JAL-2939 field/method naming more consistent

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

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 4c38aa0..aebcbb3 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -134,7 +134,7 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   private boolean hmmUseInfoLetterHeight;
 
-  private boolean showHMMSequenceLogo;
+  private boolean hmmShowSequenceLogo;
 
   private boolean hmmNormaliseSequenceLogo;
 
@@ -228,7 +228,7 @@ public class SequenceGroup implements AnnotatedCollectionI
       showSequenceLogo = seqsel.showSequenceLogo;
       normaliseSequenceLogo = seqsel.normaliseSequenceLogo;
       showConsensusHistogram = seqsel.showConsensusHistogram;
-      showHMMSequenceLogo = seqsel.showHMMSequenceLogo;
+      hmmShowSequenceLogo = seqsel.hmmShowSequenceLogo;
       hmmNormaliseSequenceLogo = seqsel.hmmNormaliseSequenceLogo;
       hmmShowHistogram = seqsel.hmmShowHistogram;
       idColour = seqsel.idColour;
@@ -617,8 +617,7 @@ public class SequenceGroup implements AnnotatedCollectionI
 
         ProfilesI info = AAFrequency.calculateHMMProfiles(hmm,
                 (endRes + 1) - startRes, startRes, endRes + 1,
-                showHMMSequenceLogo, hmmIgnoreBelowBackground,
-                hmmUseInfoLetterHeight);
+                hmmIgnoreBelowBackground, hmmUseInfoLetterHeight);
         _updateInformationRow(info);
         upd = true;
       }
@@ -1579,18 +1578,16 @@ public class SequenceGroup implements AnnotatedCollectionI
       // recalcConservation(); TODO don't know what to do here next
     }
     this.hmmShowHistogram = state;
-
   }
 
   public boolean isShowHMMSequenceLogo()
   {
-    return showHMMSequenceLogo;
+    return hmmShowSequenceLogo;
   }
 
-  public void setshowHMMSequenceLogo(boolean state)
+  public void setShowHMMSequenceLogo(boolean state)
   {
-    showHMMSequenceLogo = state;
-
+    hmmShowSequenceLogo = state;
   }
 
   public boolean isNormaliseHMMSequenceLogo()
@@ -1600,7 +1597,7 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   public void setNormaliseHMMSequenceLogo(boolean state)
   {
-    normaliseSequenceLogo = state;
+    hmmNormaliseSequenceLogo = state;
   }
 
   @Override