profile visualizations are now logos

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 51e26b8..c952ea0 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -947,7 +947,7 @@ public class Jalview2XML
         groups[i].setShowUnconserved(sg.getShowunconserved());
         groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
         groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram());
-        groups[i].setShowConsensusProfile(sg.isIncludeAllConsSymbols());
+        groups[i].setShowSequenceLogo(sg.isShowSequenceLogo());
         for (int s = 0; s < sg.getSize(); s++)
         {
           jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
@@ -1060,7 +1060,7 @@ public class Jalview2XML
     view.setTextCol2(av.textColour2.getRGB());
     view.setTextColThreshold(av.thresholdTextColour);
     view.setShowConsensusHistogram(av.isShowConsensusHistogram());
-    view.setShowConsensusProfile(av.isShowConsensusProfile());
+    view.setShowSequenceLogo(av.isShowSequenceLogo());
     view.setShowGroupConsensus(av.isShowGroupConsensus());
     view.setShowGroupConservation(av.isShowGroupConservation());
     view.setShowNPfeatureTooltip(av.isShowNpFeats());
@@ -2229,8 +2229,8 @@ public class Jalview2XML
         if (groups[i].hasShowConsensusHistogram()) {
           sg.setShowConsensusHistogram(groups[i].isShowConsensusHistogram());
         };
-        if (groups[i].hasShowConsensusProfile()) {
-          sg.setIncludeAllConsSymbols(groups[i].isShowConsensusProfile());
+        if (groups[i].hasShowSequenceLogo()) {
+          sg.setIncludeAllConsSymbols(groups[i].isShowSequenceLogo());
         }
         if (groups[i].hasIgnoreGapsinConsensus())
         {
@@ -2811,10 +2811,14 @@ public class Jalview2XML
     if (view.hasShowConsensusHistogram())
     {
       af.viewport.setShowConsensusHistogram(view.getShowConsensusHistogram());
+    } else {
+      af.viewport.setShowConsensusHistogram(true);
     }
-    if (view.hasShowConsensusProfile())
+    if (view.hasShowSequenceLogo())
     {
-      af.viewport.setShowConsensusProfile(view.getShowConsensusProfile());
+      af.viewport.setShowSequenceLogo(view.getShowSequenceLogo());
+    } else {
+      af.viewport.setShowSequenceLogo(false);
     }
     if (view.hasShowDbRefTooltip())
     {
@@ -2827,10 +2831,14 @@ public class Jalview2XML
     if (view.hasShowGroupConsensus())
     {
       af.viewport.setShowGroupConsensus(view.getShowGroupConsensus());
+    } else {
+      af.viewport.setShowGroupConsensus(false);
     }
     if (view.hasShowGroupConservation())
     {
       af.viewport.setShowGroupConservation(view.getShowGroupConservation());
+    } else {
+      af.viewport.setShowGroupConservation(false);
     }
     
     // recover featre settings