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.Toolkit;
26 import java.awt.event.MouseEvent;
27 import java.io.BufferedReader;
29 import java.io.FileOutputStream;
30 import java.io.FileReader;
31 import java.io.IOException;
32 import java.io.InputStream;
33 import java.io.InputStreamReader;
34 import java.io.Reader;
36 import java.nio.file.Files;
37 import java.nio.file.Path;
38 import java.nio.file.attribute.BasicFileAttributes;
39 import java.util.Date;
40 import java.util.Properties;
41 import java.util.logging.ConsoleHandler;
42 import java.util.logging.Level;
43 import java.util.logging.Logger;
45 import javax.swing.SwingUtilities;
47 import org.json.simple.parser.JSONParser;
48 import org.json.simple.parser.ParseException;
50 import com.stevesoft.pat.Regex;
52 import jalview.javascript.json.JSON;
53 import swingjs.api.JSUtilI;
56 * System platform information used by Applet and Application
63 private static boolean isJS = /** @j2sNative true || */
66 private static Boolean isNoJSMac = null, isNoJSWin = null, isMac = null,
69 private static Boolean isHeadless = null;
71 private static swingjs.api.JSUtilI jsutil;
77 // this is ok - it's a highly embedded method in Java; the deprecation is
78 // really a recommended best practice.
79 jsutil = ((JSUtilI) Class.forName("swingjs.JSUtil").newInstance());
80 } catch (InstantiationException | IllegalAccessException
81 | ClassNotFoundException e)
87 // private static Boolean isHeadless = null;
90 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
94 public static boolean isMac()
97 ? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0))
102 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
106 public static boolean isWin()
108 return (isWin == null
109 ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0))
115 * @return true if HTML5 JavaScript
117 public static boolean isJS()
123 * sorry folks - Macs really are different
125 * BH: disabled for SwingJS -- will need to check key-press issues
127 * @return true if we do things in a special way.
129 public static boolean isAMacAndNotJS()
131 return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac);
135 * Check if we are on a Microsoft plaform...
137 * @return true if we have to cope with another platform variation
139 public static boolean isWindowsAndNotJS()
141 return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
146 * @return true if we are running in non-interactive no UI mode
148 public static boolean isHeadless()
150 if (isHeadless == null)
152 isHeadless = "true".equals(System.getProperty("java.awt.headless"));
159 * @return nominal maximum command line length for this platform
161 public static int getMaxCommandLineLength()
163 // TODO: determine nominal limits for most platforms.
164 return 2046; // this is the max length for a windows NT system.
168 * Answers the input with every backslash replaced with a double backslash (an
169 * 'escaped' single backslash)
174 public static String escapeBackslashes(String s)
176 return s == null ? null : s.replace("\\", "\\\\");
180 * Answers true if the mouse event has Meta-down (Command key on Mac) or
181 * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
182 * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
183 * Mac, you can use e.isPopupTrigger().
188 public static boolean isControlDown(MouseEvent e)
190 return isControlDown(e, isMac());
194 * Overloaded version of method (to allow unit testing)
200 protected static boolean isControlDown(MouseEvent e, boolean aMac)
204 return e.isControlDown();
206 // Jalview 2.11 code below: above is as amended for JalviewJS
208 // * answer false for right mouse button
210 // if (e.isPopupTrigger())
215 // (jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() //
216 // .getMenuShortcutKeyMaskEx()
217 // & jalview.util.ShortcutKeyMaskExWrapper
218 // .getModifiersEx(e)) != 0; // getModifiers()) != 0;
220 // answer false for right mouse button
221 // shortcut key will be META for a Mac
222 return !e.isPopupTrigger()
223 && (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
224 & e.getModifiers()) != 0;
225 // could we use e.isMetaDown() here?
228 // BH: I don't know about that previous method. Here is what SwingJS uses.
229 // Notice the distinction in mouse events. (BUTTON3_MASK == META)
231 // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
232 // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
234 // if (id != MouseEvent.MOUSE_RELEASED)
237 //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
238 //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
240 //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
242 //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
246 // // mac, linux, unix
247 // if (id != MouseEvent.MOUSE_PRESSED)
249 // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
250 // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
251 // return rt || (ctrl && lt);
257 * Windows (not Mac, Linux, or Unix) and right button to test for the
258 * right-mouse pressed event in Windows that would have opened a menu or a
264 public static boolean isWinRightButton(MouseEvent e)
266 // was !isAMac(), but that is true also for Linux and Unix and JS,
268 return isWin() && SwingUtilities.isRightMouseButton(e);
272 * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
273 * without pressing the button.
