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;
26 import java.awt.Toolkit;
27 import java.awt.event.KeyEvent;
28 import java.awt.event.MouseEvent;
29 import java.io.BufferedReader;
31 import java.io.FileOutputStream;
32 import java.io.FileReader;
33 import java.io.IOException;
34 import java.io.InputStream;
35 import java.io.InputStreamReader;
36 import java.io.Reader;
37 import java.lang.reflect.Method;
39 import java.nio.channels.Channels;
40 import java.nio.channels.ReadableByteChannel;
41 import java.nio.file.Files;
42 import java.nio.file.Path;
43 import java.nio.file.Paths;
44 import java.nio.file.StandardCopyOption;
45 import java.nio.file.attribute.BasicFileAttributes;
46 import java.util.Date;
47 import java.util.Locale;
49 import java.util.Properties;
50 import java.util.logging.ConsoleHandler;
51 import java.util.logging.Level;
52 import java.util.logging.Logger;
54 import javax.swing.SwingUtilities;
56 import org.json.simple.parser.JSONParser;
57 import org.json.simple.parser.ParseException;
59 import com.stevesoft.pat.Regex;
61 import jalview.bin.Jalview;
62 import jalview.javascript.json.JSON;
63 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,
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)
100 // private static Boolean isHeadless = null;
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 SHIFT_DOWN_MASK = KeyEvent.SHIFT_DOWN_MASK;
116 public static int ALT_DOWN_MASK = KeyEvent.ALT_DOWN_MASK;
118 public static int SHORTCUT_KEY_MASK = (Platform.isMac() ? KeyEvent.META_DOWN_MASK : KeyEvent.CTRL_DOWN_MASK);
122 if (!GraphicsEnvironment.isHeadless())
127 Toolkit tk = Toolkit.getDefaultToolkit();
128 Method method = tk.getClass().getMethod("getMenuShortcutKeyMaskEx");
130 method = tk.getClass().getMethod("getMenuShortcutKeyMask");
131 SHORTCUT_KEY_MASK = ((int) method.invoke(tk, new Object[0]));
132 if (SHORTCUT_KEY_MASK <= 0xF)
134 // shift this into the extended region (was Java 8)
135 SHORTCUT_KEY_MASK = SHORTCUT_KEY_MASK << 6;
137 } catch (Exception e)
145 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
149 public static boolean isWin()
151 return (isWin == null
152 ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0))
158 * @return true if HTML5 JavaScript
160 public static boolean isJS()
166 * sorry folks - Macs really are different
168 * BH: disabled for SwingJS -- will need to check key-press issues
170 * @return true if we do things in a special way.
172 public static boolean isAMacAndNotJS()
174 return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac);
178 * Check if we are on a Microsoft plaform...
180 * @return true if we have to cope with another platform variation
182 public static boolean isWindowsAndNotJS()
184 return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
189 * @return true if we are running in non-interactive no UI mode
191 public static boolean isHeadless()
193 if (isHeadless == null)
195 isHeadless = "true".equals(System.getProperty("java.awt.headless"));
202 * @return nominal maximum command line length for this platform
204 public static int getMaxCommandLineLength()
206 // TODO: determine nominal limits for most platforms.
207 return 2046; // this is the max length for a windows NT system.
211 * Answers the input with every backslash replaced with a double backslash (an
212 * 'escaped' single backslash)
217 public static String escapeBackslashes(String s)
219 return s == null ? null : s.replace("\\", "\\\\");
223 * Answers true if the mouse event has Meta-down (Command key on Mac) or
224 * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
225 * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
226 * Mac, you can use e.isPopupTrigger().
231 public static boolean isControlDown(MouseEvent e)
233 return isControlDown(e, isMac());
237 * Overloaded version of method (to allow unit testing)
243 protected static boolean isControlDown(MouseEvent e, boolean aMac)
246 System.out.println(e.isPopupTrigger()
247 + " " + ((SHORTCUT_KEY_MASK & e.getModifiersEx()) != 0)
248 + " " + e.isControlDown());
249 return (aMac ? !e.isPopupTrigger()
250 && (SHORTCUT_KEY_MASK & e.getModifiersEx()) != 0
251 : e.isControlDown());
254 // BH: I don't know about that previous method. Here is what SwingJS uses.
