temp push

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 4f399f0..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(
@@ -1859,11 +1886,11 @@ public abstract class AlignmentViewport
     {
       alignment.padGaps();
     }
-    if (autoCalculateConsensus)
+    if (autoCalculateConsensusAndConservation)
     {
       updateConsensus(ap);
     }
-    if (hconsensus != null && autoCalculateConsensus)
+    if (hconsensus != null && autoCalculateConsensusAndConservation)
     {
       updateConservation(ap);
     }