd12e6d85;hp=fdc28470cd5ab6760c2e67d7fbf6f9b4b64a91c0;hpb=aa4e99f8937ce22963cf32f1e92f174ee52ad7ee;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index fdc2847..0c31a2a 100644
--- 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]);
@@ -4552,7 +4553,8 @@ public class Jalview2XML
       }
       else
       {
-        cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
+        cs = ColourSchemeProperty.getColourScheme(af.viewport, al,
+                view.getBgColour());
       }
     }
 
@@ -4892,7 +4894,7 @@ public class Jalview2XML
     else
     {
       cs = new AnnotationColourGradient(matchedAnnotation,
-              ColourSchemeProperty.getColourScheme(al,
+              ColourSchemeProperty.getColourScheme(af.viewport, al,
                       viewAnnColour.getColourScheme()),
               viewAnnColour.getAboveThreshold());
     }