3253-omnibus save

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index ae101a3..b1f595f 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -605,10 +605,30 @@ public abstract class AlignmentViewport
 
   protected ColumnSelection colSel = new ColumnSelection();
 
-  public boolean autoCalculateConsensus = true;
+  protected boolean autoCalculateConsensusAndConservation = true;
+
+  public boolean getAutoCalculateConsensusAndConservation()
+  { // BH 2019.07.24
+    return autoCalculateConsensusAndConservation;
+  }
+
+  public void setAutoCalculateConsensusAndConservation(boolean b)
+  {
+    autoCalculateConsensusAndConservation = b;
+  }
 
   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();
@@ -824,7 +844,7 @@ public abstract class AlignmentViewport
     // see note in mantis : issue number 8585
     if (alignment.isNucleotide()
             || (conservation == null && quality == null)
-            || !autoCalculateConsensus)
+            || !autoCalculateConsensusAndConservation)
     {
       return;
     }
@@ -842,7 +862,7 @@ public abstract class AlignmentViewport
   public void updateConsensus(final AlignmentViewPanel ap)
   {
     // see note in mantis : issue number 8585
-    if (consensus == null || !autoCalculateConsensus)
+    if (consensus == null || !autoCalculateConsensusAndConservation)
     {
       return;
     }
@@ -1195,6 +1215,13 @@ public abstract class AlignmentViewport
 
   public void setSequenceSetId(String newid)
   {
+    // // BH 2020.04.07 do we need to do this if it is the same?
+    // // (Jalview project files)
+    // if (newid.equals(sequenceSetID))
+    // {
+    // return;
+    // }
+
     if (sequenceSetID != null)
     {
       System.err.println(
@@ -1323,21 +1350,6 @@ public abstract class AlignmentViewport
    */
   private boolean followHighlight = true;
 
-  // private boolean disableFastPaint; // BH 2019.04.18
-  //
-  // /**
-  // * BH 2019.04.18 When gap filling is on and a modification is made to fill
-  // * those, we need to disallow fast painting for paste just once
-  // *
-  // * @return
-  // */
-  // public boolean isFastPaintDisabled()
-  // {
-  // boolean ret = disableFastPaint;
-  // disableFastPaint = false;
-  // return ret;
-  // }
-
   /**
    * Property change listener for changes in alignment
    * 
@@ -1873,17 +1885,12 @@ public abstract class AlignmentViewport
     if (isPadGaps())
     {
       alignment.padGaps();
-      // if (alignment.padGaps())
-      // {
-      // // the new alignment has been modified -- can't fast paint
-      // disableFastPaint = true;
-      // }
     }
-    if (autoCalculateConsensus)
+    if (autoCalculateConsensusAndConservation)
     {
       updateConsensus(ap);
     }
-    if (hconsensus != null && autoCalculateConsensus)
+    if (hconsensus != null && autoCalculateConsensusAndConservation)
     {
       updateConservation(ap);
     }
@@ -2287,7 +2294,7 @@ public abstract class AlignmentViewport
   public void clearSequenceColours()
   {
     sequenceColours.clear();
-  };
+  }
 
   @Override
   public AlignViewportI getCodingComplement()
@@ -2740,6 +2747,30 @@ public abstract class AlignmentViewport
     viewStyle.setProteinFontAsCdna(b);
   }
 
+  @Override
+  public void setShowComplementFeatures(boolean b)
+  {
+    viewStyle.setShowComplementFeatures(b);
+  }
+
+  @Override
+  public boolean isShowComplementFeatures()
+  {
+    return viewStyle.isShowComplementFeatures();
+  }
+
+  @Override
+  public void setShowComplementFeaturesOnTop(boolean b)
+  {
+    viewStyle.setShowComplementFeaturesOnTop(b);
+  }
+
+  @Override
+  public boolean isShowComplementFeaturesOnTop()
+  {
+    return viewStyle.isShowComplementFeaturesOnTop();
+  }
+
   /**
    * @return true if view should scroll to show the highlighted region of a
    *         sequence