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;
27 import java.awt.Toolkit;
28 import java.awt.event.KeyEvent;
29 import java.awt.event.MouseEvent;
30 import java.io.BufferedReader;
32 import java.io.FileOutputStream;
33 import java.io.FileReader;
34 import java.io.IOException;
35 import java.io.InputStream;
36 import java.io.InputStreamReader;
37 import java.io.Reader;
38 import java.lang.reflect.Method;
40 import java.nio.channels.Channels;
41 import java.nio.channels.ReadableByteChannel;
42 import java.nio.file.Files;
43 import java.nio.file.Path;
44 import java.nio.file.Paths;
45 import java.nio.file.StandardCopyOption;
46 import java.nio.file.attribute.BasicFileAttributes;
47 import java.util.Date;
48 import java.util.Locale;
50 import java.util.Properties;
51 import java.util.logging.ConsoleHandler;
52 import java.util.logging.Level;
53 import java.util.logging.Logger;
55 import javax.swing.SwingUtilities;
57 import org.json.simple.parser.JSONParser;
58 import org.json.simple.parser.ParseException;
60 import com.stevesoft.pat.Regex;
62 import jalview.bin.Jalview;
63 import jalview.javascript.json.JSON;
64 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,
77 isWin = null, isLinux = 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)
101 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
105 public static boolean isMac()
107 return (isMac == null
108 ? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0))
112 public static int SHORTCUT_KEY_MASK = (Platform.isMac()
113 ? KeyEvent.META_DOWN_MASK
114 : KeyEvent.CTRL_DOWN_MASK);
118 if (!GraphicsEnvironment.isHeadless())
120 // Using non-deprecated Extended key mask modifiers, but Java 8 has no
121 // getMenuShortcutKeyMaskEx method
122 Toolkit tk = Toolkit.getDefaultToolkit();
123 Method method = null;
126 method = tk.getClass().getMethod("getMenuShortcutKeyMaskEx");
127 } catch (Exception e)
130 "Could not find Toolkit method getMenuShortcutKeyMaskEx. Trying getMenuShortcutKeyMask.");
136 method = tk.getClass().getMethod("getMenuShortcutKeyMask");
137 } catch (Exception e)
140 "Could not find Toolkit method getMenuShortcutKeyMaskEx or getMenuShortcutKeyMask.");
148 method.setAccessible(true);
149 SHORTCUT_KEY_MASK = ((int) method.invoke(tk, new Object[0]));
150 } catch (Exception e)
155 if (SHORTCUT_KEY_MASK <= 0xF)
157 // shift this into the extended region (was Java 8)
158 SHORTCUT_KEY_MASK = SHORTCUT_KEY_MASK << 6;
163 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
167 public static boolean isWin()
169 return (isWin == null
170 ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0))
175 * added to check LaF for Linux
179 public static boolean isLinux()
181 return (isLinux == null
182 ? (isLinux = (System.getProperty("os.name")
183 .indexOf("Linux") >= 0))
189 * @return true if HTML5 JavaScript
191 public static boolean isJS()
197 * sorry folks - Macs really are different
199 * BH: disabled for SwingJS -- will need to check key-press issues
201 * @return true if we do things in a special way.
203 public static boolean isAMacAndNotJS()
205 return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac);
209 * Check if we are on a Microsoft platform...
211 * @return true if we have to cope with another platform variation
213 public static boolean isWindowsAndNotJS()
215 return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
220 * @return true if we are running in non-interactive no UI mode
222 public static boolean isHeadless()
224 if (isHeadless == null)
226 isHeadless = "true".equals(System.getProperty("java.awt.headless"));
233 * @return nominal maximum command line length for this platform
235 public static int getMaxCommandLineLength()
237 // TODO: determine nominal limits for most platforms.
238 return 2046; // this is the max length for a windows NT system.
242 * Answers the input with every backslash replaced with a double backslash (an
243 * 'escaped' single backslash)
248 public static String escapeBackslashes(String s)
250 return s == null ? null : s.replace("\\", "\\\\");
254 * Answers true if the mouse event has Meta-down (Command key on Mac) or
255 * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
256 * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
257 * Mac, you can use e.isPopupTrigger().
