Updated with latest from mchmmer branch

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index fdc2847..3840597 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1223,7 +1223,7 @@ public class Jalview2XML
         jGroup.setTextCol2(sg.textColour2.getRGB());
         jGroup.setTextColThreshold(sg.thresholdTextColour);
         jGroup.setShowUnconserved(sg.getShowNonconserved());
-        jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
+        jGroup.setIgnoreGapsinConsensus(sg.isIgnoreGapsConsensus());
         jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
         jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
         jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
@@ -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]);
@@ -4560,7 +4561,7 @@ public class Jalview2XML
     af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
             view.getIgnoreGapsinConsensus());
     af.viewport.getResidueShading()
-            .setConsensus(af.viewport.getSequenceConsensusHash());
+            .setConsensus(af.viewport.getConsensusProfiles());
     af.viewport.setColourAppliesToAllGroups(false);
 
     if (view.getConservationSelected() && cs != null)