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;
41 import java.util.Properties;
42 import java.util.logging.ConsoleHandler;
43 import java.util.logging.Level;
44 import java.util.logging.Logger;
46 import javax.swing.SwingUtilities;
48 import org.json.simple.parser.JSONParser;
49 import org.json.simple.parser.ParseException;
51 import com.stevesoft.pat.Regex;
53 import jalview.javascript.json.JSON;
54 import swingjs.api.JSUtilI;
57 * System platform information used by Applet and Application
64 private static boolean isJS = /** @j2sNative true || */
67 private static Boolean isNoJSMac = null, isNoJSWin = null, isMac = null,
70 private static Boolean isHeadless = null;
72 private static swingjs.api.JSUtilI jsutil;
78 // this is ok - it's a highly embedded method in Java; the deprecation is
79 // really a recommended best practice.
80 jsutil = ((JSUtilI) Class.forName("swingjs.JSUtil").newInstance());
81 } catch (InstantiationException | IllegalAccessException
82 | ClassNotFoundException e)
88 // private static Boolean isHeadless = null;
91 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
95 public static boolean isMac()
98 ? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0))
103 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
107 public static boolean isWin()
109 return (isWin == null
110 ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0))
116 * @return true if HTML5 JavaScript
118 public static boolean isJS()
124 * sorry folks - Macs really are different
126 * BH: disabled for SwingJS -- will need to check key-press issues
128 * @return true if we do things in a special way.
130 public static boolean isAMacAndNotJS()
132 return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac);
136 * Check if we are on a Microsoft plaform...
138 * @return true if we have to cope with another platform variation
140 public static boolean isWindowsAndNotJS()
142 return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
147 * @return true if we are running in non-interactive no UI mode
149 public static boolean isHeadless()
151 if (isHeadless == null)
153 isHeadless = "true".equals(System.getProperty("java.awt.headless"));
160 * @return nominal maximum command line length for this platform
162 public static int getMaxCommandLineLength()
164 // TODO: determine nominal limits for most platforms.
165 return 2046; // this is the max length for a windows NT system.
169 * Answers the input with every backslash replaced with a double backslash (an
170 * 'escaped' single backslash)
175 public static String escapeBackslashes(String s)
177 return s == null ? null : s.replace("\\", "\\\\");
181 * Answers true if the mouse event has Meta-down (Command key on Mac) or
182 * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
183 * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
184 * Mac, you can use e.isPopupTrigger().
189 public static boolean isControlDown(MouseEvent e)
191 return isControlDown(e, isMac());
195 * Overloaded version of method (to allow unit testing)
201 protected static boolean isControlDown(MouseEvent e, boolean aMac)
205 return e.isControlDown();
207 // Jalview 2.11 code below: above is as amended for JalviewJS
209 // * answer false for right mouse button
211 // if (e.isPopupTrigger())
216 // (jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() //
217 // .getMenuShortcutKeyMaskEx()
218 // & jalview.util.ShortcutKeyMaskExWrapper
219 // .getModifiersEx(e)) != 0; // getModifiers()) != 0;
221 // answer false for right mouse button
222 // shortcut key will be META for a Mac
223 return !e.isPopupTrigger()
224 && (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
225 & e.getModifiers()) != 0;
226 // could we use e.isMetaDown() here?
229 // BH: I don't know about that previous method. Here is what SwingJS uses.
230 // Notice the distinction in mouse events. (BUTTON3_MASK == META)
232 // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
233 // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
235 // if (id != MouseEvent.MOUSE_RELEASED)
238 //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
239 //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
241 //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
243 //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
247 // // mac, linux, unix
248 // if (id != MouseEvent.MOUSE_PRESSED)
250 // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
251 // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
252 // return rt || (ctrl && lt);
258 * Windows (not Mac, Linux, or Unix) and right button to test for the
259 * right-mouse pressed event in Windows that would have opened a menu or a
265 public static boolean isWinRightButton(MouseEvent e)
267 // was !isAMac(), but that is true also for Linux and Unix and JS,
269 return isWin() && SwingUtilities.isRightMouseButton(e);
273 * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
274 * without pressing the button.
