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 swingjs.api.JSUtilI jsutil;
87 // this is ok - it's a highly embedded method in Java; the deprecation
89 // really a recommended best practice.
90 jsutil = ((JSUtilI) Class.forName("swingjs.JSUtil").newInstance());
91 } catch (InstantiationException | IllegalAccessException
92 | ClassNotFoundException e)
100 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
104 public static boolean isMac()
106 return (isMac == null
107 ? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0))
111 public static int SHORTCUT_KEY_MASK = (Platform.isMac()
112 ? KeyEvent.META_DOWN_MASK
113 : KeyEvent.CTRL_DOWN_MASK);
117 if (!GraphicsEnvironment.isHeadless())
119 // Using non-deprecated Extended key mask modifiers, but Java 8 has no
120 // getMenuShortcutKeyMaskEx method
121 Toolkit tk = Toolkit.getDefaultToolkit();
122 Method method = null;
125 method = tk.getClass().getMethod("getMenuShortcutKeyMaskEx");
126 } catch (Exception e)
129 "Could not find Toolkit method getMenuShortcutKeyMaskEx. Trying getMenuShortcutKeyMask.");
135 method = tk.getClass().getMethod("getMenuShortcutKeyMask");
136 } catch (Exception e)
139 "Could not find Toolkit method getMenuShortcutKeyMaskEx or getMenuShortcutKeyMask.");
147 method.setAccessible(true);
148 SHORTCUT_KEY_MASK = ((int) method.invoke(tk, new Object[0]));
149 } catch (Exception e)
154 if (SHORTCUT_KEY_MASK <= 0xF)
156 // shift this into the extended region (was Java 8)
157 SHORTCUT_KEY_MASK = SHORTCUT_KEY_MASK << 6;
162 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
166 public static boolean isWin()
168 return (isWin == null
169 ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0))
175 * @return true if HTML5 JavaScript
177 public static boolean isJS()
183 * sorry folks - Macs really are different
185 * BH: disabled for SwingJS -- will need to check key-press issues
187 * @return true if we do things in a special way.
189 public static boolean isAMacAndNotJS()
191 return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac);
195 * Check if we are on a Microsoft platform...
197 * @return true if we have to cope with another platform variation
199 public static boolean isWindowsAndNotJS()
201 return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
207 * @return nominal maximum command line length for this platform
209 public static int getMaxCommandLineLength()
211 // TODO: determine nominal limits for most platforms.
212 return 2046; // this is the max length for a windows NT system.
216 * Answers the input with every backslash replaced with a double backslash (an
217 * 'escaped' single backslash)
222 public static String escapeBackslashes(String s)
224 return s == null ? null : s.replace("\\", "\\\\");
228 * Answers true if the mouse event has Meta-down (Command key on Mac) or
229 * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
230 * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
231 * Mac, you can use e.isPopupTrigger().
236 public static boolean isControlDown(MouseEvent e)
238 return isControlDown(e, isMac());
242 * Overloaded version of method (to allow unit testing)
248 protected static boolean isControlDown(MouseEvent e, boolean aMac)
251 // System.out.println(e.isPopupTrigger()
252 // + " " + ((SHORTCUT_KEY_MASK & e.getModifiersEx()) != 0)
253 // + " " + e.isControlDown());
255 ? !e.isPopupTrigger()
256 && (SHORTCUT_KEY_MASK & e.getModifiersEx()) != 0
257 : e.isControlDown());
260 // BH: I don't know about that previous method. Here is what SwingJS uses.
261 // Notice the distinction in mouse events. (BUTTON3_MASK == META)
263 // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
264 // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
266 // if (id != MouseEvent.MOUSE_RELEASED)
269 //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
270 //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
272 //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
274 //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
278 // // mac, linux, unix
279 // if (id != MouseEvent.MOUSE_PRESSED)
281 // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
282 // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
283 // return rt || (ctrl && lt);
289 * Windows (not Mac, Linux, or Unix) and right button to test for the
290 * right-mouse pressed event in Windows that would have opened a menu or a
296 public static boolean isWinRightButton(MouseEvent e)
298 // was !isAMac(), but that is true also for Linux and Unix and JS,
300 return isWin() && SwingUtilities.isRightMouseButton(e);
304 * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
305 * without pressing the button.
