X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=a746e1fe4e1a07d4ca66f37854836891089adc14;hb=19f8ee5562523508666b4472ad624b9e549a3cea;hp=a954a83be4cf8c4f15df2ceda6140a2b11997044;hpb=ef72c714cc7edbc26c4518e0c84a15b110bc6e3d;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index a954a83..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();
@@ -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))
       {
@@ -2782,5 +2789,32 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
   }
 
+  /**
+   * hold status of current selection group - defined on alignment or not.
+   */
+  private boolean selectionIsDefinedGroup = false;
 
+  @Override
+  public boolean isSelectionDefinedGroup()
+  {
+    if (selectionGroup == null)
+    {
+      return false;
+    }
+    if (isSelectionGroupChanged(true))
+    {
+      selectionIsDefinedGroup = false;
+      List<SequenceGroup> gps = alignment.getGroups();
+      if (gps == null || gps.size() == 0)
+      {
+        selectionIsDefinedGroup = false;
+      }
+      else
+      {
+        selectionIsDefinedGroup = gps.contains(selectionGroup);
+      }
+    }
+    return selectionGroup.getContext() == alignment
+            || selectionIsDefinedGroup;
+  }
 }