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.KeyEvent;
27 import java.awt.event.MouseEvent;
28 import java.io.BufferedReader;
30 import java.io.FileOutputStream;
31 import java.io.FileReader;
32 import java.io.IOException;
33 import java.io.InputStream;
34 import java.io.InputStreamReader;
35 import java.io.Reader;
36 import java.lang.reflect.Method;
38 import java.nio.channels.Channels;
39 import java.nio.channels.ReadableByteChannel;
40 import java.nio.file.Files;
41 import java.nio.file.Path;
42 import java.nio.file.Paths;
43 import java.nio.file.StandardCopyOption;
44 import java.nio.file.attribute.BasicFileAttributes;
45 import java.util.Date;
46 import java.util.Locale;
48 import java.util.Properties;
49 import java.util.logging.ConsoleHandler;
50 import java.util.logging.Level;
51 import java.util.logging.Logger;
53 import javax.swing.SwingUtilities;
55 import org.json.simple.parser.JSONParser;
56 import org.json.simple.parser.ParseException;
58 import com.stevesoft.pat.Regex;
60 import jalview.bin.Jalview;
61 import jalview.javascript.json.JSON;
62 import swingjs.api.JSUtilI;
65 * System platform information used by Applet and Application
72 private static boolean isJS = /** @j2sNative true || */
75 private static Boolean isNoJSMac = null, isNoJSWin = null, isMac = null,
78 private static Boolean isHeadless = null;
80 private static swingjs.api.JSUtilI jsutil;
88 // this is ok - it's a highly embedded method in Java; the deprecation
90 // really a recommended best practice.
91 jsutil = ((JSUtilI) Class.forName("swingjs.JSUtil").newInstance());
92 } catch (InstantiationException | IllegalAccessException
93 | ClassNotFoundException e)
99 // private static Boolean isHeadless = null;
102 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
106 public static boolean isMac()
108 return (isMac == null
109 ? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0))
113 public static int SHORTCUT_KEY_MASK = (Platform.isMac()
114 ? KeyEvent.META_DOWN_MASK
115 : KeyEvent.CTRL_DOWN_MASK);
119 if (!Jalview.isHeadlessMode())
121 // Using non-deprecated Extended key mask modifiers, but Java 8 has no
122 // getMenuShortcutKeyMaskEx method
123 Toolkit tk = Toolkit.getDefaultToolkit();
124 Method method = null;
127 method = tk.getClass().getMethod("getMenuShortcutKeyMaskEx");
128 } catch (Exception e)
131 "Could not find Toolkit method getMenuShortcutKeyMaskEx. Trying getMenuShortcutKeyMask.");
137 method = tk.getClass().getMethod("getMenuShortcutKeyMask");
138 } catch (Exception e)
141 "Could not find Toolkit method getMenuShortcutKeyMaskEx or getMenuShortcutKeyMask.");
149 method.setAccessible(true);
150 SHORTCUT_KEY_MASK = ((int) method.invoke(tk, new Object[0]));
151 } catch (Exception e)
156 if (SHORTCUT_KEY_MASK <= 0xF)
158 // shift this into the extended region (was Java 8)
159 SHORTCUT_KEY_MASK = SHORTCUT_KEY_MASK << 6;
164 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
168 public static boolean isWin()
170 return (isWin == null
171 ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0))
177 * @return true if HTML5 JavaScript
179 public static boolean isJS()
185 * sorry folks - Macs really are different
187 * BH: disabled for SwingJS -- will need to check key-press issues
189 * @return true if we do things in a special way.
191 public static boolean isAMacAndNotJS()
193 return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac);
197 * Check if we are on a Microsoft plaform...
199 * @return true if we have to cope with another platform variation
201 public static boolean isWindowsAndNotJS()
203 return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
208 * @return true if we are running in non-interactive no UI mode
210 public static boolean isHeadless()
212 if (isHeadless == null)
214 isHeadless = "true".equals(System.getProperty("java.awt.headless"));
221 * @return nominal maximum command line length for this platform
223 public static int getMaxCommandLineLength()
225 // TODO: determine nominal limits for most platforms.
226 return 2046; // this is the max length for a windows NT system.
230 * Answers the input with every backslash replaced with a double backslash (an
231 * 'escaped' single backslash)
236 public static String escapeBackslashes(String s)
238 return s == null ? null : s.replace("\\", "\\\\");
242 * Answers true if the mouse event has Meta-down (Command key on Mac) or
243 * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
244 * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
245 * Mac, you can use e.isPopupTrigger().