262 public static boolean isControlDown(MouseEvent e)
264 return isControlDown(e, isMac());
268 * Overloaded version of method (to allow unit testing)
274 protected static boolean isControlDown(MouseEvent e, boolean aMac)
277 // System.out.println(e.isPopupTrigger()
278 // + " " + ((SHORTCUT_KEY_MASK & e.getModifiersEx()) != 0)
279 // + " " + e.isControlDown());
281 ? !e.isPopupTrigger()
282 && (SHORTCUT_KEY_MASK & e.getModifiersEx()) != 0
283 : e.isControlDown());
286 // BH: I don't know about that previous method. Here is what SwingJS uses.
287 // Notice the distinction in mouse events. (BUTTON3_MASK == META)
289 // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
290 // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
292 // if (id != MouseEvent.MOUSE_RELEASED)
295 //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
296 //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
298 //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
300 //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
304 // // mac, linux, unix
305 // if (id != MouseEvent.MOUSE_PRESSED)
307 // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
308 // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
309 // return rt || (ctrl && lt);
315 * Windows (not Mac, Linux, or Unix) and right button to test for the
316 * right-mouse pressed event in Windows that would have opened a menu or a
322 public static boolean isWinRightButton(MouseEvent e)
324 // was !isAMac(), but that is true also for Linux and Unix and JS,
326 return isWin() && SwingUtilities.isRightMouseButton(e);
330 * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
331 * without pressing the button.
336 public static boolean isWinMiddleButton(MouseEvent e)
338 // was !isAMac(), but that is true also for Linux and Unix and JS
339 return isWin() && SwingUtilities.isMiddleMouseButton(e);
342 public static boolean allowMnemonics()
347 public final static int TIME_RESET = 0;
349 public final static int TIME_MARK = 1;
351 public static final int TIME_SET = 2;
353 public static final int TIME_GET = 3;
355 public static long time, mark, set, duration;
360 * Platform.timeCheck(null, Platform.TIME_MARK);
364 * Platform.timeCheck("some message", Platform.TIME_MARK);
366 * reset...[set/mark]n...get
371 public static void timeCheck(String msg, int mode)
373 long t = System.currentTimeMillis();
381 System.err.println("Platform: timer reset\t\t\t" + msg);
387 // total time between set/mark points
388 duration += (t - set);
398 System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
399 + "\t" + ((t - mark) / 1000f) + "\t" + msg);
410 System.err.println("Platform: timer dur\t" + ((t - time) / 1000f)
411 + "\t" + ((duration) / 1000f) + "\t" + msg);
418 public static void cacheFileData(String path, Object data)
420 if (isJS && data != null)
422 jsutil.cachePathData(path, data);
426 public static void cacheFileData(File file)
430 byte[] data = Platform.getFileBytes(file);
434 cacheFileData(file.toString(), data);
440 public static byte[] getFileBytes(File f)
442 return (isJS && f != null ? jsutil.getBytes(f) : null);
445 public static byte[] getFileAsBytes(String fileStr)
447 if (isJS && fileStr != null)
449 byte[] bytes = (byte[]) jsutil.getFile(fileStr, false);
450 cacheFileData(fileStr, bytes);
456 public static String getFileAsString(String url)
458 if (isJS && url != null)
460 String ret = (String) jsutil.getFile(url, true);
461 cacheFileData(url, ret);
467 public static boolean setFileBytes(File f, String urlstring)
469 if (isJS && f != null && urlstring != null)
471 @SuppressWarnings("unused")
472 byte[] bytes = getFileAsBytes(urlstring);
473 jsutil.setFileBytes(f, bytes);
479 public static void addJ2SBinaryType(String ext)
483 jsutil.addBinaryFileType(ext);
488 * Encode the URI using JavaScript encodeURIComponent
491 * @return encoded value
493 public static String encodeURI(String value)
496 * @j2sNative value = encodeURIComponent(value);
502 * Open the URL using a simple window call if this is JavaScript
505 * @return true if window has been opened
507 public static boolean openURL(String url) throws IOException
522 public static String getUniqueAppletID()
524 return (isJS ? (String) jsutil.getAppletAttribute("_uniqueId") : null);
529 * Read the Info block for this applet.
