+
+ public static Object parseJSON(String json) throws ParseException
+ {
+ return (isJS() ? JSON.parse(json) : new JSONParser().parse(json));
+ }
+
+ public static Object parseJSON(Reader r)
+ throws IOException, ParseException
+ {
+ if (r == null)
+ {
+ return null;
+ }
+
+ if (!isJS())
+ {
+ return new JSONParser().parse(r);
+ }
+ // Using a file reader is not currently supported in SwingJS JavaScript
+
+ if (r instanceof FileReader)
+ {
+ throw new IOException(
+ "StringJS does not support FileReader parsing for JSON -- but it could...");
+ }
+ return JSON.parse(r);
+ }
+
+ /**
+ * Dump the input stream to an output file.
+ *
+ * @param is
+ * @param outFile
+ * @throws IOException
+ * if the file cannot be created or there is a problem reading the
+ * input stream.
+ */
+ public static void streamToFile(InputStream is, File outFile)
+ throws IOException
+ {
+
+ if (isJS)
+ {
+ jsutil.setFileBytes(outFile, is);
+ return;
+ }
+
+ FileOutputStream fio = new FileOutputStream(outFile);
+ try
+ {
+ byte[] bb = new byte[32 * 1024];
+ int l;
+ while ((l = is.read(bb)) > 0)
+ {
+ fio.write(bb, 0, l);
+ }
+ } finally
+ {
+ fio.close();
+ }
+ }
+
+ /**
+ * Add a known domain that implements access-control-allow-origin:*
+ *
+ * These should be reviewed periodically.
+ *
+ * @param domain
+ * for a service that is not allowing ajax
+ *
+ * @author hansonr@stolaf.edu
+ *
+ */
+ public static void addJ2SDirectDatabaseCall(String domain)
+ {
+
+ if (isJS)
+ {
+ jsutil.addDirectDatabaseCall(domain);
+
+ System.out.println(
+ "Platform adding known access-control-allow-origin * for domain "
+ + domain);
+ }
+
+ }
+
+ public static void getURLCommandArguments()
+ {
+
+ /**
+ * Retrieve the first query field as command arguments to Jalview. Include
+ * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
+ * element to this value.
+ *
+ * @j2sNative var a =
+ * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
+ * + "?").split("?")[1].split("#")[0]); a &&
+ * (J2S.thisApplet.__Info.args = a.split(" "));
+ */
+
+ }
+
+ /**
+ * A (case sensitive) file path comparator that ignores the difference between
+ * / and \
+ *
+ * @param path1
+ * @param path2
+ * @return
+ */
+ public static boolean pathEquals(String path1, String path2)
+ {
+ if (path1 == null)
+ {
+ return path2 == null;
+ }
+ if (path2 == null)
+ {
+ return false;
+ }
+ String p1 = path1.replace('\\', '/');
+ String p2 = path2.replace('\\', '/');
+ return p1.equals(p2);
+ }
+
+ ///////////// JAL-3253 Applet additions //////////////
+
+ /**
+ * Retrieve the object's embedded size from a div's style on a page if
+ * embedded in SwingJS.
+ *
+ * @param frame
+ * JFrame or JInternalFrame
+ * @param defaultWidth
+ * use -1 to return null (no default size)
+ * @param defaultHeight
+ * @return the embedded dimensions or null (no default size or not embedded)
+ */
+ public static Dimension getDimIfEmbedded(Component frame,
+ int defaultWidth, int defaultHeight)
+ {
+ Dimension d = null;
+ if (isJS)
+ {
+ d = (Dimension) getEmbeddedAttribute(frame, "dim");
+ }
+ return (d == null && defaultWidth >= 0
+ ? new Dimension(defaultWidth, defaultHeight)
+ : d);
+
+ }
+
+ public static Regex newRegex(String regex)
+ {
+ return newRegex(regex, null);
+ }
+
+ public static Regex newRegex(String searchString, String replaceString)
+ {
+ ensureRegex();
+ return (replaceString == null ? new Regex(searchString)
+ : new Regex(searchString, replaceString));
+ }
+
+ public static Regex newRegexPerl(String code)
+ {
+ ensureRegex();
+ return Regex.perlCode(code);
+ }
+
+ /**
+ * Initialize Java debug logging. A representative sample -- adapt as desired.
+ */
+ public static void startJavaLogging()
+ {
+ /**
+ * @j2sIgnore
+ */
+ {
+ logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
+ "java.awt.Component", "java.awt.focus.Component",
+ "java.awt.event.Component",
+ "java.awt.focus.DefaultKeyboardFocusManager");
+ }
+ }
+
+ /**
+ * Initiate Java logging for a given class. Only for Java, not JavaScript;
+ * Allows debugging of complex event processing.
+ *
+ * @param className
+ */
+ public static void logClass(String... classNames)
+ {
+ /**
+ * @j2sIgnore
+ *
+ *
+ */
+ {
+ Logger rootLogger = Logger.getLogger("");
+ rootLogger.setLevel(Level.ALL);
+ ConsoleHandler consoleHandler = new ConsoleHandler();
+ consoleHandler.setLevel(Level.ALL);
+ for (int i = classNames.length; --i >= 0;)
+ {
+ Logger logger = Logger.getLogger(classNames[i]);
+ logger.setLevel(Level.ALL);
+ logger.addHandler(consoleHandler);
+ }
+ }
+ }
+
+ /**
+ * load a resource -- probably a core file -- if and only if a particular
+ * class has not been instantialized. We use a String here because if we used
+ * a .class object, that reference itself would simply load the class, and we
+ * want the core package to include that as well.
+ *
+ * @param resourcePath
+ * @param className
+ */
+ public static void loadStaticResource(String resourcePath,
+ String className)
+ {
+ if (isJS)
+ {
+ jsutil.loadResourceIfClassUnknown(resourcePath, className);
+ }
+ }
+
+ public static void ensureRegex()
+ {
+ if (isJS)
+ {
+ loadStaticResource("core/core_stevesoft.z.js",
+ "com.stevesoft.pat.Regex");
+ }
+ }
+
+ /**
+ * Set the "app" property of the HTML5 applet object, for example,
+ * "testApplet.app", to point to the Jalview instance. This will be the object
+ * that page developers use that is similar to the original Java applet object
+ * that was accessed via LiveConnect.
+ *
+ * @param j
+ */
+ public static void setAppClass(Object j)
+ {
+ if (isJS)
+ {
+ jsutil.setAppletAttribute("app", j);
+ }
+ }
+
+ /**
+ *
+ * If this frame ia embedded in a web page, return a known type.
+ *
+ * @param frame
+ * a JFrame or JInternalFrame
+ * @param type
+ * @return null if frame is not embedded.
+ */
+ public static Object getEmbeddedAttribute(Component frame, String type)
+ {
+ return (isJS ? jsutil.getEmbeddedAttribute(frame, type) : null);
+ }
+
+ public static void stackTrace()
+ {
+ try
+ {
+ throw new NullPointerException();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ }
+
+ public static URL getDocumentBase()
+ {
+ return (isJS ? jsutil.getDocumentBase() : null);
+ }
+
+ public static URL getCodeBase()
+ {
+ return (isJS ? jsutil.getCodeBase() : null);
+ }
+