/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.util; import java.awt.Component; import java.awt.Dimension; import java.awt.GraphicsEnvironment; import java.awt.Toolkit; import java.awt.event.KeyEvent; import java.awt.event.MouseEvent; import java.io.BufferedReader; import java.io.File; import java.io.FileOutputStream; import java.io.FileReader; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; import java.io.Reader; import java.lang.reflect.Method; import java.net.URL; import java.nio.channels.Channels; import java.nio.channels.ReadableByteChannel; import java.nio.file.Files; import java.nio.file.Path; import java.nio.file.Paths; import java.nio.file.StandardCopyOption; import java.nio.file.attribute.BasicFileAttributes; import java.util.Date; import java.util.Locale; import java.util.Map; import java.util.Properties; import java.util.logging.ConsoleHandler; import java.util.logging.Level; import java.util.logging.Logger; import javax.swing.SwingUtilities; import org.json.simple.parser.JSONParser; import org.json.simple.parser.ParseException; import com.stevesoft.pat.Regex; import jalview.bin.Jalview; import jalview.javascript.json.JSON; import swingjs.api.JSUtilI; /** * System platform information used by Applet and Application * * @author Jim Procter */ public class Platform { private static boolean isJS = /** @j2sNative true || */ false; private static Boolean isNoJSMac = null, isNoJSWin = null, isMac = null, isWin = null; private static Boolean isHeadless = null; private static swingjs.api.JSUtilI jsutil; static { if (isJS) { try { // this is ok - it's a highly embedded method in Java; the deprecation // is // really a recommended best practice. jsutil = ((JSUtilI) Class.forName("swingjs.JSUtil").newInstance()); } catch (InstantiationException | IllegalAccessException | ClassNotFoundException e) { e.printStackTrace(); } } } // private static Boolean isHeadless = null; /** * added to group mouse events into Windows and nonWindows (mac, unix, linux) * * @return */ public static boolean isMac() { return (isMac == null ? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0)) : isMac); } public static int SHORTCUT_KEY_MASK = (Platform.isMac() ? KeyEvent.META_DOWN_MASK : KeyEvent.CTRL_DOWN_MASK); static { // Using non-deprecated Extended key mask modifiers, but Java 8 has no // getMenuShortcutKeyMaskEx method Toolkit tk = Toolkit.getDefaultToolkit(); Method method = null; try { method = tk.getClass().getMethod("getMenuShortcutKeyMaskEx"); } catch (NoSuchMethodException e) { System.err.println( "Could not find Toolkit method getMenuShortcutKeyMaskEx. Trying getMenuShortcutKeyMask."); } if (method == null) { try { method = tk.getClass().getMethod("getMenuShortcutKeyMask"); } catch (NoSuchMethodException e) { System.err.println( "Could not find Toolkit method getMenuShortcutKeyMaskEx or getMenuShortcutKeyMask."); e.printStackTrace(); } } if (method != null) { try { method.setAccessible(true); SHORTCUT_KEY_MASK = ((int) method.invoke(tk, new Object[0])); } catch (Exception e) { e.printStackTrace(); } } if (SHORTCUT_KEY_MASK <= 0xF) { // shift this into the extended region (was Java 8) SHORTCUT_KEY_MASK = SHORTCUT_KEY_MASK << 6; } } } /** * added to group mouse events into Windows and nonWindows (mac, unix, linux) * * @return */ public static boolean isWin() { return (isWin == null ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0)) : isWin); } /** * * @return true if HTML5 JavaScript */ public static boolean isJS() { return isJS; } /** * sorry folks - Macs really are different * * BH: disabled for SwingJS -- will need to check key-press issues * * @return true if we do things in a special way. */ public static boolean isAMacAndNotJS() { return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac); } /** * Check if we are on a Microsoft plaform... * * @return true if we have to cope with another platform variation */ public static boolean isWindowsAndNotJS() { return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin); } /** * * @return true if we are running in non-interactive no UI mode */ public static boolean isHeadless() { if (isHeadless == null) { isHeadless = "true".equals(System.getProperty("java.awt.headless")); } return isHeadless; } /** * * @return nominal maximum command line length for this platform */ public static int getMaxCommandLineLength() { // TODO: determine nominal limits for most platforms. return 2046; // this is the max length for a windows NT system. } /** * Answers the input with every backslash replaced with a double backslash (an * 'escaped' single backslash) * * @param s * @return */ public static String escapeBackslashes(String s) { return s == null ? null : s.replace("\\", "\\\\"); } /** * Answers true if the mouse event has Meta-down (Command key on Mac) or * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on * Mac, you can use e.isPopupTrigger(). * * @param e * @return */ public static boolean