534 * @return unique id for this applet
536 public static void readInfoProperties(String prefix, Properties p)
540 String id = getUniqueAppletID();
544 @SuppressWarnings("unused")
545 Object info = jsutil.getAppletAttribute("__Info");
547 * @j2sNative for (key in info) { value = info[key];
550 if (key.indexOf(prefix) == 0)
552 System.out.println("Platform id=" + id + " reading Info." + key
564 public static void setAjaxJSON(URL url)
572 public static Object parseJSON(InputStream response)
573 throws IOException, ParseException
577 return JSON.parse(response);
580 BufferedReader br = null;
583 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
584 return new JSONParser().parse(br);
592 } catch (IOException e)
600 public static Object parseJSON(String json) throws ParseException
602 return (isJS() ? JSON.parse(json) : new JSONParser().parse(json));
605 public static Object parseJSON(Reader r)
606 throws IOException, ParseException
615 return new JSONParser().parse(r);
617 // Using a file reader is not currently supported in SwingJS JavaScript
619 if (r instanceof FileReader)
621 throw new IOException(
622 "StringJS does not support FileReader parsing for JSON -- but it could...");
624 return JSON.parse(r);
629 * Dump the input stream to an output file.
633 * @throws IOException
634 * if the file cannot be created or there is a problem reading the
637 public static void streamToFile(InputStream is, File outFile)
642 jsutil.setFileBytes(outFile, is);
645 FileOutputStream fio = new FileOutputStream(outFile);
648 byte[] bb = new byte[32 * 1024];
650 while ((l = is.read(bb)) > 0)
661 * Add a known domain that implements access-control-allow-origin:*
663 * These should be reviewed periodically.
666 * for a service that is not allowing ajax
668 * @author hansonr@stolaf.edu
671 public static void addJ2SDirectDatabaseCall(String domain)
676 jsutil.addDirectDatabaseCall(domain);
678 "Platform adding known access-control-allow-origin * for domain "
683 * J2S.addDirectDatabaseCall(domain);
690 * Allow for URL-line command arguments. Untested.
693 public static void getURLCommandArguments()
697 * Retrieve the first query field as command arguments to Jalview. Include
698 * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's
699 * __Info.args element to this value.
702 * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
703 * + "?").split("?")[1].split("#")[0]); a && (System.out.println("URL arguments detected were "+a)) &&
704 * (J2S.thisApplet.__Info.urlargs = a.split(" "));
705 * (!J2S.thisApplet.__Info.args || J2S.thisApplet.__Info.args == "" || J2S.thisApplet.__Info.args == "??") && (J2S.thisApplet.__Info.args = a) && (System.out.println("URL arguments were passed to J2S main."));
707 } catch (Throwable t)
713 * A (case sensitive) file path comparator that ignores the difference between
720 public static boolean pathEquals(String path1, String path2)
724 return path2 == null;
730 String p1 = path1.replace('\\', '/');
731 String p2 = path2.replace('\\', '/');
732 return p1.equals(p2);
734 ///////////// JAL-3253 Applet additions //////////////
737 * Retrieve the object's embedded size from a div's style on a page if
738 * embedded in SwingJS.
741 * JFrame or JInternalFrame
742 * @param defaultWidth
743 * use -1 to return null (no default size)
744 * @param defaultHeight
745 * @return the embedded dimensions or null (no default size or not embedded)
747 public static Dimension getDimIfEmbedded(Component frame,
748 int defaultWidth, int defaultHeight)
753 d = (Dimension) getEmbeddedAttribute(frame, "dim");
755 return (d == null && defaultWidth >= 0
756 ? new Dimension(defaultWidth, defaultHeight)
761 public static Regex newRegex(String regex)
763 return newRegex(regex, null);
766 public static Regex newRegex(String searchString, String replaceString)
769 return (replaceString == null ? new Regex(searchString)
770 : new Regex(searchString, replaceString));
773 public static Regex newRegexPerl(String code)
776 return Regex.perlCode(code);
780 * Initialize Java debug logging. A representative sample -- adapt as desired.
782 public static void startJavaLogging()
788 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
789 "java.awt.Component", "java.awt.focus.Component",
790 "java.awt.event.Component",
791 "java.awt.focus.DefaultKeyboardFocusManager");
796 * Initiate Java logging for a given class. Only for Java, not JavaScript;
797 * Allows debugging of complex event processing.
801 public static void logClass(String... classNames)
809 Logger rootLogger = Logger.getLogger("");
810 rootLogger.setLevel(Level.ALL);
811 ConsoleHandler consoleHandler = new ConsoleHandler();
812 consoleHandler.setLevel(Level.ALL);
813 for (int i = classNames.length; --i >= 0;)
815 Logger logger = Logger.getLogger(classNames[i]);
816 logger.setLevel(Level.ALL);
817 logger.addHandler(consoleHandler);
823 * load a resource -- probably a core file -- if and only if a particular
824 * class has not been instantialized. We use a String here because if we used
825 * a .class object, that reference itself would simply load the class, and we
826 * want the core package to include that as well.
