+ startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
+ format);
+ getFeatures = checkDasArguments(aparser);
+ // extract groovy arguments before anything else.
+ }
+ // Once all loading is done. Retrieve features.
+ if (getFeatures != null)
+ {
+ if (startUpAlframe != null)
+ {
+ startFeatureFetching(getFeatures);
+ }
+ }
+ 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 = null;
+ if (groovyscript.trim().equals("STDIN"))
+ {
+ // read from stdin into a tempfile and execute it
+ try
+ {
+ sfile = File.createTempFile("jalview", "groovy");
+ PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
+ new FileOutputStream(sfile)));
+ BufferedReader br = new BufferedReader(
+ new java.io.InputStreamReader(System.in));
+ String line = null;
+ while ((line = br.readLine()) != null)
+ {
+ outfile.write(line + "\n");
+ }
+ br.close();
+ outfile.flush();
+ outfile.close();
+
+ } catch (Exception ex)
+ {
+ System.err.println("Failed to read from STDIN into tempfile "
+ + ((sfile == null) ? "(tempfile wasn't created)" : sfile
+ .toString()));
+ ex.printStackTrace();
+ return;
+ }
+ }
+ else
+ {
+ 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;
+ }
+ boolean success = false;
+ 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[]
+ { URL[].class }); // String[].class });
+ Object gse = gseccons.newInstance(new Object[]
+ { new URL[]
+ { sfile.toURL() } }); // .toString() } });
+ java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
+ { String.class, gbindingc });
+ run.invoke(gse, new Object[]
+ { sfile.getName(), gbinding });
+ success = true;
+ } catch (Exception e)
+ {
+ System.err.println("Exception Whilst trying to execute file " + sfile
+ + " as a groovy script.");
+ e.printStackTrace(System.err);
+
+ }
+ if (success && groovyscript.equals("STDIN"))
+ {
+ // delete temp file that we made - but only if it was successfully
+ // executed
+ sfile.delete();
+ }
+ }
+
+ /**
+ * Check commandline for any das server definitions or any fetchfrom switches
+ *
+ * @return vector of DAS source nicknames to retrieve from
+ */
+ private static Vector checkDasArguments(ArgsParser aparser)
+ {
+ Vector source = null;
+ String data;
+ String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
+ while ((data = aparser.getValue("dasserver")) != null)
+ {
+ String nickname = null;
+ String url = null;
+ boolean seq=false,feat=true;
+ int pos = data.indexOf('=');
+ // determine capabilities
+ if (pos > 0)
+ {
+ nickname = data.substring(0, pos);
+ }
+ url = data.substring(pos + 1);
+ if (url != null && (url.startsWith("http:") || url.startsWith("sequence:http:")))
+ {
+ if (nickname == null)
+ {
+ nickname = url;
+ }
+ if (locsources == null)
+ {
+ locsources = "";
+ }
+ else
+ {
+ locsources += "\t";
+ }
+ locsources = locsources + nickname + "|" + url;
+ System.err
+ .println("NOTE! dasserver parameter not yet really supported (got args of "
+ + nickname + "|" + url);
+ if (source == null)
+ {
+ source = new Vector();
+ }
+ source.addElement(nickname);
+ }
+ } // loop until no more server entries are found.
+ if (locsources != null && locsources.indexOf('|') > -1)
+ {
+ Cache.log.debug("Setting local source list in properties file to:\n"
+ + locsources);
+ Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
+ }
+ while ((data = aparser.getValue("fetchfrom")) != null)
+ {
+ System.out.println("adding source '" + data + "'");
+ if (source == null)
+ {
+ source = new Vector();
+ }
+ source.addElement(data);
+ }
+ return source;
+ }
+
+ /**
+ * start a feature fetcher for every alignment frame
+ *
+ * @param dasSources
+ */
+ private static void startFeatureFetching(final Vector dasSources)
+ {
+ AlignFrame afs[] = Desktop.getAlignframes();
+ if (afs == null || afs.length == 0)
+ {
+ return;
+ }
+ for (int i = 0; i < afs.length; i++)
+ {
+ final AlignFrame af = afs[i];
+ SwingUtilities.invokeLater(new Runnable()
+ {
+
+ public void run()
+ {
+ af.featureSettings_actionPerformed(null);
+ af.featureSettings.fetchDasFeatures(dasSources);
+ }
+ });
+ }
+ }
+
+ private static String checkProtocol(String file)
+ {
+ String protocol = jalview.io.FormatAdapter.FILE;