Merge branch 'develop' into releases/Release_2_10_Branch

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index bd55668..a746e1f 100644 (file)
--- 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))
       {