X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=b080a25341af9267b3eb8f6b33d889715ee342ac;hb=985fd5ff517f3eb5221a7aefec88138341514779;hp=bf9569b85119899dab22c86dda60e0cd52c9df74;hpb=ea976fa3d06c5fa75d9b89dafe5560dbae7fdb1d;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index bf9569b..b080a25 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -964,6 +964,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return progressBar.operationInProgress();
   }
 
+  /**
+   * Sets the text of the status bar. Note that setting a null or empty value
+   * will cause the status bar to be hidden, with possibly undesirable flicker
+   * of the screen layout.
+   */
   @Override
   public void setStatus(String text)
   {
@@ -2408,15 +2413,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    SequenceGroup sg = new SequenceGroup();
-
-    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
-    {
-      sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
-    }
+    SequenceGroup sg = new SequenceGroup(
+            viewport.getAlignment().getSequences());
 
     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
     viewport.setSelectionGroup(sg);
+    viewport.isSelectionGroupChanged(true);
     viewport.sendSelection();
     // JAL-2034 - should delegate to
     // alignPanel to decide if overview needs
@@ -2900,7 +2902,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.setFollowHighlight(state);
     if (state)
     {
-      alignPanel.scrollToPosition(viewport.getSearchResults(), false);
+      alignPanel.scrollToPosition(viewport.getSearchResults());
     }
   }
 
@@ -3047,6 +3049,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.expandColSelection(sg, false);
     viewport.hideAllSelectedSeqs();
     viewport.hideSelectedColumns();
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
@@ -3071,6 +3074,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hideSelColumns_actionPerformed(ActionEvent e)
   {
     viewport.hideSelectedColumns();
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }