+ if (groovyscript!=null)
+ {
+ if (jalview.bin.Cache.groovyJarsPresent())
+ {
+ System.out.println("Executing script "+groovyscript);
+ executeGroovyScript(groovyscript, desktop);
+ } else {
+ System.err.println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "+groovyscript);
+ }
+ }
+
+ // Once all other stuff is done, execute any groovy scripts (in order)
+ }
+ /**
+ * Locate the given string as a file and pass it to the groovy interpreter.
+ * @param groovyscript the script to execute
+ * @param jalviewContext the Jalview Desktop object passed in to the groovy binding as the 'Jalview' object.
+ */
+ private static void executeGroovyScript(String groovyscript, Object jalviewContext)
+ {
+ if (jalviewContext==null)
+ {
+ System.err.println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
+ }
+ File sfile = new File(groovyscript);
+ if (!sfile.exists())
+ {
+ System.err.println("File '"+groovyscript+"' does not exist.");
+ return;
+ }
+ if (!sfile.canRead())
+ {
+ System.err.println("File '"+groovyscript+"' cannot be read.");
+ return;
+ }
+ if (sfile.length()<1)
+ {
+ System.err.println("File '"+groovyscript+"' is empty.");
+ return;
+ }
+ try {
+ /* The following code performs the GroovyScriptEngine invocation using reflection,
+ * and is equivalent to this fragment from the embedding groovy documentation on
+ * the groovy site:
+ * <code>
+ import groovy.lang.Binding;
+ import groovy.util.GroovyScriptEngine;
+
+ String[] roots = new String[] { "/my/groovy/script/path" };
+ GroovyScriptEngine gse = new GroovyScriptEngine(roots);
+ Binding binding = new Binding();
+ binding.setVariable("input", "world");
+ gse.run("hello.groovy", binding);
+ * </code>
+ */
+ ClassLoader cl = jalviewContext.getClass().getClassLoader();
+ Class gbindingc = cl.loadClass("groovy.lang.Binding");
+ Constructor gbcons = gbindingc.getConstructor(null);
+ Object gbinding = gbcons.newInstance(null);
+ java.lang.reflect.Method setvar = gbindingc.getMethod("setVariable", new Class[] { String.class, Object.class} );
+ setvar.invoke(gbinding, new Object[] { "Jalview", jalviewContext});
+ Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
+ Constructor gseccons = gsec.getConstructor(new Class[] { String[].class });
+ Object gse = gseccons.newInstance(new Object[] { new String[] { groovyscript } });
+ java.lang.reflect.Method run = gsec.getMethod("run", new Class[]{ String.class, gbindingc });
+ run.invoke(gse, new Object[] { sfile.getName(), gbinding });
+ } catch (Exception e)
+ {
+ System.err.println("Exception Whilst trying to execute file "+sfile+" as a groovy script.");
+ e.printStackTrace(System.err);
+ }