2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import java.awt.Component;
24 import java.awt.Dimension;
25 import java.awt.GraphicsEnvironment;
26 import java.awt.Toolkit;
27 import java.awt.event.KeyEvent;
28 import java.awt.event.MouseEvent;
29 import java.io.BufferedReader;
31 import java.io.FileOutputStream;
32 import java.io.FileReader;
33 import java.io.IOException;
34 import java.io.InputStream;
35 import java.io.InputStreamReader;
36 import java.io.Reader;
37 import java.lang.reflect.Method;
39 import java.nio.channels.Channels;
40 import java.nio.channels.ReadableByteChannel;
41 import java.nio.file.Files;
42 import java.nio.file.Path;
43 import java.nio.file.Paths;
44 import java.nio.file.StandardCopyOption;
45 import java.nio.file.attribute.BasicFileAttributes;
46 import java.util.Date;
47 import java.util.Locale;
49 import java.util.Properties;
50 import java.util.logging.ConsoleHandler;
51 import java.util.logging.Level;
52 import java.util.logging.Logger;
54 import javax.swing.SwingUtilities;
56 import org.json.simple.parser.JSONParser;
57 import org.json.simple.parser.ParseException;
59 import com.stevesoft.pat.Regex;
61 import jalview.bin.Jalview;
62 import jalview.javascript.json.JSON;
63 import swingjs.api.JSUtilI;
66 * System platform information used by Applet and Application
73 private static boolean isJS = /** @j2sNative true || */
76 private static Boolean isNoJSMac = null, isNoJSWin = null, isMac = null,
79 private static Boolean isHeadless = null;
81 private static swingjs.api.JSUtilI jsutil;
89 // this is ok - it's a highly embedded method in Java; the deprecation
91 // really a recommended best practice.
92 jsutil = ((JSUtilI) Class.forName("swingjs.JSUtil").newInstance());
93 } catch (InstantiationException | IllegalAccessException
94 | ClassNotFoundException e)
100 // private static Boolean isHeadless = null;
103 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
107 public static boolean isMac()
109 return (isMac == null
110 ? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0))
114 public static int SHORTCUT_KEY_MASK = (Platform.isMac() ? KeyEvent.META_DOWN_MASK : KeyEvent.CTRL_DOWN_MASK);
118 if (!GraphicsEnvironment.isHeadless())
123 Toolkit tk = Toolkit.getDefaultToolkit();
124 Method method = tk.getClass().getMethod("getMenuShortcutKeyMaskEx");
126 method = tk.getClass().getMethod("getMenuShortcutKeyMask");
127 SHORTCUT_KEY_MASK = ((int) method.invoke(tk, new Object[0]));
128 if (SHORTCUT_KEY_MASK <= 0xF)
130 // shift this into the extended region (was Java 8)
131 SHORTCUT_KEY_MASK = SHORTCUT_KEY_MASK << 6;
133 } catch (Exception e)
141 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
145 public static boolean isWin()
147 return (isWin == null
148 ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0))
154 * @return true if HTML5 JavaScript
156 public static boolean isJS()
162 * sorry folks - Macs really are different
164 * BH: disabled for SwingJS -- will need to check key-press issues
166 * @return true if we do things in a special way.
168 public static boolean isAMacAndNotJS()
170 return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac);
174 * Check if we are on a Microsoft plaform...
176 * @return true if we have to cope with another platform variation
178 public static boolean isWindowsAndNotJS()
180 return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
185 * @return true if we are running in non-interactive no UI mode
187 public static boolean isHeadless()
189 if (isHeadless == null)
191 isHeadless = "true".equals(System.getProperty("java.awt.headless"));
198 * @return nominal maximum command line length for this platform
200 public static int getMaxCommandLineLength()
202 // TODO: determine nominal limits for most platforms.
203 return 2046; // this is the max length for a windows NT system.
207 * Answers the input with every backslash replaced with a double backslash (an
208 * 'escaped' single backslash)
213 public static String escapeBackslashes(String s)
215 return s == null ? null : s.replace("\\", "\\\\");
219 * Answers true if the mouse event has Meta-down (Command key on Mac) or
220 * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
221 * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
222 * Mac, you can use e.isPopupTrigger().
