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;
80 private static Boolean isHeadless = null;
82 private static swingjs.api.JSUtilI jsutil;
90 // this is ok - it's a highly embedded method in Java; the deprecation
92 // really a recommended best practice.
93 jsutil = ((JSUtilI) Class.forName("swingjs.JSUtil").newInstance());
94 } catch (InstantiationException | IllegalAccessException
95 | ClassNotFoundException e)
103 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
107 public static boolean isMac()
109 return (isMac == null
110 ? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0))
114 public static int SHORTCUT_KEY_MASK = (Platform.isMac()
115 ? KeyEvent.META_DOWN_MASK
116 : KeyEvent.CTRL_DOWN_MASK);
120 if (!GraphicsEnvironment.isHeadless())
122 // Using non-deprecated Extended key mask modifiers, but Java 8 has no
123 // getMenuShortcutKeyMaskEx method
124 Toolkit tk = Toolkit.getDefaultToolkit();
125 Method method = null;
128 method = tk.getClass().getMethod("getMenuShortcutKeyMaskEx");
129 } catch (Exception e)
132 "Could not find Toolkit method getMenuShortcutKeyMaskEx. Trying getMenuShortcutKeyMask.");
138 method = tk.getClass().getMethod("getMenuShortcutKeyMask");
139 } catch (Exception e)
142 "Could not find Toolkit method getMenuShortcutKeyMaskEx or getMenuShortcutKeyMask.");
150 method.setAccessible(true);
151 SHORTCUT_KEY_MASK = ((int) method.invoke(tk, new Object[0]));
152 } catch (Exception e)
157 if (SHORTCUT_KEY_MASK <= 0xF)
159 // shift this into the extended region (was Java 8)
160 SHORTCUT_KEY_MASK = SHORTCUT_KEY_MASK << 6;
165 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
169 public static boolean isWin()
171 return (isWin == null
172 ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0))
177 * added to check LaF for Linux
181 public static boolean isLinux()
183 return (isLinux == null
184 ? (isLinux = (System.getProperty("os.name").indexOf("Linux") >= 0))
190 * @return true if HTML5 JavaScript
192 public static boolean isJS()
198 * sorry folks - Macs really are different
200 * BH: disabled for SwingJS -- will need to check key-press issues
202 * @return true if we do things in a special way.
204 public static boolean isAMacAndNotJS()
206 return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac);
210 * Check if we are on a Microsoft platform...
212 * @return true if we have to cope with another platform variation
214 public static boolean isWindowsAndNotJS()
216 return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
221 * @return true if we are running in non-interactive no UI mode
223 public static boolean isHeadless()
225 if (isHeadless == null)
227 isHeadless = "true".equals(System.getProperty("java.awt.headless"));
234 * @return nominal maximum command line length for this platform
236 public static int getMaxCommandLineLength()
238 // TODO: determine nominal limits for most platforms.
239 return 2046; // this is the max length for a windows NT system.
243 * Answers the input with every backslash replaced with a double backslash (an
244 * 'escaped' single backslash)
249 public static String escapeBackslashes(String s)
251 return s == null ? null : s.replace("\\", "\\\\");
255 * Answers true if the mouse event has Meta-down (Command key on Mac) or
256 * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
257 * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
258 * Mac, you can use e.isPopupTrigger().
263 public static boolean isControlDown(MouseEvent e)
265 return isControlDown(e, isMac());
269 * Overloaded version of method (to allow unit testing)
275 protected static boolean isControlDown(MouseEvent e, boolean aMac)
278 // System.out.println(e.isPopupTrigger()
279 // + " " + ((SHORTCUT_KEY_MASK & e.getModifiersEx()) != 0)
280 // + " " + e.isControlDown());
282 ? !e.isPopupTrigger()
283 && (SHORTCUT_KEY_MASK & e.getModifiersEx()) != 0
284 : e.isControlDown());
287 // BH: I don't know about that previous method. Here is what SwingJS uses.
