JAL-958 store/recover normalised flag

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 4533b25..e283f27 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1004,6 +1004,7 @@ public class Jalview2XML
         groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
         groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram());
         groups[i].setShowSequenceLogo(sg.isShowSequenceLogo());
+        groups[i].setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
         for (int s = 0; s < sg.getSize(); s++)
         {
           jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
@@ -1117,6 +1118,7 @@ public class Jalview2XML
     view.setTextColThreshold(av.thresholdTextColour);
     view.setShowConsensusHistogram(av.isShowConsensusHistogram());
     view.setShowSequenceLogo(av.isShowSequenceLogo());
+    view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
     view.setShowGroupConsensus(av.isShowGroupConsensus());
     view.setShowGroupConservation(av.isShowGroupConservation());
     view.setShowNPfeatureTooltip(av.isShowNpFeats());
@@ -2480,6 +2482,10 @@ public class Jalview2XML
         {
           sg.setshowSequenceLogo(groups[i].isShowSequenceLogo());
         }
+        if (groups[i].hasNormaliseSequenceLogo())
+        {
+          sg.setNormaliseSequenceLogo(groups[i].isNormaliseSequenceLogo());
+        }
         if (groups[i].hasIgnoreGapsinConsensus())
         {
           sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus());
@@ -3297,6 +3303,10 @@ public class Jalview2XML
     {
       af.viewport.setShowSequenceLogo(false);
     }
+    if (view.hasNormaliseSequenceLogo())
+    {
+      af.viewport.setNormaliseSequenceLogo(view.getNormaliseSequenceLogo());
+    } 
     if (view.hasShowDbRefTooltip())
     {
       af.viewport.setShowDbRefs(view.getShowDbRefTooltip());