250 public static boolean isControlDown(MouseEvent e)
252 return isControlDown(e, isMac());
256 * Overloaded version of method (to allow unit testing)
262 protected static boolean isControlDown(MouseEvent e, boolean aMac)
265 // System.out.println(e.isPopupTrigger()
266 // + " " + ((SHORTCUT_KEY_MASK & e.getModifiersEx()) != 0)
267 // + " " + e.isControlDown());
269 ? !e.isPopupTrigger()
270 && (SHORTCUT_KEY_MASK & e.getModifiersEx()) != 0
271 : e.isControlDown());
274 // BH: I don't know about that previous method. Here is what SwingJS uses.
275 // Notice the distinction in mouse events. (BUTTON3_MASK == META)
277 // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
278 // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
280 // if (id != MouseEvent.MOUSE_RELEASED)
283 //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
284 //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
286 //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
288 //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
292 // // mac, linux, unix
293 // if (id != MouseEvent.MOUSE_PRESSED)
295 // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
296 // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
297 // return rt || (ctrl && lt);
303 * Windows (not Mac, Linux, or Unix) and right button to test for the
304 * right-mouse pressed event in Windows that would have opened a menu or a
310 public static boolean isWinRightButton(MouseEvent e)
312 // was !isAMac(), but that is true also for Linux and Unix and JS,
314 return isWin() && SwingUtilities.isRightMouseButton(e);
318 * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
319 * without pressing the button.
324 public static boolean isWinMiddleButton(MouseEvent e)
326 // was !isAMac(), but that is true also for Linux and Unix and JS
327 return isWin() && SwingUtilities.isMiddleMouseButton(e);
330 public static boolean allowMnemonics()
335 public final static int TIME_RESET = 0;
337 public final static int TIME_MARK = 1;
339 public static final int TIME_SET = 2;
341 public static final int TIME_GET = 3;
343 public static long time, mark, set, duration;
348 * Platform.timeCheck(null, Platform.TIME_MARK);
352 * Platform.timeCheck("some message", Platform.TIME_MARK);
354 * reset...[set/mark]n...get
359 public static void timeCheck(String msg, int mode)
361 long t = System.currentTimeMillis();
369 System.err.println("Platform: timer reset\t\t\t" + msg);
375 // total time between set/mark points
376 duration += (t - set);
386 System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
387 + "\t" + ((t - mark) / 1000f) + "\t" + msg);
398 System.err.println("Platform: timer dur\t" + ((t - time) / 1000f)
399 + "\t" + ((duration) / 1000f) + "\t" + msg);
406 public static void cacheFileData(String path, Object data)
408 if (isJS && data != null)
410 jsutil.cachePathData(path, data);
414 public static void cacheFileData(File file)
418 byte[] data = Platform.getFileBytes(file);
422 cacheFileData(file.toString(), data);
428 public static byte[] getFileBytes(File f)
430 return (isJS && f != null ? jsutil.getBytes(f) : null);
433 public static byte[] getFileAsBytes(String fileStr)
435 if (isJS && fileStr != null)
437 byte[] bytes = (byte[]) jsutil.getFile(fileStr, false);
438 cacheFileData(fileStr, bytes);
444 public static String getFileAsString(String url)
446 if (isJS && url != null)
448 String ret = (String) jsutil.getFile(url, true);
449 cacheFileData(url, ret);
455 public static boolean setFileBytes(File f, String urlstring)
457 if (isJS && f != null && urlstring != null)
459 @SuppressWarnings("unused")
460 byte[] bytes = getFileAsBytes(urlstring);
461 jsutil.setFileBytes(f, bytes);
467 public static void addJ2SBinaryType(String ext)
471 jsutil.addBinaryFileType(ext);
476 * Encode the URI using JavaScript encodeURIComponent
479 * @return encoded value
481 public static String encodeURI(String value)
484 * @j2sNative value = encodeURIComponent(value);
490 * Open the URL using a simple window call if this is JavaScript
493 * @return true if window has been opened
495 public static boolean openURL(String url) throws IOException
510 public static String getUniqueAppletID()
512 return (isJS ? (String) jsutil.getAppletAttribute("_uniqueId") : null);
516 * Read the Info block for this applet.