isControlDown(MouseEvent e) { return isControlDown(e, isMac()); } /** * Overloaded version of method (to allow unit testing) * * @param e * @param aMac * @return */ protected static boolean isControlDown(MouseEvent e, boolean aMac) { // // System.out.println(e.isPopupTrigger() // + " " + ((SHORTCUT_KEY_MASK & e.getModifiersEx()) != 0) // + " " + e.isControlDown()); return (aMac ? !e.isPopupTrigger() && (SHORTCUT_KEY_MASK & e.getModifiersEx()) != 0 : e.isControlDown()); } // BH: I don't know about that previous method. Here is what SwingJS uses. // Notice the distinction in mouse events. (BUTTON3_MASK == META) // // private static boolean isPopupTrigger(int id, int mods, boolean isWin) { // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0); // if (isWin) { // if (id != MouseEvent.MOUSE_RELEASED) // return false; //// //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both. //// //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue, // because //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers. //// // return rt; // } else { // // mac, linux, unix // if (id != MouseEvent.MOUSE_PRESSED) // return false; // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0); // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0); // return rt || (ctrl && lt); // } // } // /** * Windows (not Mac, Linux, or Unix) and right button to test for the * right-mouse pressed event in Windows that would have opened a menu or a * Mac. * * @param e * @return */ public static boolean isWinRightButton(MouseEvent e) { // was !isAMac(), but that is true also for Linux and Unix and JS, return isWin() && SwingUtilities.isRightMouseButton(e); } /** * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling * without pressing the button. * * @param e * @return */ public static boolean isWinMiddleButton(MouseEvent e) { // was !isAMac(), but that is true also for Linux and Unix and JS return isWin() && SwingUtilities.isMiddleMouseButton(e); } public static boolean allowMnemonics() { return !isMac(); } public final static int TIME_RESET = 0; public final static int TIME_MARK = 1; public static final int TIME_SET = 2; public static final int TIME_GET = 3; public static long time, mark, set, duration; /** * typical usage: * * Platform.timeCheck(null, Platform.TIME_MARK); * * ... * * Platform.timeCheck("some message", Platform.TIME_MARK); * * reset...[set/mark]n...get * * @param msg * @param mode */ public static void timeCheck(String msg, int mode) { long t = System.currentTimeMillis(); switch (mode) { case TIME_RESET: time = mark = t; duration = 0; if (msg != null) { System.err.println("Platform: timer reset\t\t\t" + msg); } break; case TIME_MARK: if (set > 0) { // total time between set/mark points duration += (t - set); } else { if (time == 0) { time = mark = t; } if (msg != null) { System.err.println("Platform: timer mark\t" + ((t - time) / 1000f) + "\t" + ((t - mark) / 1000f) + "\t" + msg); } mark = t; } break; case TIME_SET: set = t; break; case TIME_GET: if (msg != null) { System.err.println("Platform: timer dur\t" + ((t - time) / 1000f) + "\t" + ((duration) / 1000f) + "\t" + msg); } set = 0; break; } } public static void cacheFileData(String path, Object data) { if (isJS && data != null) { jsutil.cachePathData(path, data); } } public static void cacheFileData(File file) { if (isJS) { byte[] data = Platform.getFileBytes(file); { if (data != null) { cacheFileData(file.toString(), data); } } } } public static byte[] getFileBytes(File f) { return (isJS && f != null ? jsutil.getBytes(f) : null); } public static byte[] getFileAsBytes(String fileStr) { if (isJS && fileStr != null) { byte[] bytes = (byte[]) jsutil.getFile(fileStr, false); cacheFileData(fileStr, bytes); return bytes; } return null; } public static String getFileAsString(String url) { if (isJS && url != null) { String ret = (String) jsutil.getFile(url, true); cacheFileData(url, ret); return ret; } return null; } public static boolean setFileBytes(File f, String urlstring) { if (isJS && f != null && urlstring != null) { @SuppressWarnings("unused") byte[] bytes = getFileAsBytes(urlstring); jsutil.setFileBytes(f, bytes); return true; } return false; } public static void addJ2SBinaryType(String ext) { if (isJS) { jsutil.addBinaryFileType(ext); } } /** * Encode the URI using JavaScript encodeURIComponent * * @param value * @return encoded value */ public static String encodeURI(String value) { /** * @j2sNative value = encodeURIComponent(value); */ return value; } /** * Open the URL using a simple window call if this is JavaScript * * @param url * @return true if window has been opened */ public static boolean openURL(String url) throws IOException { if (!isJS()) { return false; } /** * @j2sNative * * * window.open(url); */ return true; } public static String getUniqueAppletID() { return (isJS ? (String) jsutil.getAppletAttribute("_uniqueId") : null); } /** * Read the Info block for this applet. * * @param