288 // Notice the distinction in mouse events. (BUTTON3_MASK == META)
290 // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
291 // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
293 // if (id != MouseEvent.MOUSE_RELEASED)
296 //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
297 //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
299 //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
301 //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
305 // // mac, linux, unix
306 // if (id != MouseEvent.MOUSE_PRESSED)
308 // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
309 // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
310 // return rt || (ctrl && lt);
316 * Windows (not Mac, Linux, or Unix) and right button to test for the
317 * right-mouse pressed event in Windows that would have opened a menu or a
323 public static boolean isWinRightButton(MouseEvent e)
325 // was !isAMac(), but that is true also for Linux and Unix and JS,
327 return isWin() && SwingUtilities.isRightMouseButton(e);
331 * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
332 * without pressing the button.
337 public static boolean isWinMiddleButton(MouseEvent e)
339 // was !isAMac(), but that is true also for Linux and Unix and JS
340 return isWin() && SwingUtilities.isMiddleMouseButton(e);
343 public static boolean allowMnemonics()
348 public final static int TIME_RESET = 0;
350 public final static int TIME_MARK = 1;
352 public static final int TIME_SET = 2;
354 public static final int TIME_GET = 3;
356 public static long time, mark, set, duration;
361 * Platform.timeCheck(null, Platform.TIME_MARK);
365 * Platform.timeCheck("some message", Platform.TIME_MARK);
367 * reset...[set/mark]n...get
372 public static void timeCheck(String msg, int mode)
374 long t = System.currentTimeMillis();
382 System.err.println("Platform: timer reset\t\t\t" + msg);
388 // total time between set/mark points
389 duration += (t - set);
399 System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
400 + "\t" + ((t - mark) / 1000f) + "\t" + msg);
411 System.err.println("Platform: timer dur\t" + ((t - time) / 1000f)
412 + "\t" + ((duration) / 1000f) + "\t" + msg);
419 public static void cacheFileData(String path, Object data)
421 if (isJS && data != null)
423 jsutil.cachePathData(path, data);
427 public static void cacheFileData(File file)
431 byte[] data = Platform.getFileBytes(file);
435 cacheFileData(file.toString(), data);
441 public static byte[] getFileBytes(File f)
443 return (isJS && f != null ? jsutil.getBytes(f) : null);
446 public static byte[] getFileAsBytes(String fileStr)
448 if (isJS && fileStr != null)
450 byte[] bytes = (byte[]) jsutil.getFile(fileStr, false);
451 cacheFileData(fileStr, bytes);
457 public static String getFileAsString(String url)
459 if (isJS && url != null)
461 String ret = (String) jsutil.getFile(url, true);
462 cacheFileData(url, ret);
468 public static boolean setFileBytes(File f, String urlstring)
470 if (isJS && f != null && urlstring != null)
472 @SuppressWarnings("unused")
473 byte[] bytes = getFileAsBytes(urlstring);
474 jsutil.setFileBytes(f, bytes);
480 public static void addJ2SBinaryType(String ext)
484 jsutil.addBinaryFileType(ext);
489 * Encode the URI using JavaScript encodeURIComponent
492 * @return encoded value
494 public static String encodeURI(String value)
497 * @j2sNative value = encodeURIComponent(value);
503 * Open the URL using a simple window call if this is JavaScript
506 * @return true if window has been opened
508 public static boolean openURL(String url) throws IOException
523 public static String getUniqueAppletID()
525 return (isJS ? (String) jsutil.getAppletAttribute("_uniqueId") : null);
530 * Read the Info block for this applet.
535 * @return unique id for this applet
537 public static void readInfoProperties(String prefix, Properties p)
541 String id = getUniqueAppletID();
545 @SuppressWarnings("unused")
546 Object info = jsutil.getAppletAttribute("__Info");
548 * @j2sNative for (key in info) { value = info[key];
551 if (key.indexOf(prefix) == 0)
553 System.out.println("Platform id=" + id + " reading Info." + key
565 public static void setAjaxJSON(URL url)
573 public static Object parseJSON(InputStream response)
574 throws IOException, ParseException
578 return JSON.parse(response);
581 BufferedReader br = null;
584 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
585 return new JSONParser().parse(br);
593 } catch (IOException e)
601 public static Object parseJSON(String json) throws ParseException
603 return (isJS() ? JSON.parse(json) : new JSONParser().parse(json));
606 public static Object parseJSON(Reader r)
607 throws IOException, ParseException
616 return new JSONParser().parse(r);
618 // Using a file reader is not currently supported in SwingJS JavaScript
620 if (r instanceof FileReader)
622 throw new IOException(
623 "StringJS does not support FileReader parsing for JSON -- but it could...");
625 return JSON.parse(r);
630 * Dump the input stream to an output file.
