JAL-1812 set/return currentAlFrame for Groovy in headless mode

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index dfd0924..462f5a7 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -387,7 +387,7 @@ public class Jalview
       }
       else
       {
-
+        Desktop.setCurrentAlignFrame(af);
         data = aparser.getValue("colour", true);
         if (data != null)
         {

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index c957444..d3b8afc 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -23,6 +23,7 @@ package jalview.gui;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
+import jalview.bin.Jalview;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
@@ -2381,6 +2382,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   public static AlignFrame[] getAlignFrames()
   {
+    if (Jalview.isHeadlessMode())
+    {
+      // Desktop.desktop is null in headless mode
+      return new AlignFrame[] { currentAlignFrame };
+    }
+
     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 
     if (frames == null)