521 * @return unique id for this applet
523 public static void readInfoProperties(String prefix, Properties p)
527 String id = getUniqueAppletID();
531 @SuppressWarnings("unused")
532 Object info = jsutil.getAppletAttribute("__Info");
534 * @j2sNative for (key in info) { value = info[key];
537 if (key.indexOf(prefix) == 0)
539 System.out.println("Platform id=" + id + " reading Info." + key
551 public static void setAjaxJSON(URL url)
559 public static Object parseJSON(InputStream response)
560 throws IOException, ParseException
564 return JSON.parse(response);
567 BufferedReader br = null;
570 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
571 return new JSONParser().parse(br);
579 } catch (IOException e)
587 public static Object parseJSON(String json) throws ParseException
589 return (isJS() ? JSON.parse(json) : new JSONParser().parse(json));
592 public static Object parseJSON(Reader r)
593 throws IOException, ParseException
602 return new JSONParser().parse(r);
604 // Using a file reader is not currently supported in SwingJS JavaScript
606 if (r instanceof FileReader)
608 throw new IOException(
609 "StringJS does not support FileReader parsing for JSON -- but it could...");
611 return JSON.parse(r);
615 * Dump the input stream to an output file.
619 * @throws IOException
620 * if the file cannot be created or there is a problem reading the
623 public static void streamToFile(InputStream is, File outFile)
629 jsutil.setFileBytes(outFile, is);
633 FileOutputStream fio = new FileOutputStream(outFile);
636 byte[] bb = new byte[32 * 1024];
638 while ((l = is.read(bb)) > 0)
649 * Add a known domain that implements access-control-allow-origin:*
651 * These should be reviewed periodically.
654 * for a service that is not allowing ajax
656 * @author hansonr@stolaf.edu
659 public static void addJ2SDirectDatabaseCall(String domain)
664 jsutil.addDirectDatabaseCall(domain);
667 "Platform adding known access-control-allow-origin * for domain "
674 * Allow for URL-line command arguments. Untested.
677 public static void getURLCommandArguments()
683 * Retrieve the first query field as command arguments to Jalview. Include
684 * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's
685 * __Info.args element to this value.
688 * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
689 * + "?").split("?")[1].split("#")[0]); a &&
690 * (J2S.thisApplet.__Info.args = a.split(" "));
692 * System.out.println("URL arguments: " + a);
694 } catch (Throwable t)
700 * A (case sensitive) file path comparator that ignores the difference between
707 public static boolean pathEquals(String path1, String path2)
711 return path2 == null;
717 String p1 = path1.replace('\\', '/');
718 String p2 = path2.replace('\\', '/');
719 return p1.equals(p2);
722 ///////////// JAL-3253 Applet additions //////////////
725 * Retrieve the object's embedded size from a div's style on a page if
726 * embedded in SwingJS.
729 * JFrame or JInternalFrame
730 * @param defaultWidth
731 * use -1 to return null (no default size)
732 * @param defaultHeight
733 * @return the embedded dimensions or null (no default size or not embedded)
735 public static Dimension getDimIfEmbedded(Component frame,
736 int defaultWidth, int defaultHeight)
741 d = (Dimension) getEmbeddedAttribute(frame, "dim");
743 return (d == null && defaultWidth >= 0
744 ? new Dimension(defaultWidth, defaultHeight)
749 public static Regex newRegex(String regex)
751 return newRegex(regex, null);
754 public static Regex newRegex(String searchString, String replaceString)
757 return (replaceString == null ? new Regex(searchString)
758 : new Regex(searchString, replaceString));
761 public static Regex newRegexPerl(String code)
764 return Regex.perlCode(code);
768 * Initialize Java debug logging. A representative sample -- adapt as desired.
770 public static void startJavaLogging()
776 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
777 "java.awt.Component", "java.awt.focus.Component",
778 "java.awt.event.Component",
779 "java.awt.focus.DefaultKeyboardFocusManager");
784 * Initiate Java logging for a given class. Only for Java, not JavaScript;
785 * Allows debugging of complex event processing.
789 public static void logClass(String... classNames)
797 Logger rootLogger = Logger.getLogger("");
798 rootLogger.setLevel(Level.ALL);
799 ConsoleHandler consoleHandler = new ConsoleHandler();
800 consoleHandler.setLevel(Level.ALL);
801 for (int i = classNames.length; --i >= 0;)
803 Logger logger = Logger.getLogger(classNames[i]);
804 logger.setLevel(Level.ALL);
805 logger.addHandler(consoleHandler);
811 * load a resource -- probably a core file -- if and only if a particular
812 * class has not been instantialized. We use a String here because if we used
813 * a .class object, that reference itself would simply load the class, and we
814 * want the core package to include that as well.