310 public static boolean isWinMiddleButton(MouseEvent e)
312 // was !isAMac(), but that is true also for Linux and Unix and JS
313 return isWin() && SwingUtilities.isMiddleMouseButton(e);
316 public static boolean allowMnemonics()
321 public final static int TIME_RESET = 0;
323 public final static int TIME_MARK = 1;
325 public static final int TIME_SET = 2;
327 public static final int TIME_GET = 3;
329 public static long time, mark, set, duration;
334 * Platform.timeCheck(null, Platform.TIME_MARK);
338 * Platform.timeCheck("some message", Platform.TIME_MARK);
340 * reset...[set/mark]n...get
345 public static void timeCheck(String msg, int mode)
347 long t = System.currentTimeMillis();
355 System.err.println("Platform: timer reset\t\t\t" + msg);
361 // total time between set/mark points
362 duration += (t - set);
372 System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
373 + "\t" + ((t - mark) / 1000f) + "\t" + msg);
384 System.err.println("Platform: timer dur\t" + ((t - time) / 1000f)
385 + "\t" + ((duration) / 1000f) + "\t" + msg);
392 public static void cacheFileData(String path, Object data)
394 if (isJS && data != null)
396 jsutil.cachePathData(path, data);
400 public static void cacheFileData(File file)
404 byte[] data = Platform.getFileBytes(file);
408 cacheFileData(file.toString(), data);
414 public static byte[] getFileBytes(File f)
416 return (isJS && f != null ? jsutil.getBytes(f) : null);
419 public static byte[] getFileAsBytes(String fileStr)
421 if (isJS && fileStr != null)
423 byte[] bytes = (byte[]) jsutil.getFile(fileStr, false);
424 cacheFileData(fileStr, bytes);
430 public static String getFileAsString(String url)
432 if (isJS && url != null)
434 String ret = (String) jsutil.getFile(url, true);
435 cacheFileData(url, ret);
441 public static boolean setFileBytes(File f, String urlstring)
443 if (isJS && f != null && urlstring != null)
445 @SuppressWarnings("unused")
446 byte[] bytes = getFileAsBytes(urlstring);
447 jsutil.setFileBytes(f, bytes);
453 public static void addJ2SBinaryType(String ext)
457 jsutil.addBinaryFileType(ext);
462 * Encode the URI using JavaScript encodeURIComponent
465 * @return encoded value
467 public static String encodeURI(String value)
470 * @j2sNative value = encodeURIComponent(value);
476 * Open the URL using a simple window call if this is JavaScript
479 * @return true if window has been opened
481 public static boolean openURL(String url) throws IOException
496 public static String getUniqueAppletID()
498 return (isJS ? (String) jsutil.getAppletAttribute("_uniqueId") : null);
502 * Read the Info block for this applet.
507 * @return unique id for this applet
509 public static void readInfoProperties(String prefix, Properties p)
513 String id = getUniqueAppletID();
517 @SuppressWarnings("unused")
518 Object info = jsutil.getAppletAttribute("__Info");
520 * @j2sNative for (key in info) { value = info[key];
523 if (key.indexOf(prefix) == 0)
525 System.out.println("Platform id=" + id + " reading Info." + key
537 public static void setAjaxJSON(URL url)
545 public static Object parseJSON(InputStream response)
546 throws IOException, ParseException
550 return JSON.parse(response);
553 BufferedReader br = null;
556 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
557 return new JSONParser().parse(br);
565 } catch (IOException e)
573 public static Object parseJSON(String json) throws ParseException
575 return (isJS() ? JSON.parse(json) : new JSONParser().parse(json));
578 public static Object parseJSON(Reader r)
579 throws IOException, ParseException
588 return new JSONParser().parse(r);
590 // Using a file reader is not currently supported in SwingJS JavaScript
592 if (r instanceof FileReader)
594 throw new IOException(
595 "StringJS does not support FileReader parsing for JSON -- but it could...");
597 return JSON.parse(r);
601 * Dump the input stream to an output file.
