JAL-2629 storage and lifecycle of alignment/group HMM annotations revised

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index fdc2847..730bcb0 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());
@@ -4560,7 +4560,7 @@ 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)