interactive/batch mode test for groovy scripting (See JAL-611)

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index fc6d23e..b599f0f 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -179,6 +179,7 @@ public class Jalview
     if (!headless)
     {
       desktop = new Desktop();
+      desktop.setInBatchMode(true); // indicate we are starting up
       desktop.setVisible(true);
       desktop.startServiceDiscovery();
       if (!aparser.contains("nousagestats"))
@@ -536,7 +537,7 @@ public class Jalview
         startFeatureFetching(getFeatures);
       }
     }
-    // execute a groovy script.
+    // Once all other stuff is done, execute any groovy scripts (in order)
     if (groovyscript != null)
     {
       if (jalview.bin.Cache.groovyJarsPresent())
@@ -551,8 +552,11 @@ public class Jalview
                         + groovyscript);
       }
     }
-
-    // Once all other stuff is done, execute any groovy scripts (in order)
+    // and finally, turn off batch mode indicator - if the desktop still exists
+    if (desktop!=null)
+    {
+      desktop.setInBatchMode(false);
+    }
   }
 
   private static void startUsageStats(final Desktop desktop)

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 0bf029c..b35495f 100755 (executable)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -2088,6 +2088,29 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     return v_client;
 
   }
+  /**
+   * flag set if jalview GUI is being operated programmatically
+   */
+  private boolean inBatchMode=false;
+
+  /**
+   * check if jalview GUI is being operated programmatically
+   * @return inBatchMode
+   */
+  public boolean isInBatchMode()
+  {
+    return inBatchMode;
+  }
+
+  /**
+   * set flag if jalview GUI is being operated programmatically
+   * @param inBatchMode 
+   */
+  public void setInBatchMode(boolean inBatchMode)
+  {
+    this.inBatchMode = inBatchMode;
+  }
+
 
   public void startServiceDiscovery()
   {