JAL-629 Run non-alignframe linked groovy scripts. Use multiple specified groovy...

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 5d3b50d..3006f1f 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -775,10 +775,11 @@ public class Commands
                   // RESTORE SESSION AFTER EXPORT IF NEED BE
                   if (sessionToRestore != null)
                   {
-                    Console.debug("Restoring session from "
-                            + sessionToRestore);
-                    
-                    sview.getBinding().restoreSession(sessionToRestore.getAbsolutePath());
+                    Console.debug(
+                            "Restoring session from " + sessionToRestore);
+
+                    sview.getBinding().restoreSession(
+                            sessionToRestore.getAbsolutePath());
 
                   }
                 } catch (ImageOutputException ioexec)
@@ -789,11 +790,14 @@ public class Commands
                   continue;
                 } finally
                 {
-                  try {
+                  try
+                  {
                     this.colourAlignFrame(af, originalColourScheme);
                   } catch (Exception t)
                   {
-                    addError("Unexpected error when restoring colourscheme to alignment after temporary change for export.",t);
+                    addError(
+                            "Unexpected error when restoring colourscheme to alignment after temporary change for export.",
+                            t);
                   }
                 }
               }
@@ -838,21 +842,30 @@ public class Commands
     ArgValuesMap avm = argParser.getLinkedArgs(id);
     AlignFrame af = afMap.get(id);
 
+    if (avm != null && !avm.containsArg(Arg.GROOVY))
+    {
+      // nothing to do
+      return;
+    }
+
     if (af == null)
     {
-      addWarn("Did not have an alignment window for id=" + id);
+      addWarn("Groovy script does not have an alignment window.  Proceeding with caution!");
       return;
     }
 
     if (avm.containsArg(Arg.GROOVY))
     {
-      String groovyscript = avm.getValue(Arg.GROOVY);
-      if (groovyscript != null)
+      for (ArgValue groovyAv : avm.getArgValueList(Arg.GROOVY))
       {
-        // Execute the groovy script after we've done all the rendering stuff
-        // and before any images or figures are generated.
-        Console.info("Executing script " + groovyscript);
-        Jalview.getInstance().executeGroovyScript(groovyscript, af);
+        String groovyscript = groovyAv.getValue();
+        if (groovyscript != null)
+        {
+          // Execute the groovy script after we've done all the rendering stuff
+          // and before any images or figures are generated.
+          Console.info("Executing script " + groovyscript);
+          Jalview.getInstance().executeGroovyScript(groovyscript, af);
+        }
       }
     }
   }
@@ -862,9 +875,16 @@ public class Commands
     ArgValuesMap avm = argParser.getLinkedArgs(id);
     AlignFrame af = afMap.get(id);
 
+    if (avm != null && !avm.containsArg(Arg.IMAGE))
+    {
+      // nothing to do
+      return true;
+    }
+
     if (af == null)
     {
-      addWarn("Did not have an alignment window for id=" + id);
+      addWarn("Do not have an alignment window to create image from (id="
+              + id + ").  Not proceeding.");
       return false;
     }
 
@@ -991,9 +1011,16 @@ public class Commands
     ArgValuesMap avm = argParser.getLinkedArgs(id);
     AlignFrame af = afMap.get(id);
 
+    if (avm != null && !avm.containsArg(Arg.OUTPUT))
+    {
+      // nothing to do
+      return true;
+    }
+
     if (af == null)
     {
-      addWarn("Did not have an alignment window for id=" + id);
+      addWarn("Do not have an alignment window (id=" + id
+              + ").  Not proceeding.");
       return false;
     }