278 public static boolean isWinMiddleButton(MouseEvent e)
280 // was !isAMac(), but that is true also for Linux and Unix and JS
281 return isWin() && SwingUtilities.isMiddleMouseButton(e);
284 public static boolean allowMnemonics()
289 public final static int TIME_RESET = 0;
291 public final static int TIME_MARK = 1;
293 public static final int TIME_SET = 2;
295 public static final int TIME_GET = 3;
297 public static long time, mark, set, duration;
302 * Platform.timeCheck(null, Platform.TIME_MARK);
306 * Platform.timeCheck("some message", Platform.TIME_MARK);
308 * reset...[set/mark]n...get
313 public static void timeCheck(String msg, int mode)
315 long t = System.currentTimeMillis();
323 System.err.println("Platform: timer reset\t\t\t" + msg);
329 // total time between set/mark points
330 duration += (t - set);
340 System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
341 + "\t" + ((t - mark) / 1000f) + "\t" + msg);
352 System.err.println("Platform: timer dur\t" + ((t - time) / 1000f)
353 + "\t" + ((duration) / 1000f) + "\t" + msg);
360 public static void cacheFileData(String path, Object data)
362 if (isJS && data != null)
364 jsutil.cachePathData(path, data);
369 public static void cacheFileData(File file)
373 byte[] data = Platform.getFileBytes(file);
377 cacheFileData(file.toString(), data);
383 public static byte[] getFileBytes(File f)
385 return (isJS && f != null ? jsutil.getBytes(f) : null);
388 public static byte[] getFileAsBytes(String fileStr)
390 if (isJS && fileStr != null)
392 byte[] bytes = (byte[]) jsutil.getFile(fileStr, false);
393 cacheFileData(fileStr, bytes);
399 public static String getFileAsString(String url)
401 if (isJS && url != null)
403 String ret = (String) jsutil.getFile(url, true);
404 cacheFileData(url, ret);
410 public static boolean setFileBytes(File f, String urlstring)
412 if (isJS && f != null && urlstring != null)
414 @SuppressWarnings("unused")
415 byte[] bytes = getFileAsBytes(urlstring);
416 jsutil.setFileBytes(f, bytes);
423 public static void addJ2SBinaryType(String ext)
427 jsutil.addBinaryFileType(ext);
432 * Encode the URI using JavaScript encodeURIComponent
435 * @return encoded value
437 public static String encodeURI(String value)
440 * @j2sNative value = encodeURIComponent(value);
446 * Open the URL using a simple window call if this is JavaScript
449 * @return true if window has been opened
451 public static boolean openURL(String url) throws IOException
466 public static String getUniqueAppletID()
468 return (isJS ? (String) jsutil.getAppletAttribute("_uniqueId") : null);
473 * Read the Info block for this applet.
478 * @return unique id for this applet
480 public static void readInfoProperties(String prefix, Properties p)
484 String id = getUniqueAppletID();
488 @SuppressWarnings("unused")
489 Object info = jsutil.getAppletAttribute("__Info");
491 * @j2sNative for (key in info) { value = info[key];
494 if (key.indexOf(prefix) == 0)
496 System.out.println("Platform id=" + id + " reading Info." + key
508 public static void setAjaxJSON(URL url)
516 public static Object parseJSON(InputStream response)
517 throws IOException, ParseException
521 return JSON.parse(response);
524 BufferedReader br = null;
527 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
528 return new JSONParser().parse(br);
536 } catch (IOException e)
544 public static Object parseJSON(String json) throws ParseException
546 return (isJS() ? JSON.parse(json)
547 : new JSONParser().parse(json));
550 public static Object parseJSON(Reader r)
551 throws IOException, ParseException
560 return new JSONParser().parse(r);
562 // Using a file reader is not currently supported in SwingJS JavaScript
564 if (r instanceof FileReader)
566 throw new IOException(
567 "StringJS does not support FileReader parsing for JSON -- but it could...");
569 return JSON.parse(r);
573 * Dump the input stream to an output file.
577 * @throws IOException
578 * if the file cannot be created or there is a problem
579 * reading the input stream.
581 public static void streamToFile(InputStream is, File outFile)
587 jsutil.setFileBytes(outFile, is);
591 FileOutputStream fio = new FileOutputStream(outFile);
594 byte[] bb = new byte[32 * 1024];
596 while ((l = is.read(bb)) > 0)
607 * Add a known domain that implements access-control-allow-origin:*
609 * These should be reviewed periodically.
612 * for a service that is not allowing ajax
614 * @author hansonr@stolaf.edu
617 public static void addJ2SDirectDatabaseCall(String domain)
622 jsutil.addDirectDatabaseCall(domain);
625 "Platform adding known access-control-allow-origin * for domain "
631 public static void getURLCommandArguments()
635 * Retrieve the first query field as command arguments to Jalview. Include
636 * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
637 * element to this value.
