JAL-3210 Barebones gradle/buildship/eclipse. See README

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 4116c3b..536f767 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -605,30 +605,10 @@ public abstract class AlignmentViewport
 
   protected ColumnSelection colSel = new ColumnSelection();
 
-  protected boolean autoCalculateConsensusAndConservation = true;
-
-  public boolean getAutoCalculateConsensusAndConservation()
-  { // BH 2019.07.24
-    return autoCalculateConsensusAndConservation;
-  }
-
-  public void setAutoCalculateConsensusAndConservation(boolean b)
-  {
-    autoCalculateConsensusAndConservation = b;
-  }
+  public boolean autoCalculateConsensus = true;
 
   protected boolean autoCalculateStrucConsensus = true;
 
-  public boolean getAutoCalculateStrucConsensus()
-  { // BH 2019.07.24
-    return autoCalculateStrucConsensus;
-  }
-
-  public void setAutoCalculateStrucConsensus(boolean b)
-  {
-    autoCalculateStrucConsensus = b;
-  }
-
   protected boolean ignoreGapsInConsensusCalculation = false;
 
   protected ResidueShaderI residueShading = new ResidueShader();
@@ -844,7 +824,7 @@ public abstract class AlignmentViewport
     // see note in mantis : issue number 8585
     if (alignment.isNucleotide()
             || (conservation == null && quality == null)
-            || !autoCalculateConsensusAndConservation)
+            || !autoCalculateConsensus)
     {
       return;
     }
@@ -862,7 +842,7 @@ public abstract class AlignmentViewport
   public void updateConsensus(final AlignmentViewPanel ap)
   {
     // see note in mantis : issue number 8585
-    if (consensus == null || !autoCalculateConsensusAndConservation)
+    if (consensus == null || !autoCalculateConsensus)
     {
       return;
     }
@@ -1879,11 +1859,11 @@ public abstract class AlignmentViewport
     {
       alignment.padGaps();
     }
-    if (autoCalculateConsensusAndConservation)
+    if (autoCalculateConsensus)
     {
       updateConsensus(ap);
     }
-    if (hconsensus != null && autoCalculateConsensusAndConservation)
+    if (hconsensus != null && autoCalculateConsensus)
     {
       updateConservation(ap);
     }