605 * @throws IOException
606 * if the file cannot be created or there is a problem reading the
609 public static void streamToFile(InputStream is, File outFile)
615 jsutil.setFileBytes(outFile, is);
619 FileOutputStream fio = new FileOutputStream(outFile);
622 byte[] bb = new byte[32 * 1024];
624 while ((l = is.read(bb)) > 0)
635 * Add a known domain that implements access-control-allow-origin:*
637 * These should be reviewed periodically.
640 * for a service that is not allowing ajax
642 * @author hansonr@stolaf.edu
645 public static void addJ2SDirectDatabaseCall(String domain)
650 jsutil.addDirectDatabaseCall(domain);
653 "Platform adding known access-control-allow-origin * for domain "
660 * Allow for URL-line command arguments. Untested.
663 public static void getURLCommandArguments()
669 * Retrieve the first query field as command arguments to Jalview. Include
670 * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's
671 * __Info.args element to this value.
674 * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
675 * + "?").split("?")[1].split("#")[0]); a &&
676 * (J2S.thisApplet.__Info.args = a.split(" "));
678 * System.out.println("URL arguments: " + a);
680 } catch (Throwable t)
686 * A (case sensitive) file path comparator that ignores the difference between
693 public static boolean pathEquals(String path1, String path2)
697 return path2 == null;
703 String p1 = path1.replace('\\', '/');
704 String p2 = path2.replace('\\', '/');
705 return p1.equals(p2);
708 ///////////// JAL-3253 Applet additions //////////////
711 * Retrieve the object's embedded size from a div's style on a page if
712 * embedded in SwingJS.
715 * JFrame or JInternalFrame
716 * @param defaultWidth
717 * use -1 to return null (no default size)
718 * @param defaultHeight
719 * @return the embedded dimensions or null (no default size or not embedded)
721 public static Dimension getDimIfEmbedded(Component frame,
722 int defaultWidth, int defaultHeight)
727 d = (Dimension) getEmbeddedAttribute(frame, "dim");
729 return (d == null && defaultWidth >= 0
730 ? new Dimension(defaultWidth, defaultHeight)
735 public static Regex newRegex(String regex)
737 return newRegex(regex, null);
740 public static Regex newRegex(String searchString, String replaceString)
743 return (replaceString == null ? new Regex(searchString)
744 : new Regex(searchString, replaceString));
747 public static Regex newRegexPerl(String code)
750 return Regex.perlCode(code);
754 * Initialize Java debug logging. A representative sample -- adapt as desired.
756 public static void startJavaLogging()
762 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
763 "java.awt.Component", "java.awt.focus.Component",
764 "java.awt.event.Component",
765 "java.awt.focus.DefaultKeyboardFocusManager");
770 * Initiate Java logging for a given class. Only for Java, not JavaScript;
771 * Allows debugging of complex event processing.
775 public static void logClass(String... classNames)
783 Logger rootLogger = Logger.getLogger("");
784 rootLogger.setLevel(Level.ALL);
785 ConsoleHandler consoleHandler = new ConsoleHandler();
786 consoleHandler.setLevel(Level.ALL);
787 for (int i = classNames.length; --i >= 0;)
789 Logger logger = Logger.getLogger(classNames[i]);
790 logger.setLevel(Level.ALL);
791 logger.addHandler(consoleHandler);
797 * load a resource -- probably a core file -- if and only if a particular
798 * class has not been instantialized. We use a String here because if we used
799 * a .class object, that reference itself would simply load the class, and we
800 * want the core package to include that as well.
802 * @param resourcePath
805 public static void loadStaticResource(String resourcePath,
810 jsutil.loadResourceIfClassUnknown(resourcePath, className);
814 public static void ensureRegex()
818 loadStaticResource("core/core_stevesoft.z.js",
819 "com.stevesoft.pat.Regex");
824 * Set the "app" property of the HTML5 applet object, for example,
825 * "testApplet.app", to point to the Jalview instance. This will be the object
826 * that page developers use that is similar to the original Java applet object
827 * that was accessed via LiveConnect.