227 public static boolean isControlDown(MouseEvent e)
229 return isControlDown(e, isMac());
233 * Overloaded version of method (to allow unit testing)
239 protected static boolean isControlDown(MouseEvent e, boolean aMac)
242 System.out.println(e.isPopupTrigger()
243 + " " + ((SHORTCUT_KEY_MASK & e.getModifiersEx()) != 0)
244 + " " + e.isControlDown());
245 return (aMac ? !e.isPopupTrigger()
246 && (SHORTCUT_KEY_MASK & e.getModifiersEx()) != 0
247 : e.isControlDown());
250 // BH: I don't know about that previous method. Here is what SwingJS uses.
251 // Notice the distinction in mouse events. (BUTTON3_MASK == META)
253 // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
254 // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
256 // if (id != MouseEvent.MOUSE_RELEASED)
259 //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
260 //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
262 //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
264 //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
268 // // mac, linux, unix
269 // if (id != MouseEvent.MOUSE_PRESSED)
271 // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
272 // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
273 // return rt || (ctrl && lt);
279 * Windows (not Mac, Linux, or Unix) and right button to test for the
280 * right-mouse pressed event in Windows that would have opened a menu or a
286 public static boolean isWinRightButton(MouseEvent e)
288 // was !isAMac(), but that is true also for Linux and Unix and JS,
290 return isWin() && SwingUtilities.isRightMouseButton(e);
294 * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
295 * without pressing the button.
300 public static boolean isWinMiddleButton(MouseEvent e)
302 // was !isAMac(), but that is true also for Linux and Unix and JS
303 return isWin() && SwingUtilities.isMiddleMouseButton(e);
306 public static boolean allowMnemonics()
311 public final static int TIME_RESET = 0;
313 public final static int TIME_MARK = 1;
315 public static final int TIME_SET = 2;
317 public static final int TIME_GET = 3;
319 public static long time, mark, set, duration;
324 * Platform.timeCheck(null, Platform.TIME_MARK);
328 * Platform.timeCheck("some message", Platform.TIME_MARK);
330 * reset...[set/mark]n...get
335 public static void timeCheck(String msg, int mode)
337 long t = System.currentTimeMillis();
345 System.err.println("Platform: timer reset\t\t\t" + msg);
351 // total time between set/mark points
352 duration += (t - set);
362 System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
363 + "\t" + ((t - mark) / 1000f) + "\t" + msg);
374 System.err.println("Platform: timer dur\t" + ((t - time) / 1000f)
375 + "\t" + ((duration) / 1000f) + "\t" + msg);
382 public static void cacheFileData(String path, Object data)
384 if (isJS && data != null)
386 jsutil.cachePathData(path, data);
390 public static void cacheFileData(File file)
394 byte[] data = Platform.getFileBytes(file);
398 cacheFileData(file.toString(), data);
404 public static byte[] getFileBytes(File f)
406 return (isJS && f != null ? jsutil.getBytes(f) : null);
409 public static byte[] getFileAsBytes(String fileStr)
411 if (isJS && fileStr != null)
413 byte[] bytes = (byte[]) jsutil.getFile(fileStr, false);
414 cacheFileData(fileStr, bytes);
420 public static String getFileAsString(String url)
422 if (isJS && url != null)
424 String ret = (String) jsutil.getFile(url, true);
425 cacheFileData(url, ret);
431 public static boolean setFileBytes(File f, String urlstring)
433 if (isJS && f != null && urlstring != null)
435 @SuppressWarnings("unused")
436 byte[] bytes = getFileAsBytes(urlstring);
437 jsutil.setFileBytes(f, bytes);
443 public static void addJ2SBinaryType(String ext)
447 jsutil.addBinaryFileType(ext);
452 * Encode the URI using JavaScript encodeURIComponent
455 * @return encoded value
457 public static String encodeURI(String value)
460 * @j2sNative value = encodeURIComponent(value);
466 * Open the URL using a simple window call if this is JavaScript
469 * @return true if window has been opened
471 public static boolean openURL(String url) throws IOException
486 public static String getUniqueAppletID()
488 return (isJS ? (String) jsutil.getAppletAttribute("_uniqueId") : null);
492 * Read the Info block for this applet.
