patched for JAL-531 - only display full symbol distribution stats on tooltip/annotati...

[jalview.git] / src / jalview / datamodel / SequenceGroup.java

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 9d3e6db..451250e 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -49,7 +49,7 @@ public class SequenceGroup
   /**
    * after Olivier's non-conserved only character display
    */
-  boolean showUnconserved = false;
+  boolean showNonconserved = false;
 
   /**
    * group members
@@ -957,18 +957,18 @@ public class SequenceGroup
   /**
    * @return the showUnconserved
    */
-  public boolean getShowunconserved()
+  public boolean getShowNonconserved()
   {
-    return showUnconserved;
+    return showNonconserved;
   }
 
   /**
-   * @param showUnconserved
+   * @param showNonconserved
    *          the showUnconserved to set
    */
-  public void setShowunconserved(boolean displayNonconserved)
+  public void setShowNonconserved(boolean displayNonconserved)
   {
-    this.showUnconserved = displayNonconserved;
+    this.showNonconserved = displayNonconserved;
   }
 
   AlignmentAnnotation consensus = null, conservation = null;
@@ -1079,17 +1079,18 @@ public class SequenceGroup
   }
 
   /**
-   * @param includeAllConsSymbols
-   *          the includeAllConsSymbols to set
+   * @param showSequenceLogo
+   *          indicates if a sequence logo is shown for consensus annotation
    */
-  public void setIncludeAllConsSymbols(boolean includeAllConsSymbols)
+  public void setshowSequenceLogo(boolean showSequenceLogo)
   {
-    if (this.showSequenceLogo != includeAllConsSymbols && consensus != null)
+    // TODO: decouple calculation from settings update
+    if (this.showSequenceLogo != showSequenceLogo && consensus != null)
     {
-      this.showSequenceLogo = includeAllConsSymbols;
+      this.showSequenceLogo = showSequenceLogo;
       recalcConservation();
     }
-    this.showSequenceLogo = includeAllConsSymbols;
+    this.showSequenceLogo = showSequenceLogo;
   }
 
   /**