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.Locale;
42 import java.util.Properties;
43 import java.util.logging.ConsoleHandler;
44 import java.util.logging.Level;
45 import java.util.logging.Logger;
47 import javax.swing.SwingUtilities;
49 import org.json.simple.parser.JSONParser;
50 import org.json.simple.parser.ParseException;
52 import com.stevesoft.pat.Regex;
54 import jalview.bin.Jalview;
55 import jalview.javascript.json.JSON;
56 import swingjs.api.JSUtilI;
59 * System platform information used by Applet and Application
66 private static boolean isJS = /** @j2sNative true || */
69 private static Boolean isNoJSMac = null, isNoJSWin = null, isMac = null,
72 private static Boolean isHeadless = null;
74 private static swingjs.api.JSUtilI jsutil;
82 // this is ok - it's a highly embedded method in Java; the deprecation
84 // really a recommended best practice.
85 jsutil = ((JSUtilI) Class.forName("swingjs.JSUtil").newInstance());
86 } catch (InstantiationException | IllegalAccessException
87 | ClassNotFoundException e)
93 // private static Boolean isHeadless = null;
96 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
100 public static boolean isMac()
102 return (isMac == null
103 ? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0))
108 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
112 public static boolean isWin()
114 return (isWin == null
115 ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0))
121 * @return true if HTML5 JavaScript
123 public static boolean isJS()
129 * sorry folks - Macs really are different
131 * BH: disabled for SwingJS -- will need to check key-press issues
133 * @return true if we do things in a special way.
135 public static boolean isAMacAndNotJS()
137 return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac);
141 * Check if we are on a Microsoft plaform...
143 * @return true if we have to cope with another platform variation
145 public static boolean isWindowsAndNotJS()
147 return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
152 * @return true if we are running in non-interactive no UI mode
154 public static boolean isHeadless()
156 if (isHeadless == null)
158 isHeadless = "true".equals(System.getProperty("java.awt.headless"));
165 * @return nominal maximum command line length for this platform
167 public static int getMaxCommandLineLength()
169 // TODO: determine nominal limits for most platforms.
170 return 2046; // this is the max length for a windows NT system.
174 * Answers the input with every backslash replaced with a double backslash (an
175 * 'escaped' single backslash)
180 public static String escapeBackslashes(String s)
182 return s == null ? null : s.replace("\\", "\\\\");
186 * Answers true if the mouse event has Meta-down (Command key on Mac) or
187 * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
188 * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
189 * Mac, you can use e.isPopupTrigger().
194 public static boolean isControlDown(MouseEvent e)
196 return isControlDown(e, isMac());
200 * Overloaded version of method (to allow unit testing)
206 protected static boolean isControlDown(MouseEvent e, boolean aMac)
210 return e.isControlDown();
212 // Jalview 2.11 code below: above is as amended for JalviewJS
214 // * answer false for right mouse button
216 // if (e.isPopupTrigger())
221 // (jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() //
222 // .getMenuShortcutKeyMaskEx()
223 // & jalview.util.ShortcutKeyMaskExWrapper
224 // .getModifiersEx(e)) != 0; // getModifiers()) != 0;
226 // answer false for right mouse button
227 // shortcut key will be META for a Mac
228 return !e.isPopupTrigger()
229 && (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
230 & e.getModifiers()) != 0;
231 // could we use e.isMetaDown() here?
234 // BH: I don't know about that previous method. Here is what SwingJS uses.
235 // Notice the distinction in mouse events. (BUTTON3_MASK == META)
237 // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
238 // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
240 // if (id != MouseEvent.MOUSE_RELEASED)
243 //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
244 //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
246 //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
248 //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
252 // // mac, linux, unix
253 // if (id != MouseEvent.MOUSE_PRESSED)
255 // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
256 // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
257 // return rt || (ctrl && lt);
263 * Windows (not Mac, Linux, or Unix) and right button to test for the
264 * right-mouse pressed event in Windows that would have opened a menu or a
270 public static boolean isWinRightButton(MouseEvent e)
272 // was !isAMac(), but that is true also for Linux and Unix and JS,
274 return isWin() && SwingUtilities.isRightMouseButton(e);
278 * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
279 * without pressing the button.