497 * @return unique id for this applet
499 public static void readInfoProperties(String prefix, Properties p)
503 String id = getUniqueAppletID();
507 @SuppressWarnings("unused")
508 Object info = jsutil.getAppletAttribute("__Info");
510 * @j2sNative for (key in info) { value = info[key];
513 if (key.indexOf(prefix) == 0)
515 System.out.println("Platform id=" + id + " reading Info." + key
527 public static void setAjaxJSON(URL url)
535 public static Object parseJSON(InputStream response)
536 throws IOException, ParseException
540 return JSON.parse(response);
543 BufferedReader br = null;
546 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
547 return new JSONParser().parse(br);
555 } catch (IOException e)
563 public static Object parseJSON(String json) throws ParseException
565 return (isJS() ? JSON.parse(json) : new JSONParser().parse(json));
568 public static Object parseJSON(Reader r)
569 throws IOException, ParseException
578 return new JSONParser().parse(r);
580 // Using a file reader is not currently supported in SwingJS JavaScript
582 if (r instanceof FileReader)
584 throw new IOException(
585 "StringJS does not support FileReader parsing for JSON -- but it could...");
587 return JSON.parse(r);
591 * Dump the input stream to an output file.
595 * @throws IOException
596 * if the file cannot be created or there is a problem reading the
599 public static void streamToFile(InputStream is, File outFile)
605 jsutil.setFileBytes(outFile, is);
609 FileOutputStream fio = new FileOutputStream(outFile);
612 byte[] bb = new byte[32 * 1024];
614 while ((l = is.read(bb)) > 0)
625 * Add a known domain that implements access-control-allow-origin:*
627 * These should be reviewed periodically.
630 * for a service that is not allowing ajax
632 * @author hansonr@stolaf.edu
635 public static void addJ2SDirectDatabaseCall(String domain)
640 jsutil.addDirectDatabaseCall(domain);
643 "Platform adding known access-control-allow-origin * for domain "
650 * Allow for URL-line command arguments. Untested.
653 public static void getURLCommandArguments()
658 * Retrieve the first query field as command arguments to Jalview. Include
659 * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
660 * element to this value.
663 * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
664 * + "?").split("?")[1].split("#")[0]); a &&
665 * (J2S.thisApplet.__Info.args = a.split(" "));
667 * System.out.println("URL arguments: " + a);
669 } catch (Throwable t) {
674 * A (case sensitive) file path comparator that ignores the difference between
681 public static boolean pathEquals(String path1, String path2)
685 return path2 == null;
691 String p1 = path1.replace('\\', '/');
692 String p2 = path2.replace('\\', '/');
693 return p1.equals(p2);
696 ///////////// JAL-3253 Applet additions //////////////
699 * Retrieve the object's embedded size from a div's style on a page if
700 * embedded in SwingJS.
703 * JFrame or JInternalFrame
704 * @param defaultWidth
705 * use -1 to return null (no default size)
706 * @param defaultHeight
707 * @return the embedded dimensions or null (no default size or not embedded)
709 public static Dimension getDimIfEmbedded(Component frame,
710 int defaultWidth, int defaultHeight)
715 d = (Dimension) getEmbeddedAttribute(frame, "dim");
717 return (d == null && defaultWidth >= 0
718 ? new Dimension(defaultWidth, defaultHeight)
723 public static Regex newRegex(String regex)
725 return newRegex(regex, null);
728 public static Regex newRegex(String searchString, String replaceString)
731 return (replaceString == null ? new Regex(searchString)
732 : new Regex(searchString, replaceString));
735 public static Regex newRegexPerl(String code)
738 return Regex.perlCode(code);
742 * Initialize Java debug logging. A representative sample -- adapt as desired.
744 public static void startJavaLogging()
750 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
751 "java.awt.Component", "java.awt.focus.Component",
752 "java.awt.event.Component",
753 "java.awt.focus.DefaultKeyboardFocusManager");
758 * Initiate Java logging for a given class. Only for Java, not JavaScript;
759 * Allows debugging of complex event processing.
763 public static void logClass(String... classNames)
771 Logger rootLogger = Logger.getLogger("");
772 rootLogger.setLevel(Level.ALL);
773 ConsoleHandler consoleHandler = new ConsoleHandler();
774 consoleHandler.setLevel(Level.ALL);
775 for (int i = classNames.length; --i >= 0;)
777 Logger logger = Logger.getLogger(classNames[i]);
778 logger.setLevel(Level.ALL);
779 logger.addHandler(consoleHandler);
785 * load a resource -- probably a core file -- if and only if a particular
786 * class has not been instantialized. We use a String here because if we used
787 * a .class object, that reference itself would simply load the class, and we
788 * want the core package to include that as well.
