X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=a746e1fe4e1a07d4ca66f37854836891089adc14;hb=19f8ee5562523508666b4472ad624b9e549a3cea;hp=bd55668e752504025d0984783cbb370e84c8b2d7;hpb=47abd39554b389bbd420367a3291872e7b098727;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index bd55668..a746e1f 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -807,7 +807,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void updateConservation(final AlignmentViewPanel ap)
   {
     // see note in mantis : issue number 8585
-    if (alignment.isNucleotide() || conservation == null
+    if (alignment.isNucleotide()
+            || (conservation == null && quality == null)
             || !autoCalculateConsensus)
     {
       return;
@@ -1107,6 +1108,13 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
+  public boolean hasSelectedColumns()
+  {
+    ColumnSelection columnSelection = getColumnSelection();
+    return columnSelection != null && columnSelection.hasSelectedColumns();
+  }
+
+  @Override
   public boolean hasHiddenColumns()
   {
     return colSel != null && colSel.hasHiddenColumns();
@@ -2730,7 +2738,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
       }
       seqMappings = MappingUtils
               .findMappingsForSequenceAndOthers(sequence, mappings,
-                      getCodingComplement().getAlignment());
+                      getCodingComplement().getAlignment().getSequences());
       if (!seqMappings.isEmpty())
       {
         break;
@@ -2763,8 +2771,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     if (sg != null
             && (sgs = sg.getStartRes()) >= 0
             && sg.getStartRes() <= (sge = sg.getEndRes())
-            && (colSel == null || colSel.getSelected() == null || colSel
-                    .getSelected().size() == 0))
+            && !this.hasSelectedColumns())
     {
       if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
       {