816 * @param resourcePath
819 public static void loadStaticResource(String resourcePath,
824 jsutil.loadResourceIfClassUnknown(resourcePath, className);
828 public static void ensureRegex()
832 loadStaticResource("core/core_stevesoft.z.js",
833 "com.stevesoft.pat.Regex");
838 * Set the "app" property of the HTML5 applet object, for example,
839 * "testApplet.app", to point to the Jalview instance. This will be the object
840 * that page developers use that is similar to the original Java applet object
841 * that was accessed via LiveConnect.
845 public static void setAppClass(Object j)
849 jsutil.setAppClass(j);
855 * If this frame is embedded in a web page, return a known type.
858 * a JFrame or JInternalFrame
860 * "name", "node", "init", "dim", or any DOM attribute, such as "id"
861 * @return null if frame is not embedded.
863 public static Object getEmbeddedAttribute(Component frame, String type)
865 return (isJS ? jsutil.getEmbeddedAttribute(frame, type) : null);
868 public static void stackTrace()
872 throw new NullPointerException();
873 } catch (Exception e)
880 public static URL getDocumentBase()
882 return (isJS ? jsutil.getDocumentBase() : null);
885 public static URL getCodeBase()
887 return (isJS ? jsutil.getCodeBase() : null);
890 public static String getUserPath(String subpath)
892 char sep = File.separatorChar;
893 return System.getProperty("user.home") + sep
894 + subpath.replace('/', sep);
898 * This method enables checking if a cached file has exceeded a certain
904 * the threshold in days
907 public static boolean isFileOlderThanThreshold(File file, int noOfDays)
911 // not meaningful in SwingJS -- this is a session-specific temp file. It
912 // doesn't have a timestamp.
915 Path filePath = file.toPath();
916 BasicFileAttributes attr;
920 attr = Files.readAttributes(filePath, BasicFileAttributes.class);
921 diffInDays = (int) ((new Date().getTime()
922 - attr.lastModifiedTime().toMillis())
923 / (1000 * 60 * 60 * 24));
924 // System.out.println("Diff in days : " + diffInDays);
925 } catch (IOException e)
929 return noOfDays <= diffInDays;
933 * Get the leading integer part of a string that begins with an integer.
936 * - the string input to process
938 * - value returned if unsuccessful
941 public static int getLeadingIntegerValue(String input, int failValue)
949 int val = /** @j2sNative 1 ? parseInt(input) : */
951 return (val == val + 0 ? val : failValue);
953 // JavaScript does not support Regex ? lookahead
954 String[] parts = input.split("(?=\\D)(?<=\\d)");
955 if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+"))
957 return Integer.valueOf(parts[0]);
962 public static Map<String, Object> getAppletInfoAsMap()
964 return (isJS ? jsutil.getAppletInfoAsMap() : null);
968 * Get the SwingJS applet ID and combine that with the frameType
971 * "alignment", "desktop", etc., or null
974 public static String getAppID(String frameType)
977 String id = Jalview.getInstance().j2sAppletID;
980 Jalview.getInstance().j2sAppletID = id = (isJS
981 ? (String) jsutil.getAppletAttribute("_id")
984 return id + (frameType == null ? "" : "-" + frameType);
988 * Option to avoid unnecessary seeking of nonexistent resources in JavaScript.
989 * Works in Java as well.
994 public static Locale getLocaleOrNone(Locale loc)
996 return (isJS && loc.getLanguage() == "en" ? new Locale("") : loc);
1000 * From UrlDownloadClient; trivial in JavaScript; painful in Java.
1004 * @throws IOException
1006 public static void download(String urlstring, String outfile)
1010 try (InputStream is = new URL(urlstring).openStream())
1013 { // so much easier!
1014 streamToFile(is, new File(outfile));
1017 temp = Files.createTempFile(".jalview_", ".tmp");
1018 try (FileOutputStream fos = new FileOutputStream(temp.toString());
1019 ReadableByteChannel rbc = Channels.newChannel(is))
1021 fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
1022 // copy tempfile to outfile once our download completes
1023 // incase something goes wrong
1024 Files.copy(temp, Paths.get(outfile),
1025 StandardCopyOption.REPLACE_EXISTING);
1027 } catch (IOException e)
1036 Files.deleteIfExists(temp);
1038 } catch (IOException e)
1040 System.out.println("Exception while deleting download temp file: "