790 * @param resourcePath
793 public static void loadStaticResource(String resourcePath,
798 jsutil.loadResourceIfClassUnknown(resourcePath, className);
802 public static void ensureRegex()
806 loadStaticResource("core/core_stevesoft.z.js",
807 "com.stevesoft.pat.Regex");
812 * Set the "app" property of the HTML5 applet object, for example,
813 * "testApplet.app", to point to the Jalview instance. This will be the object
814 * that page developers use that is similar to the original Java applet object
815 * that was accessed via LiveConnect.
819 public static void setAppClass(Object j)
823 jsutil.setAppClass(j);
829 * If this frame is embedded in a web page, return a known type.
832 * a JFrame or JInternalFrame
833 * @param type "name", "node", "init", "dim", or any DOM attribute, such as "id"
834 * @return null if frame is not embedded.
836 public static Object getEmbeddedAttribute(Component frame, String type)
838 return (isJS ? jsutil.getEmbeddedAttribute(frame, type) : null);
841 public static void stackTrace()
845 throw new NullPointerException();
846 } catch (Exception e)
853 public static URL getDocumentBase()
855 return (isJS ? jsutil.getDocumentBase() : null);
858 public static URL getCodeBase()
860 return (isJS ? jsutil.getCodeBase() : null);
863 public static String getUserPath(String subpath)
865 char sep = File.separatorChar;
866 return System.getProperty("user.home") + sep
867 + subpath.replace('/', sep);
871 * This method enables checking if a cached file has exceeded a certain
877 * the threshold in days
880 public static boolean isFileOlderThanThreshold(File file, int noOfDays)
884 // not meaningful in SwingJS -- this is a session-specific temp file. It
885 // doesn't have a timestamp.
888 Path filePath = file.toPath();
889 BasicFileAttributes attr;
893 attr = Files.readAttributes(filePath, BasicFileAttributes.class);
894 diffInDays = (int) ((new Date().getTime()
895 - attr.lastModifiedTime().toMillis())
896 / (1000 * 60 * 60 * 24));
897 // System.out.println("Diff in days : " + diffInDays);
898 } catch (IOException e)
902 return noOfDays <= diffInDays;
906 * Get the leading integer part of a string that begins with an integer.
909 * - the string input to process
911 * - value returned if unsuccessful
914 public static int getLeadingIntegerValue(String input, int failValue)
922 int val = /** @j2sNative 1 ? parseInt(input) : */
924 return (val == val + 0 ? val : failValue);
926 // JavaScript does not support Regex ? lookahead
927 String[] parts = input.split("(?=\\D)(?<=\\d)");
928 if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+"))
930 return Integer.valueOf(parts[0]);
935 public static Map<String, Object> getAppletInfoAsMap()
937 return (isJS ? jsutil.getAppletInfoAsMap() : null);
941 * Get the SwingJS applet ID and combine that with the frameType
944 * "alignment", "desktop", etc., or null
947 public static String getAppID(String frameType)
950 String id = Jalview.getInstance().j2sAppletID;
953 Jalview.getInstance().j2sAppletID = id = (isJS ? (String) jsutil
954 .getAppletAttribute("_id") : "jalview");
956 return id + (frameType == null ? "" : "-" + frameType);
961 * Option to avoid unnecessary seeking of nonexistent resources in JavaScript.
962 * Works in Java as well.
967 public static Locale getLocaleOrNone(Locale loc)
969 return (isJS && loc.getLanguage() == "en" ? new Locale("") : loc);
973 * From UrlDownloadClient; trivial in JavaScript; painful in Java.
977 * @throws IOException
979 public static void download(String urlstring, String outfile)
983 try (InputStream is = new URL(urlstring).openStream())
987 streamToFile(is, new File(outfile));
990 temp = Files.createTempFile(".jalview_", ".tmp");
991 try (FileOutputStream fos = new FileOutputStream(temp.toString());
992 ReadableByteChannel rbc = Channels.newChannel(is))
994 fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
995 // copy tempfile to outfile once our download completes
996 // incase something goes wrong
997 Files.copy(temp, Paths.get(outfile),
998 StandardCopyOption.REPLACE_EXISTING);
1000 } catch (IOException e)
1009 Files.deleteIfExists(temp);
1011 } catch (IOException e)
1013 System.out.println("Exception while deleting download temp file: "