255 // Notice the distinction in mouse events. (BUTTON3_MASK == META)
257 // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
258 // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
260 // if (id != MouseEvent.MOUSE_RELEASED)
263 //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
264 //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
266 //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
268 //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
272 // // mac, linux, unix
273 // if (id != MouseEvent.MOUSE_PRESSED)
275 // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
276 // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
277 // return rt || (ctrl && lt);
283 * Windows (not Mac, Linux, or Unix) and right button to test for the
284 * right-mouse pressed event in Windows that would have opened a menu or a
290 public static boolean isWinRightButton(MouseEvent e)
292 // was !isAMac(), but that is true also for Linux and Unix and JS,
294 return isWin() && SwingUtilities.isRightMouseButton(e);
298 * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
299 * without pressing the button.
304 public static boolean isWinMiddleButton(MouseEvent e)
306 // was !isAMac(), but that is true also for Linux and Unix and JS
307 return isWin() && SwingUtilities.isMiddleMouseButton(e);
310 public static boolean allowMnemonics()
315 public final static int TIME_RESET = 0;
317 public final static int TIME_MARK = 1;
319 public static final int TIME_SET = 2;
321 public static final int TIME_GET = 3;
323 public static long time, mark, set, duration;
328 * Platform.timeCheck(null, Platform.TIME_MARK);
332 * Platform.timeCheck("some message", Platform.TIME_MARK);
334 * reset...[set/mark]n...get
339 public static void timeCheck(String msg, int mode)
341 long t = System.currentTimeMillis();
349 System.err.println("Platform: timer reset\t\t\t" + msg);
355 // total time between set/mark points
356 duration += (t - set);
366 System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
367 + "\t" + ((t - mark) / 1000f) + "\t" + msg);
378 System.err.println("Platform: timer dur\t" + ((t - time) / 1000f)
379 + "\t" + ((duration) / 1000f) + "\t" + msg);
386 public static void cacheFileData(String path, Object data)
388 if (isJS && data != null)
390 jsutil.cachePathData(path, data);
394 public static void cacheFileData(File file)
398 byte[] data = Platform.getFileBytes(file);
402 cacheFileData(file.toString(), data);
408 public static byte[] getFileBytes(File f)
410 return (isJS && f != null ? jsutil.getBytes(f) : null);
413 public static byte[] getFileAsBytes(String fileStr)
415 if (isJS && fileStr != null)
417 byte[] bytes = (byte[]) jsutil.getFile(fileStr, false);
418 cacheFileData(fileStr, bytes);
424 public static String getFileAsString(String url)
426 if (isJS && url != null)
428 String ret = (String) jsutil.getFile(url, true);
429 cacheFileData(url, ret);
435 public static boolean setFileBytes(File f, String urlstring)
437 if (isJS && f != null && urlstring != null)
439 @SuppressWarnings("unused")
440 byte[] bytes = getFileAsBytes(urlstring);
441 jsutil.setFileBytes(f, bytes);
447 public static void addJ2SBinaryType(String ext)
451 jsutil.addBinaryFileType(ext);
456 * Encode the URI using JavaScript encodeURIComponent
459 * @return encoded value
461 public static String encodeURI(String value)
464 * @j2sNative value = encodeURIComponent(value);
470 * Open the URL using a simple window call if this is JavaScript
473 * @return true if window has been opened
475 public static boolean openURL(String url) throws IOException
490 public static String getUniqueAppletID()
492 return (isJS ? (String) jsutil.getAppletAttribute("_uniqueId") : null);
496 * Read the Info block for this applet.
501 * @return unique id for this applet
503 public static void readInfoProperties(String prefix, Properties p)
507 String id = getUniqueAppletID();
511 @SuppressWarnings("unused")
512 Object info = jsutil.getAppletAttribute("__Info");
514 * @j2sNative for (key in info) { value = info[key];
517 if (key.indexOf(prefix) == 0)
519 System.out.println("Platform id=" + id + " reading Info." + key
531 public static void setAjaxJSON(URL url)
539 public static Object parseJSON(InputStream response)
540 throws IOException, ParseException
544 return JSON.parse(response);
547 BufferedReader br = null;
550 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
551 return new JSONParser().parse(br);
559 } catch (IOException e)
567 public static Object parseJSON(String json) throws ParseException
569 return (isJS() ? JSON.parse(json) : new JSONParser().parse(json));
572 public static Object parseJSON(Reader r)
573 throws IOException, ParseException
582 return new JSONParser().parse(r);
584 // Using a file reader is not currently supported in SwingJS JavaScript
586 if (r instanceof FileReader)
588 throw new IOException(
589 "StringJS does not support FileReader parsing for JSON -- but it could...");
591 return JSON.parse(r);
595 * Dump the input stream to an output file.