828 * @param resourcePath
831 public static void loadStaticResource(String resourcePath,
836 jsutil.loadResourceIfClassUnknown(resourcePath, className);
840 public static void ensureRegex()
844 loadStaticResource("core/core_stevesoft.z.js",
845 "com.stevesoft.pat.Regex");
850 * Set the "app" property of the HTML5 applet object, for example,
851 * "testApplet.app", to point to the Jalview instance. This will be the object
852 * that page developers use that is similar to the original Java applet object
853 * that was accessed via LiveConnect.
857 public static void setAppClass(Object j)
861 jsutil.setAppClass(j);
867 * If this frame is embedded in a web page, return a known type.
870 * a JFrame or JInternalFrame
872 * "name", "node", "init", "dim", or any DOM attribute, such as "id"
873 * @return null if frame is not embedded.
875 public static Object getEmbeddedAttribute(Component frame, String type)
877 return (isJS ? jsutil.getEmbeddedAttribute(frame, type) : null);
880 public static void stackTrace()
884 throw new NullPointerException();
885 } catch (Exception e)
892 public static URL getDocumentBase()
894 return (isJS ? jsutil.getDocumentBase() : null);
897 public static URL getCodeBase()
899 return (isJS ? jsutil.getCodeBase() : null);
902 public static String getUserPath(String subpath)
904 char sep = File.separatorChar;
905 return System.getProperty("user.home") + sep
906 + subpath.replace('/', sep);
910 * This method enables checking if a cached file has exceeded a certain
916 * the threshold in days
919 public static boolean isFileOlderThanThreshold(File file, int noOfDays)
923 // not meaningful in SwingJS -- this is a session-specific temp file. It
924 // doesn't have a timestamp.
927 Path filePath = file.toPath();
928 BasicFileAttributes attr;
932 attr = Files.readAttributes(filePath, BasicFileAttributes.class);
933 diffInDays = (int) ((new Date().getTime()
934 - attr.lastModifiedTime().toMillis())
935 / (1000 * 60 * 60 * 24));
936 // System.out.println("Diff in days : " + diffInDays);
937 } catch (IOException e)
941 return noOfDays <= diffInDays;
945 * Get the leading integer part of a string that begins with an integer.
948 * - the string input to process
950 * - value returned if unsuccessful
953 public static int getLeadingIntegerValue(String input, int failValue)
961 int val = /** @j2sNative 1 ? parseInt(input) : */
963 return (val == val + 0 ? val : failValue);
965 // JavaScript does not support Regex ? lookahead
966 String[] parts = input.split("(?=\\D)(?<=\\d)");
967 if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+"))
969 return Integer.valueOf(parts[0]);
974 public static Map<String, Object> getAppletInfoAsMap()
976 return (isJS ? jsutil.getAppletInfoAsMap() : null);
980 * Get the SwingJS applet ID and combine that with the frameType
983 * "alignment", "desktop", etc., or null
986 public static String getAppID(String frameType)
989 String id = Jalview.getInstance().j2sAppletID;
992 Jalview.getInstance().j2sAppletID = id = (isJS
993 ? (String) jsutil.getAppletAttribute("_id")
996 return id + (frameType == null ? "" : "-" + frameType);
1000 * Option to avoid unnecessary seeking of nonexistent resources in JavaScript.
1001 * Works in Java as well.
1006 public static Locale getLocaleOrNone(Locale loc)
1008 return (isJS && loc.getLanguage() == "en" ? new Locale("") : loc);
1012 * From UrlDownloadClient; trivial in JavaScript; painful in Java.
1016 * @throws IOException
1018 public static void download(String urlstring, String outfile)
1022 try (InputStream is = new URL(urlstring).openStream())
1025 { // so much easier!
1026 streamToFile(is, new File(outfile));
1029 temp = Files.createTempFile(".jalview_", ".tmp");
1030 try (FileOutputStream fos = new FileOutputStream(temp.toString());
1031 ReadableByteChannel rbc = Channels.newChannel(is))
1033 fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
1034 // copy tempfile to outfile once our download completes
1035 // incase something goes wrong
1036 Files.copy(temp, Paths.get(outfile),
1037 StandardCopyOption.REPLACE_EXISTING);
1039 } catch (IOException e)
1048 Files.deleteIfExists(temp);
1050 } catch (IOException e)
1052 System.out.println("Exception while deleting download temp file: "