640 * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
641 * + "?").split("?")[1].split("#")[0]); a &&
642 * (J2S.thisApplet.__Info.args = a.split(" "));
648 * A (case sensitive) file path comparator that ignores the difference between /
655 public static boolean pathEquals(String path1, String path2)
659 return path2 == null;
665 String p1 = path1.replace('\\', '/');
666 String p2 = path2.replace('\\', '/');
667 return p1.equals(p2);
672 ///////////// JAL-3253 Applet additions //////////////
676 * Retrieve the object's embedded size from a div's style on a page if
677 * embedded in SwingJS.
680 * JFrame or JInternalFrame
681 * @param defaultWidth
682 * use -1 to return null (no default size)
683 * @param defaultHeight
684 * @return the embedded dimensions or null (no default size or not embedded)
686 public static Dimension getDimIfEmbedded(Component frame,
687 int defaultWidth, int defaultHeight)
692 d = (Dimension) getEmbeddedAttribute(frame, "dim");
694 return (d == null && defaultWidth >= 0
695 ? new Dimension(defaultWidth, defaultHeight)
700 public static Regex newRegex(String regex)
702 return newRegex(regex, null);
705 public static Regex newRegex(String searchString, String replaceString)
708 return (replaceString == null ? new Regex(searchString)
709 : new Regex(searchString, replaceString));
712 public static Regex newRegexPerl(String code)
715 return Regex.perlCode(code);
719 * Initialize Java debug logging. A representative sample -- adapt as desired.
721 public static void startJavaLogging()
727 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
728 "java.awt.Component", "java.awt.focus.Component",
729 "java.awt.event.Component",
730 "java.awt.focus.DefaultKeyboardFocusManager");
735 * Initiate Java logging for a given class. Only for Java, not JavaScript;
736 * Allows debugging of complex event processing.
740 public static void logClass(String... classNames)
748 Logger rootLogger = Logger.getLogger("");
749 rootLogger.setLevel(Level.ALL);
750 ConsoleHandler consoleHandler = new ConsoleHandler();
751 consoleHandler.setLevel(Level.ALL);
752 for (int i = classNames.length; --i >= 0;)
754 Logger logger = Logger.getLogger(classNames[i]);
755 logger.setLevel(Level.ALL);
756 logger.addHandler(consoleHandler);
763 * load a resource -- probably a core file -- if and only if a particular
764 * class has not been instantialized. We use a String here because if we used
765 * a .class object, that reference itself would simply load the class, and we
766 * want the core package to include that as well.
768 * @param resourcePath
771 public static void loadStaticResource(String resourcePath,
776 jsutil.loadResourceIfClassUnknown(resourcePath, className);
780 public static void ensureRegex()
784 loadStaticResource("core/core_stevesoft.z.js",
785 "com.stevesoft.pat.Regex");
790 * Set the "app" property of the HTML5 applet object, for example,
791 * "testApplet.app", to point to the Jalview instance. This will be the object
792 * that page developers use that is similar to the original Java applet object
793 * that was accessed via LiveConnect.
797 public static void setAppClass(Object j)
801 jsutil.setAppletAttribute("app", j);
807 * If this frame ia embedded in a web page, return a known type.
810 * a JFrame or JInternalFrame
812 * @return null if frame is not embedded.
814 public static Object getEmbeddedAttribute(Component frame, String type)
816 return (isJS ? jsutil.getEmbeddedAttribute(frame, type) : null);
819 public static void stackTrace()
823 throw new NullPointerException();
824 } catch (Exception e)
831 public static URL getDocumentBase()
833 return (isJS ? jsutil.getDocumentBase() : null);
836 public static URL getCodeBase()
838 return (isJS ? jsutil.getCodeBase() : null);
841 public static String getUserPath(String subpath)
843 char sep = File.separatorChar;
844 return System.getProperty("user.home") + sep + subpath.replace('/', sep);
848 * This method enables checking if a cached file has exceeded a certain
854 * the threshold in days
857 public static boolean isFileOlderThanThreshold(File file, int noOfDays)
860 // not meaningful in SwingJS -- this is a session-specific temp file. It doesn't have a timestamp.
863 Path filePath = file.toPath();
864 BasicFileAttributes attr;
868 attr = Files.readAttributes(filePath, BasicFileAttributes.class);
869 diffInDays = (int) ((new Date().getTime()
870 - attr.lastModifiedTime().toMillis())
871 / (1000 * 60 * 60 * 24));
872 // System.out.println("Diff in days : " + diffInDays);
873 } catch (IOException e)
877 return noOfDays <= diffInDays;
881 * Get the leading integer part of a string that begins with an integer.
884 * - the string input to process
886 * - value returned if unsuccessful
889 public static int getLeadingIntegerValue(String input, int failValue)
896 int val = /** @j2sNative 1 ? parseInt(input) : */ 0;
897 return (val == val + 0 ? val : failValue);
899 // JavaScript does not support Regex ? lookahead
900 String[] parts = input.split("(?=\\D)(?<=\\d)");
901 if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+"))
903 return Integer.valueOf(parts[0]);