634 * @throws IOException
635 * if the file cannot be created or there is a problem reading the
638 public static void streamToFile(InputStream is, File outFile)
643 jsutil.setFileBytes(outFile, is);
646 FileOutputStream fio = new FileOutputStream(outFile);
649 byte[] bb = new byte[32 * 1024];
651 while ((l = is.read(bb)) > 0)
662 * Add a known domain that implements access-control-allow-origin:*
664 * These should be reviewed periodically.
667 * for a service that is not allowing ajax
669 * @author hansonr@stolaf.edu
672 public static void addJ2SDirectDatabaseCall(String domain)
677 jsutil.addDirectDatabaseCall(domain);
679 "Platform adding known access-control-allow-origin * for domain "
686 * Allow for URL-line command arguments. Untested.
689 public static void getURLCommandArguments()
694 * Retrieve the first query field as command arguments to Jalview. Include
695 * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's
696 * __Info.args element to this value.
699 * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
700 * + "?").split("?")[1].split("#")[0]); a && (System.out.println("URL arguments detected were "+a)) &&
701 * (J2S.thisApplet.__Info.urlargs = a.split(" "));
702 * (!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."));
704 } catch (Throwable t)
711 * A (case sensitive) file path comparator that ignores the difference between
718 public static boolean pathEquals(String path1, String path2)
722 return path2 == null;
728 String p1 = path1.replace('\\', '/');
729 String p2 = path2.replace('\\', '/');
730 return p1.equals(p2);
732 ///////////// JAL-3253 Applet additions //////////////
735 * Retrieve the object's embedded size from a div's style on a page if
736 * embedded in SwingJS.
739 * JFrame or JInternalFrame
740 * @param defaultWidth
741 * use -1 to return null (no default size)
742 * @param defaultHeight
743 * @return the embedded dimensions or null (no default size or not embedded)
745 public static Dimension getDimIfEmbedded(Component frame,
746 int defaultWidth, int defaultHeight)
751 d = (Dimension) getEmbeddedAttribute(frame, "dim");
753 return (d == null && defaultWidth >= 0
754 ? new Dimension(defaultWidth, defaultHeight)
759 public static Regex newRegex(String regex)
761 return newRegex(regex, null);
764 public static Regex newRegex(String searchString, String replaceString)
767 return (replaceString == null ? new Regex(searchString)
768 : new Regex(searchString, replaceString));
771 public static Regex newRegexPerl(String code)
774 return Regex.perlCode(code);
778 * Initialize Java debug logging. A representative sample -- adapt as desired.
780 public static void startJavaLogging()
786 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
787 "java.awt.Component", "java.awt.focus.Component",
788 "java.awt.event.Component",
789 "java.awt.focus.DefaultKeyboardFocusManager");
794 * Initiate Java logging for a given class. Only for Java, not JavaScript;
795 * Allows debugging of complex event processing.
799 public static void logClass(String... classNames)
807 Logger rootLogger = Logger.getLogger("");
808 rootLogger.setLevel(Level.ALL);
809 ConsoleHandler consoleHandler = new ConsoleHandler();
810 consoleHandler.setLevel(Level.ALL);
811 for (int i = classNames.length; --i >= 0;)
813 Logger logger = Logger.getLogger(classNames[i]);
814 logger.setLevel(Level.ALL);
815 logger.addHandler(consoleHandler);
821 * load a resource -- probably a core file -- if and only if a particular
822 * class has not been instantialized. We use a String here because if we used
823 * a .class object, that reference itself would simply load the class, and we
824 * want the core package to include that as well.