284 public static boolean isWinMiddleButton(MouseEvent e)
286 // was !isAMac(), but that is true also for Linux and Unix and JS
287 return isWin() && SwingUtilities.isMiddleMouseButton(e);
290 public static boolean allowMnemonics()
295 public final static int TIME_RESET = 0;
297 public final static int TIME_MARK = 1;
299 public static final int TIME_SET = 2;
301 public static final int TIME_GET = 3;
303 public static long time, mark, set, duration;
308 * Platform.timeCheck(null, Platform.TIME_MARK);
312 * Platform.timeCheck("some message", Platform.TIME_MARK);
314 * reset...[set/mark]n...get
319 public static void timeCheck(String msg, int mode)
321 long t = System.currentTimeMillis();
329 System.err.println("Platform: timer reset\t\t\t" + msg);
335 // total time between set/mark points
336 duration += (t - set);
346 System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
347 + "\t" + ((t - mark) / 1000f) + "\t" + msg);
358 System.err.println("Platform: timer dur\t" + ((t - time) / 1000f)
359 + "\t" + ((duration) / 1000f) + "\t" + msg);
366 public static void cacheFileData(String path, Object data)
368 if (isJS && data != null)
370 jsutil.cachePathData(path, data);
374 public static void cacheFileData(File file)
378 byte[] data = Platform.getFileBytes(file);
382 cacheFileData(file.toString(), data);
388 public static byte[] getFileBytes(File f)
390 return (isJS && f != null ? jsutil.getBytes(f) : null);
393 public static byte[] getFileAsBytes(String fileStr)
395 if (isJS && fileStr != null)
397 byte[] bytes = (byte[]) jsutil.getFile(fileStr, false);
398 cacheFileData(fileStr, bytes);
404 public static String getFileAsString(String url)
406 if (isJS && url != null)
408 String ret = (String) jsutil.getFile(url, true);
409 cacheFileData(url, ret);
415 public static boolean setFileBytes(File f, String urlstring)
417 if (isJS && f != null && urlstring != null)
419 @SuppressWarnings("unused")
420 byte[] bytes = getFileAsBytes(urlstring);
421 jsutil.setFileBytes(f, bytes);
427 public static void addJ2SBinaryType(String ext)
431 jsutil.addBinaryFileType(ext);
436 * Encode the URI using JavaScript encodeURIComponent
439 * @return encoded value
441 public static String encodeURI(String value)
444 * @j2sNative value = encodeURIComponent(value);
450 * Open the URL using a simple window call if this is JavaScript
453 * @return true if window has been opened
455 public static boolean openURL(String url) throws IOException
470 public static String getUniqueAppletID()
472 return (isJS ? (String) jsutil.getAppletAttribute("_uniqueId") : null);
476 * Read the Info block for this applet.
481 * @return unique id for this applet
483 public static void readInfoProperties(String prefix, Properties p)
487 String id = getUniqueAppletID();
491 @SuppressWarnings("unused")
492 Object info = jsutil.getAppletAttribute("__Info");
494 * @j2sNative for (key in info) { value = info[key];
497 if (key.indexOf(prefix) == 0)
499 System.out.println("Platform id=" + id + " reading Info." + key
511 public static void setAjaxJSON(URL url)
519 public static Object parseJSON(InputStream response)
520 throws IOException, ParseException
524 return JSON.parse(response);
527 BufferedReader br = null;
530 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
531 return new JSONParser().parse(br);
539 } catch (IOException e)
547 public static Object parseJSON(String json) throws ParseException
549 return (isJS() ? JSON.parse(json) : new JSONParser().parse(json));
552 public static Object parseJSON(Reader r)
553 throws IOException, ParseException
562 return new JSONParser().parse(r);
564 // Using a file reader is not currently supported in SwingJS JavaScript
566 if (r instanceof FileReader)
568 throw new IOException(
569 "StringJS does not support FileReader parsing for JSON -- but it could...");
571 return JSON.parse(r);
575 * Dump the input stream to an output file.
579 * @throws IOException
580 * if the file cannot be created or there is a problem reading the
583 public static void streamToFile(InputStream is, File outFile)
589 jsutil.setFileBytes(outFile, is);
593 FileOutputStream fio = new FileOutputStream(outFile);
596 byte[] bb = new byte[32 * 1024];
598 while ((l = is.read(bb)) > 0)
609 * Add a known domain that implements access-control-allow-origin:*
611 * These should be reviewed periodically.
614 * for a service that is not allowing ajax
616 * @author hansonr@stolaf.edu
619 public static void addJ2SDirectDatabaseCall(String domain)
624 jsutil.addDirectDatabaseCall(domain);
627 "Platform adding known access-control-allow-origin * for domain "
634 * Allow for URL-line command arguments. Untested.
637 public static void getURLCommandArguments()
642 * Retrieve the first query field as command arguments to Jalview. Include
643 * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
644 * element to this value.
647 * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
648 * + "?").split("?")[1].split("#")[0]); a &&
649 * (J2S.thisApplet.__Info.args = a.split(" "));
651 * System.out.println("URL arguments: " + a);
653 } catch (Throwable t) {
658 * A (case sensitive) file path comparator that ignores the difference between
665 public static boolean pathEquals(String path1, String path2)
669 return path2 == null;
675 String p1 = path1.replace('\\', '/');
676 String p2 = path2.replace('\\', '/');
677 return p1.equals(p2);
680 ///////////// JAL-3253 Applet additions //////////////
683 * Retrieve the object's embedded size from a div's style on a page if
684 * embedded in SwingJS.