599 * @throws IOException
600 * if the file cannot be created or there is a problem reading the
603 public static void streamToFile(InputStream is, File outFile)
609 jsutil.setFileBytes(outFile, is);
613 FileOutputStream fio = new FileOutputStream(outFile);
616 byte[] bb = new byte[32 * 1024];
618 while ((l = is.read(bb)) > 0)
629 * Add a known domain that implements access-control-allow-origin:*
631 * These should be reviewed periodically.
634 * for a service that is not allowing ajax
636 * @author hansonr@stolaf.edu
639 public static void addJ2SDirectDatabaseCall(String domain)
644 jsutil.addDirectDatabaseCall(domain);
647 "Platform adding known access-control-allow-origin * for domain "
654 * Allow for URL-line command arguments. Untested.
657 public static void getURLCommandArguments()
662 * Retrieve the first query field as command arguments to Jalview. Include
663 * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
664 * element to this value.
667 * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
668 * + "?").split("?")[1].split("#")[0]); a &&
669 * (J2S.thisApplet.__Info.args = a.split(" "));
671 * System.out.println("URL arguments: " + a);
673 } catch (Throwable t) {
678 * A (case sensitive) file path comparator that ignores the difference between
685 public static boolean pathEquals(String path1, String path2)
689 return path2 == null;
695 String p1 = path1.replace('\\', '/');
696 String p2 = path2.replace('\\', '/');
697 return p1.equals(p2);
700 ///////////// JAL-3253 Applet additions //////////////
703 * Retrieve the object's embedded size from a div's style on a page if
704 * embedded in SwingJS.
707 * JFrame or JInternalFrame
708 * @param defaultWidth
709 * use -1 to return null (no default size)
710 * @param defaultHeight
711 * @return the embedded dimensions or null (no default size or not embedded)
713 public static Dimension getDimIfEmbedded(Component frame,
714 int defaultWidth, int defaultHeight)
719 d = (Dimension) getEmbeddedAttribute(frame, "dim");
721 return (d == null && defaultWidth >= 0
722 ? new Dimension(defaultWidth, defaultHeight)
727 public static Regex newRegex(String regex)
729 return newRegex(regex, null);
732 public static Regex newRegex(String searchString, String replaceString)
735 return (replaceString == null ? new Regex(searchString)
736 : new Regex(searchString, replaceString));
739 public static Regex newRegexPerl(String code)
742 return Regex.perlCode(code);
746 * Initialize Java debug logging. A representative sample -- adapt as desired.
748 public static void startJavaLogging()
754 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
755 "java.awt.Component", "java.awt.focus.Component",
756 "java.awt.event.Component",
757 "java.awt.focus.DefaultKeyboardFocusManager");
762 * Initiate Java logging for a given class. Only for Java, not JavaScript;
763 * Allows debugging of complex event processing.
767 public static void logClass(String... classNames)
775 Logger rootLogger = Logger.getLogger("");
776 rootLogger.setLevel(Level.ALL);
777 ConsoleHandler consoleHandler = new ConsoleHandler();
778 consoleHandler.setLevel(Level.ALL);
779 for (int i = classNames.length; --i >= 0;)
781 Logger logger = Logger.getLogger(classNames[i]);
782 logger.setLevel(Level.ALL);
783 logger.addHandler(consoleHandler);
789 * load a resource -- probably a core file -- if and only if a particular
790 * class has not been instantialized. We use a String here because if we used
791 * a .class object, that reference itself would simply load the class, and we
792 * want the core package to include that as well.
