showConservation, quality, identity not used

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index f9f32e4..c0e9dc9 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -51,9 +51,6 @@ public class AlignViewport
     boolean renderGaps = true;
     boolean showSequenceFeatures = false;
     boolean showAnnotation = true;
-    boolean showConservation = true;
-    boolean showQuality = true;
-    boolean showIdentity = true;
     boolean colourAppliesToAllGroups = true;
     ColourSchemeI globalColourScheme = null;
     boolean conservationColourSelected = false;
@@ -155,10 +152,6 @@ public class AlignViewport
 
       showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
       showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
-      showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
-
-      showQuality = Cache.getDefault("SHOW_QUALITY", true);
-      showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
 
       autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
 
@@ -199,12 +192,13 @@ public class AlignViewport
                 AlignmentAnnotation.BAR_GRAPH);
             conservation.hasText = true;
 
-            if (showConservation)
+
+            if (Cache.getDefault("SHOW_CONSERVATION", true))
             {
               alignment.addAnnotation(conservation);
             }
 
-            if (showQuality)
+            if (Cache.getDefault("SHOW_QUALITY", true))
             {
               quality = new AlignmentAnnotation("Quality",
                                                 "Alignment Quality based on Blosum62 scores",
@@ -223,7 +217,7 @@ public class AlignViewport
                                                AlignmentAnnotation.BAR_GRAPH);
           consensus.hasText = true;
 
-           if (showIdentity)
+           if (Cache.getDefault("SHOW_IDENTITY", true))
            {
              alignment.addAnnotation(consensus);
            }
@@ -504,6 +498,8 @@ public class AlignViewport
         }
         catch (OutOfMemoryError error)
         {
+          consensus = null;
+          hconsensus = null;
           javax.swing.SwingUtilities.invokeLater(new Runnable()
           {
             public void run()

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 056555a..fef8a83 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1338,10 +1338,6 @@ public class Jalview2XML
         af.viewport.setStartRes(view.getStartRes());
         af.viewport.setStartSeq(view.getStartSeq());
         af.viewport.setShowAnnotation(view.getShowAnnotation());
-        af.viewport.showConservation = !hideConservation;
-        af.viewport.showQuality = !hideQuality;
-        af.viewport.showIdentity = !hideConsensus;
-
         af.viewport.setAbovePIDThreshold(view.getPidSelected());
         af.abovePIDThreshold.setSelected(view.getPidSelected());
         af.viewport.setColourText(view.getShowColourText());