831 public static void setAppClass(Object j)
835 jsutil.setAppClass(j);
841 * If this frame is embedded in a web page, return a known type.
844 * a JFrame or JInternalFrame
846 * "name", "node", "init", "dim", or any DOM attribute, such as "id"
847 * @return null if frame is not embedded.
849 public static Object getEmbeddedAttribute(Component frame, String type)
851 return (isJS ? jsutil.getEmbeddedAttribute(frame, type) : null);
854 public static void stackTrace()
858 throw new NullPointerException();
859 } catch (Exception e)
866 public static URL getDocumentBase()
868 return (isJS ? jsutil.getDocumentBase() : null);
871 public static URL getCodeBase()
873 return (isJS ? jsutil.getCodeBase() : null);
876 public static String getUserPath(String subpath)
878 char sep = File.separatorChar;
879 return System.getProperty("user.home") + sep
880 + subpath.replace('/', sep);
884 * This method enables checking if a cached file has exceeded a certain
890 * the threshold in days
893 public static boolean isFileOlderThanThreshold(File file, int noOfDays)
897 // not meaningful in SwingJS -- this is a session-specific temp file. It
898 // doesn't have a timestamp.
901 Path filePath = file.toPath();
902 BasicFileAttributes attr;
906 attr = Files.readAttributes(filePath, BasicFileAttributes.class);
907 diffInDays = (int) ((new Date().getTime()
908 - attr.lastModifiedTime().toMillis())
909 / (1000 * 60 * 60 * 24));
910 // System.out.println("Diff in days : " + diffInDays);
911 } catch (IOException e)
915 return noOfDays <= diffInDays;
919 * Get the leading integer part of a string that begins with an integer.
922 * - the string input to process
924 * - value returned if unsuccessful
927 public static int getLeadingIntegerValue(String input, int failValue)
935 int val = /** @j2sNative 1 ? parseInt(input) : */
937 return (val == val + 0 ? val : failValue);
939 // JavaScript does not support Regex ? lookahead
940 String[] parts = input.split("(?=\\D)(?<=\\d)");
941 if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+"))
943 return Integer.valueOf(parts[0]);
948 public static Map<String, Object> getAppletInfoAsMap()
950 return (isJS ? jsutil.getAppletInfoAsMap() : null);
954 * Get the SwingJS applet ID and combine that with the frameType
957 * "alignment", "desktop", etc., or null
960 public static String getAppID(String frameType)
963 String id = Jalview.getInstance().j2sAppletID;
966 Jalview.getInstance().j2sAppletID = id = (isJS
967 ? (String) jsutil.getAppletAttribute("_id")
970 return id + (frameType == null ? "" : "-" + frameType);
974 * Option to avoid unnecessary seeking of nonexistent resources in JavaScript.
975 * Works in Java as well.
980 public static Locale getLocaleOrNone(Locale loc)
982 return (isJS && loc.getLanguage() == "en" ? new Locale("") : loc);
986 * From UrlDownloadClient; trivial in JavaScript; painful in Java.
990 * @throws IOException
992 public static void download(String urlstring, String outfile)
996 try (InputStream is = new URL(urlstring).openStream())
1000 streamToFile(is, new File(outfile));
1003 temp = Files.createTempFile(".jalview_", ".tmp");
1004 try (FileOutputStream fos = new FileOutputStream(temp.toString());
1005 ReadableByteChannel rbc = Channels.newChannel(is))
1007 fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
1008 // copy tempfile to outfile once our download completes
1009 // incase something goes wrong
1010 Files.copy(temp, Paths.get(outfile),
1011 StandardCopyOption.REPLACE_EXISTING);
1013 } catch (IOException e)
1022 Files.deleteIfExists(temp);
1024 } catch (IOException e)
1026 System.out.println("Exception while deleting download temp file: "