Merge branch 'patchJAL-674_offset' into Release_2_8_2_Branch

diff --combined src/jalview/gui/AlignFrame.java
index 2a804ad,0087e8d..31652c1
--- 1/src/jalview/gui/AlignFrame.java
--- 2/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@@ -30,6 -30,7 +30,7 @@@ import jalview.analysis.ParseProperties
  import jalview.analysis.SequenceIdMatcher;
  import jalview.api.AlignViewControllerGuiI;
  import jalview.api.AlignViewControllerI;
+ import jalview.api.AlignmentViewPanel;
  import jalview.api.analysis.ScoreModelI;
  import jalview.bin.Cache;
  import jalview.commands.CommandI;
@@@ -115,6 -116,7 +116,7 @@@ import java.beans.PropertyChangeEvent
  import java.io.File;
  import java.net.URL;
  import java.util.ArrayList;
+ import java.util.Arrays;
  import java.util.Enumeration;
  import java.util.Hashtable;
  import java.util.List;
@@@ -4184,21 -4186,6 +4186,21 @@@ public class AlignFrame extends GAlignF
         */
        msa = viewport.getAlignmentView(true);
      }
 +    else if (viewport.getSelectionGroup() != null
 +            && viewport.getSelectionGroup().getSize() == 1)
 +    {
 +      int option = JOptionPane
 +              .showConfirmDialog(
 +this,
 +                      "More than one sequece group selection is required for this Job, click \n'Cancel' to edit your selection or 'Ok' to submit the entire sequence.",
 +                      "Invalid selection",
 +                      JOptionPane.OK_CANCEL_OPTION);
 +      if (option == JOptionPane.OK_OPTION)
 +      {
 +        msa = viewport.getAlignmentView(false);
 +      }
 +
 +    }
      else
      {
        /*
@@@ -5831,6 -5818,15 +5833,15 @@@
              .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
      alignPanel.paintAlignment(true);
    }
+ 
+   /**
+    * 
+    * @return alignment panels in this alignemnt frame
+    */
+   public List<AlignmentViewPanel> getAlignPanels()
+   {
+     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+   }
  }
  
  class PrintThread extends Thread