826 * @param resourcePath
829 public static void loadStaticResource(String resourcePath,
834 jsutil.loadResourceIfClassUnknown(resourcePath, className);
838 public static void ensureRegex()
842 loadStaticResource("core/core_stevesoft.z.js",
843 "com.stevesoft.pat.Regex");
848 * Set the "app" property of the HTML5 applet object, for example,
849 * "testApplet.app", to point to the Jalview instance. This will be the object
850 * that page developers use that is similar to the original Java applet object
851 * that was accessed via LiveConnect.
855 public static void setAppClass(Object j)
859 jsutil.setAppClass(j);
865 * If this frame is embedded in a web page, return a known type.
868 * a JFrame or JInternalFrame
870 * "name", "node", "init", "dim", or any DOM attribute, such as "id"
871 * @return null if frame is not embedded.
873 public static Object getEmbeddedAttribute(Component frame, String type)
875 return (isJS ? jsutil.getEmbeddedAttribute(frame, type) : null);
878 public static void stackTrace()
882 throw new NullPointerException();
883 } catch (Exception e)
890 public static URL getDocumentBase()
892 return (isJS ? jsutil.getDocumentBase() : null);
895 public static URL getCodeBase()
897 return (isJS ? jsutil.getCodeBase() : null);
900 public static String getUserPath(String subpath)
902 char sep = File.separatorChar;
903 return System.getProperty("user.home") + sep
904 + subpath.replace('/', sep);
908 * This method enables checking if a cached file has exceeded a certain
914 * the threshold in days
917 public static boolean isFileOlderThanThreshold(File file, int noOfDays)
921 // not meaningful in SwingJS -- this is a session-specific temp file. It
922 // doesn't have a timestamp.
925 Path filePath = file.toPath();
926 BasicFileAttributes attr;
930 attr = Files.readAttributes(filePath, BasicFileAttributes.class);
931 diffInDays = (int) ((new Date().getTime()
932 - attr.lastModifiedTime().toMillis())
933 / (1000 * 60 * 60 * 24));
934 // System.out.println("Diff in days : " + diffInDays);
935 } catch (IOException e)
939 return noOfDays <= diffInDays;
943 * Get the leading integer part of a string that begins with an integer.
946 * - the string input to process
948 * - value returned if unsuccessful
951 public static int getLeadingIntegerValue(String input, int failValue)
959 int val = /** @j2sNative 1 ? parseInt(input) : */
961 return (val == val + 0 ? val : failValue);
963 // JavaScript does not support Regex ? lookahead
964 String[] parts = input.split("(?=\\D)(?<=\\d)");
965 if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+"))
967 return Integer.valueOf(parts[0]);
972 public static Map<String, Object> getAppletInfoAsMap()
974 return (isJS ? jsutil.getAppletInfoAsMap() : null);
978 * Get the SwingJS applet ID and combine that with the frameType
981 * "alignment", "desktop", etc., or null
984 public static String getAppID(String frameType)
987 String id = Jalview.getInstance().j2sAppletID;
990 Jalview.getInstance().j2sAppletID = id = (isJS
991 ? (String) jsutil.getAppletAttribute("_id")
994 return id + (frameType == null ? "" : "-" + frameType);
998 * Option to avoid unnecessary seeking of nonexistent resources in JavaScript.
999 * Works in Java as well.
1004 public static Locale getLocaleOrNone(Locale loc)
1006 return (isJS && loc.getLanguage() == "en" ? new Locale("") : loc);
1010 * From UrlDownloadClient; trivial in JavaScript; painful in Java.
1014 * @throws IOException
1016 public static void download(String urlstring, String outfile)
1020 try (InputStream is = new URL(urlstring).openStream())
1023 { // so much easier!
1024 streamToFile(is, new File(outfile));
1027 temp = Files.createTempFile(".jalview_", ".tmp");
1028 try (FileOutputStream fos = new FileOutputStream(temp.toString());
1029 ReadableByteChannel rbc = Channels.newChannel(is))
1031 fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
1032 // copy tempfile to outfile once our download completes
1033 // incase something goes wrong
1034 Files.copy(temp, Paths.get(outfile),
1035 StandardCopyOption.REPLACE_EXISTING);
1037 } catch (IOException e)
1046 Files.deleteIfExists(temp);
1048 } catch (IOException e)
1050 System.out.println("Exception while deleting download temp file: "