794 * @param resourcePath
797 public static void loadStaticResource(String resourcePath,
802 jsutil.loadResourceIfClassUnknown(resourcePath, className);
806 public static void ensureRegex()
810 loadStaticResource("core/core_stevesoft.z.js",
811 "com.stevesoft.pat.Regex");
816 * Set the "app" property of the HTML5 applet object, for example,
817 * "testApplet.app", to point to the Jalview instance. This will be the object
818 * that page developers use that is similar to the original Java applet object
819 * that was accessed via LiveConnect.
823 public static void setAppClass(Object j)
827 jsutil.setAppClass(j);
833 * If this frame is embedded in a web page, return a known type.
836 * a JFrame or JInternalFrame
837 * @param type "name", "node", "init", "dim", or any DOM attribute, such as "id"
838 * @return null if frame is not embedded.
840 public static Object getEmbeddedAttribute(Component frame, String type)
842 return (isJS ? jsutil.getEmbeddedAttribute(frame, type) : null);
845 public static void stackTrace()
849 throw new NullPointerException();
850 } catch (Exception e)
857 public static URL getDocumentBase()
859 return (isJS ? jsutil.getDocumentBase() : null);
862 public static URL getCodeBase()
864 return (isJS ? jsutil.getCodeBase() : null);
867 public static String getUserPath(String subpath)
869 char sep = File.separatorChar;
870 return System.getProperty("user.home") + sep
871 + subpath.replace('/', sep);
875 * This method enables checking if a cached file has exceeded a certain
881 * the threshold in days
884 public static boolean isFileOlderThanThreshold(File file, int noOfDays)
888 // not meaningful in SwingJS -- this is a session-specific temp file. It
889 // doesn't have a timestamp.
892 Path filePath = file.toPath();
893 BasicFileAttributes attr;
897 attr = Files.readAttributes(filePath, BasicFileAttributes.class);
898 diffInDays = (int) ((new Date().getTime()
899 - attr.lastModifiedTime().toMillis())
900 / (1000 * 60 * 60 * 24));
901 // System.out.println("Diff in days : " + diffInDays);
902 } catch (IOException e)
906 return noOfDays <= diffInDays;
910 * Get the leading integer part of a string that begins with an integer.
913 * - the string input to process
915 * - value returned if unsuccessful
918 public static int getLeadingIntegerValue(String input, int failValue)
926 int val = /** @j2sNative 1 ? parseInt(input) : */
928 return (val == val + 0 ? val : failValue);
930 // JavaScript does not support Regex ? lookahead
931 String[] parts = input.split("(?=\\D)(?<=\\d)");
932 if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+"))
934 return Integer.valueOf(parts[0]);
939 public static Map<String, Object> getAppletInfoAsMap()
941 return (isJS ? jsutil.getAppletInfoAsMap() : null);
945 * Get the SwingJS applet ID and combine that with the frameType
948 * "alignment", "desktop", etc., or null
951 public static String getAppID(String frameType)
954 String id = Jalview.getInstance().j2sAppletID;
957 Jalview.getInstance().j2sAppletID = id = (isJS ? (String) jsutil
958 .getAppletAttribute("_id") : "jalview");
960 return id + (frameType == null ? "" : "-" + frameType);
965 * Option to avoid unnecessary seeking of nonexistent resources in JavaScript.
966 * Works in Java as well.
971 public static Locale getLocaleOrNone(Locale loc)
973 return (isJS && loc.getLanguage() == "en" ? new Locale("") : loc);
977 * From UrlDownloadClient; trivial in JavaScript; painful in Java.
981 * @throws IOException
983 public static void download(String urlstring, String outfile)
987 try (InputStream is = new URL(urlstring).openStream())
991 streamToFile(is, new File(outfile));
994 temp = Files.createTempFile(".jalview_", ".tmp");
995 try (FileOutputStream fos = new FileOutputStream(temp.toString());
996 ReadableByteChannel rbc = Channels.newChannel(is))
998 fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
999 // copy tempfile to outfile once our download completes
1000 // incase something goes wrong
1001 Files.copy(temp, Paths.get(outfile),
1002 StandardCopyOption.REPLACE_EXISTING);
1004 } catch (IOException e)
1013 Files.deleteIfExists(temp);
1015 } catch (IOException e)
1017 System.out.println("Exception while deleting download temp file: "