prefix * "jalview_" * @param p * @return unique id for this applet */ public static void readInfoProperties(String prefix, Properties p) { if (isJS) { String id = getUniqueAppletID(); String key = ""; String value = ""; @SuppressWarnings("unused") Object info = jsutil.getAppletAttribute("__Info"); /** * @j2sNative for (key in info) { value = info[key]; */ if (key.indexOf(prefix) == 0) { System.out.println("Platform id=" + id + " reading Info." + key + " = " + value); p.put(key, value); } /** * @j2sNative } */ } } public static void setAjaxJSON(URL url) { if (isJS()) { JSON.setAjax(url); } } public static Object parseJSON(InputStream response) throws IOException, ParseException { if (isJS()) { return JSON.parse(response); } BufferedReader br = null; try { br = new BufferedReader(new InputStreamReader(response, "UTF-8")); return new JSONParser().parse(br); } finally { if (br != null) { try { br.close(); } catch (IOException e) { // ignore } } } } 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); } } /** * Allow for URL-line command arguments. Untested. * */ public static void getURLCommandArguments() { try { /** * 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(" ")); * * System.out.println("URL arguments: " + a); */ } catch (Throwable t) { } } /** * 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.setAppClass(j); } } /** * * If this frame is embedded in a web page, return a known type. * * @param frame * a JFrame or JInternalFrame * @param type "name", "node", "init", "dim", or any DOM attribute, such as "id" * @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); } public static String getUserPath(String subpath) { char sep = File.separatorChar; return System.getProperty("user.home") + sep + subpath.replace('/', sep); } /** * This method enables checking if a cached file has exceeded a certain * threshold(in days) * * @param file * the cached file * @param noOfDays * the threshold in days * @return */ public static boolean isFileOlderThanThreshold(File file, int noOfDays) { if (isJS()) { // not meaningful in SwingJS -- this is a session-specific temp file. It // doesn't have a timestamp. return false; } Path filePath = file.toPath(); BasicFileAttributes attr; int diffInDays = 0; try { attr = Files.readAttributes(filePath, BasicFileAttributes.class); diffInDays = (int) ((new Date().getTime() - attr.lastModifiedTime().toMillis()) / (1000 * 60 * 60 * 24)); // System.out.println("Diff in days : " + diffInDays); } catch (IOException e) { e.printStackTrace(); } return noOfDays <= diffInDays; } /** * Get the leading integer part of a string that begins with an integer. * * @param input * - the string input to process * @param failValue * - value returned if unsuccessful * @return */ public static int getLeadingIntegerValue(String input, int failValue) { if (input == null) { return failValue; } if (isJS) { int val = /** @j2sNative 1 ? parseInt(input) : */ 0; return (val == val + 0 ? val : failValue); } // JavaScript does not support Regex ? lookahead String[] parts = input.split("(?=\\D)(?<=\\d)"); if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+")) { return Integer.valueOf(parts[0]); } return failValue; } public static Map getAppletInfoAsMap() { return (isJS ? jsutil.getAppletInfoAsMap() : null); } /** * Get the SwingJS applet ID and combine that with the frameType * * @param frameType * "alignment", "desktop", etc., or null * @return */ public static String getAppID(String frameType) { String id = Jalview.getInstance().j2sAppletID; if (id == null) { Jalview.getInstance().j2sAppletID = id = (isJS ? (String) jsutil .getAppletAttribute("_id") : "jalview"); } return id + (frameType == null ? "" : "-" + frameType); } /** * Option to avoid unnecessary seeking of nonexistent resources in JavaScript. * Works in Java as well. * * @param loc * @return */ public static Locale getLocaleOrNone(Locale loc) { return (isJS && loc.getLanguage() == "en" ? new Locale("") : loc); } /** * From UrlDownloadClient; trivial in JavaScript; painful in Java. * * @param urlstring * @param outfile * @throws IOException */ public static void download(String urlstring, String outfile) throws IOException { Path temp = null; try (InputStream is = new URL(urlstring).openStream()) { if (isJS) { // so much easier! streamToFile(is, new File(outfile)); return; } temp = Files.createTempFile(".jalview_", ".tmp"); try (FileOutputStream fos = new FileOutputStream(temp.toString()); ReadableByteChannel rbc = Channels.newChannel(is)) { fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE); // copy tempfile to outfile once our download completes // incase something goes wrong Files.copy(temp, Paths.get(outfile), StandardCopyOption.REPLACE_EXISTING); } } catch (IOException e) { throw e; } finally { try { if (temp != null) { Files.deleteIfExists(temp); } } catch (IOException e) { System.out.println("Exception while deleting download temp file: " + e.getMessage()); } } } }