Merge branch 'patchJAL-674_offset' into develop

diff --combined src/jalview/gui/AlignFrame.java
index 52bd121,0087e8d..4f174d3
--- 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;
@@@ -54,7 -55,6 +55,7 @@@ import jalview.datamodel.SequenceGroup
  import jalview.datamodel.SequenceI;
  import jalview.io.AlignmentProperties;
  import jalview.io.AnnotationFile;
 +import jalview.io.BioJsHTMLOutput;
  import jalview.io.FeaturesFile;
  import jalview.io.FileLoader;
  import jalview.io.FormatAdapter;
@@@ -116,6 -116,7 +117,7 @@@ 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;
@@@ -1233,12 -1234,6 +1235,12 @@@ public class AlignFrame extends GAlignF
              alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
    }
  
 +  @Override
 +  public void bioJSMenuItem_actionPerformed(ActionEvent e)
 +  {
 +    new BioJsHTMLOutput(alignPanel,
 +            alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
 +  }
    public void createImageMap(File file, String image)
    {
      alignPanel.makePNGImageMap(file, image);
@@@ -4191,21 -4186,6 +4193,21 @@@
         */
        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
      {
        /*
@@@ -5838,6 -5818,15 +5840,15 @@@
              .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