JAL-3285 delete duplicate variables in AlignmentViewport from merge

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 1a9684f..23c1d00 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -108,33 +108,11 @@ public abstract class AlignmentViewport
    * alignment
    */
 
-  private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
-
-  protected ColumnSelection colSel = new ColumnSelection();
-
-  public boolean autoCalculateConsensus = true;
-
-  protected boolean autoCalculateStrucConsensus = true;
-
-  protected boolean ignoreGapsInConsensusCalculation = false;
-
   protected boolean ignoreBelowBackGroundFrequencyCalculation = false;
 
   protected boolean infoLetterHeight = false;
 
-  protected ResidueShaderI residueShading = new ResidueShader();
-
-  protected AlignmentAnnotation consensus;
-
-  protected AlignmentAnnotation complementConsensus;
-
   protected AlignmentAnnotation occupancy;
-
-  protected AlignmentAnnotation strucConsensus;
-
-  protected AlignmentAnnotation conservation;
-
-  protected AlignmentAnnotation quality;
   
   /**
    * results of alignment consensus analysis for visible portion of view
@@ -146,19 +124,6 @@ public abstract class AlignmentViewport
    */
   protected ProfilesI hmmProfiles;
 
-  /**
-   * results of cDNA complement consensus visible portion of view
-   */
-  protected Hashtable[] hcomplementConsensus;
-
-  /**
-   * results of secondary structure base pair consensus for visible portion of
-   * view
-   */
-  protected Hashtable[] hStrucConsensus;
-
-  protected Conservation hconservation;
-
   public AlignmentViewport(AlignmentI al)
   {
     setAlignment(al);