687 * JFrame or JInternalFrame
688 * @param defaultWidth
689 * use -1 to return null (no default size)
690 * @param defaultHeight
691 * @return the embedded dimensions or null (no default size or not embedded)
693 public static Dimension getDimIfEmbedded(Component frame,
694 int defaultWidth, int defaultHeight)
699 d = (Dimension) getEmbeddedAttribute(frame, "dim");
701 return (d == null && defaultWidth >= 0
702 ? new Dimension(defaultWidth, defaultHeight)
707 public static Regex newRegex(String regex)
709 return newRegex(regex, null);
712 public static Regex newRegex(String searchString, String replaceString)
715 return (replaceString == null ? new Regex(searchString)
716 : new Regex(searchString, replaceString));
719 public static Regex newRegexPerl(String code)
722 return Regex.perlCode(code);
726 * Initialize Java debug logging. A representative sample -- adapt as desired.
728 public static void startJavaLogging()
734 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
735 "java.awt.Component", "java.awt.focus.Component",
736 "java.awt.event.Component",
737 "java.awt.focus.DefaultKeyboardFocusManager");
742 * Initiate Java logging for a given class. Only for Java, not JavaScript;
743 * Allows debugging of complex event processing.
747 public static void logClass(String... classNames)
755 Logger rootLogger = Logger.getLogger("");
756 rootLogger.setLevel(Level.ALL);
757 ConsoleHandler consoleHandler = new ConsoleHandler();
758 consoleHandler.setLevel(Level.ALL);
759 for (int i = classNames.length; --i >= 0;)
761 Logger logger = Logger.getLogger(classNames[i]);
762 logger.setLevel(Level.ALL);
763 logger.addHandler(consoleHandler);
769 * load a resource -- probably a core file -- if and only if a particular
770 * class has not been instantialized. We use a String here because if we used
771 * a .class object, that reference itself would simply load the class, and we
772 * want the core package to include that as well.
774 * @param resourcePath
777 public static void loadStaticResource(String resourcePath,
782 jsutil.loadResourceIfClassUnknown(resourcePath, className);
786 public static void ensureRegex()
790 loadStaticResource("core/core_stevesoft.z.js",
791 "com.stevesoft.pat.Regex");
796 * Set the "app" property of the HTML5 applet object, for example,
797 * "testApplet.app", to point to the Jalview instance. This will be the object
798 * that page developers use that is similar to the original Java applet object
799 * that was accessed via LiveConnect.
803 public static void setAppClass(Object j)
807 jsutil.setAppletAttribute("app", j);
813 * If this frame ia embedded in a web page, return a known type.
816 * a JFrame or JInternalFrame
818 * @return null if frame is not embedded.
820 public static Object getEmbeddedAttribute(Component frame, String type)
822 return (isJS ? jsutil.getEmbeddedAttribute(frame, type) : null);
825 public static void stackTrace()
829 throw new NullPointerException();
830 } catch (Exception e)
837 public static URL getDocumentBase()
839 return (isJS ? jsutil.getDocumentBase() : null);
842 public static URL getCodeBase()
844 return (isJS ? jsutil.getCodeBase() : null);
847 public static String getUserPath(String subpath)
849 char sep = File.separatorChar;
850 return System.getProperty("user.home") + sep
851 + subpath.replace('/', sep);
855 * This method enables checking if a cached file has exceeded a certain
861 * the threshold in days
864 public static boolean isFileOlderThanThreshold(File file, int noOfDays)
868 // not meaningful in SwingJS -- this is a session-specific temp file. It
869 // doesn't have a timestamp.
872 Path filePath = file.toPath();
873 BasicFileAttributes attr;
877 attr = Files.readAttributes(filePath, BasicFileAttributes.class);
878 diffInDays = (int) ((new Date().getTime()
879 - attr.lastModifiedTime().toMillis())
880 / (1000 * 60 * 60 * 24));
881 // System.out.println("Diff in days : " + diffInDays);
882 } catch (IOException e)
886 return noOfDays <= diffInDays;
890 * Get the leading integer part of a string that begins with an integer.
893 * - the string input to process
895 * - value returned if unsuccessful
898 public static int getLeadingIntegerValue(String input, int failValue)
906 int val = /** @j2sNative 1 ? parseInt(input) : */
908 return (val == val + 0 ? val : failValue);
910 // JavaScript does not support Regex ? lookahead
911 String[] parts = input.split("(?=\\D)(?<=\\d)");
912 if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+"))
914 return Integer.valueOf(parts[0]);
919 public static Map<String, Object> getAppletInfoAsMap()
921 return (isJS ? jsutil.getAppletInfoAsMap() : null);
925 * Get the SwingJS applet ID and combine that with the frameType
928 * "alignment", "desktop", etc., or null
931 public static String getAppID(String frameType)
933 String id = Jalview.getInstance().j2sAppletID;
936 Jalview.getInstance().j2sAppletID = id = (String) jsutil
937 .getAppletAttribute("_id");
939 return id + (frameType == null ? "" : "-" + frameType);
944 * Option to avoid unnecessary seeking of nonexistent resources in JavaScript.
945 * Works in Java as well.
950 public static Locale getLocaleOrNone(Locale loc)
952 return (isJS && loc.getCountry() == "en" ? new Locale("") : loc);