279 public static boolean isWinMiddleButton(MouseEvent e)
281 // was !isAMac(), but that is true also for Linux and Unix and JS
282 return isWin() && SwingUtilities.isMiddleMouseButton(e);
285 public static boolean allowMnemonics()
290 public final static int TIME_RESET = 0;
292 public final static int TIME_MARK = 1;
294 public static final int TIME_SET = 2;
296 public static final int TIME_GET = 3;
298 public static long time, mark, set, duration;
303 * Platform.timeCheck(null, Platform.TIME_MARK);
307 * Platform.timeCheck("some message", Platform.TIME_MARK);
309 * reset...[set/mark]n...get
314 public static void timeCheck(String msg, int mode)
316 long t = System.currentTimeMillis();
324 System.err.println("Platform: timer reset\t\t\t" + msg);
330 // total time between set/mark points
331 duration += (t - set);
341 System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
342 + "\t" + ((t - mark) / 1000f) + "\t" + msg);
353 System.err.println("Platform: timer dur\t" + ((t - time) / 1000f)
354 + "\t" + ((duration) / 1000f) + "\t" + msg);
361 public static void cacheFileData(String path, Object data)
363 if (isJS && data != null)
365 jsutil.cachePathData(path, data);
370 public static void cacheFileData(File file)
374 byte[] data = Platform.getFileBytes(file);
378 cacheFileData(file.toString(), data);
384 public static byte[] getFileBytes(File f)
386 return (isJS && f != null ? jsutil.getBytes(f) : null);
389 public static byte[] getFileAsBytes(String fileStr)
391 if (isJS && fileStr != null)
393 byte[] bytes = (byte[]) jsutil.getFile(fileStr, false);
394 cacheFileData(fileStr, bytes);
400 public static String getFileAsString(String url)
402 if (isJS && url != null)
404 String ret = (String) jsutil.getFile(url, true);
405 cacheFileData(url, ret);
411 public static boolean setFileBytes(File f, String urlstring)
413 if (isJS && f != null && urlstring != null)
415 @SuppressWarnings("unused")
416 byte[] bytes = getFileAsBytes(urlstring);
417 jsutil.setFileBytes(f, bytes);
424 public static void addJ2SBinaryType(String ext)
428 jsutil.addBinaryFileType(ext);
433 * Encode the URI using JavaScript encodeURIComponent
436 * @return encoded value
438 public static String encodeURI(String value)
441 * @j2sNative value = encodeURIComponent(value);
447 * Open the URL using a simple window call if this is JavaScript
450 * @return true if window has been opened
452 public static boolean openURL(String url) throws IOException
467 public static String getUniqueAppletID()
469 return (isJS ? (String) jsutil.getAppletAttribute("_uniqueId") : null);
474 * Read the Info block for this applet.
479 * @return unique id for this applet
481 public static void readInfoProperties(String prefix, Properties p)
485 String id = getUniqueAppletID();
489 @SuppressWarnings("unused")
490 Object info = jsutil.getAppletAttribute("__Info");
492 * @j2sNative for (key in info) { value = info[key];
495 if (key.indexOf(prefix) == 0)
497 System.out.println("Platform id=" + id + " reading Info." + key
509 public static void setAjaxJSON(URL url)
517 public static Object parseJSON(InputStream response)
518 throws IOException, ParseException
522 return JSON.parse(response);
525 BufferedReader br = null;
528 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
529 return new JSONParser().parse(br);
537 } catch (IOException e)
545 public static Object parseJSON(String json) throws ParseException
547 return (isJS() ? JSON.parse(json)
548 : new JSONParser().parse(json));
551 public static Object parseJSON(Reader r)
552 throws IOException, ParseException
561 return new JSONParser().parse(r);
563 // Using a file reader is not currently supported in SwingJS JavaScript
565 if (r instanceof FileReader)
567 throw new IOException(
568 "StringJS does not support FileReader parsing for JSON -- but it could...");
570 return JSON.parse(r);
574 * Dump the input stream to an output file.
578 * @throws IOException
579 * if the file cannot be created or there is a problem
580 * reading the input stream.
582 public static void streamToFile(InputStream is, File outFile)
588 jsutil.setFileBytes(outFile, is);
592 FileOutputStream fio = new FileOutputStream(outFile);
595 byte[] bb = new byte[32 * 1024];
597 while ((l = is.read(bb)) > 0)
608 * Add a known domain that implements access-control-allow-origin:*
610 * These should be reviewed periodically.
613 * for a service that is not allowing ajax
615 * @author hansonr@stolaf.edu
618 public static void addJ2SDirectDatabaseCall(String domain)
623 jsutil.addDirectDatabaseCall(domain);
626 "Platform adding known access-control-allow-origin * for domain "
632 public static void getURLCommandArguments()
636 * Retrieve the first query field as command arguments to Jalview. Include
637 * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
638 * element to this value.
641 * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
642 * + "?").split("?")[1].split("#")[0]); a &&
643 * (J2S.thisApplet.__Info.args = a.split(" "));
649 * A (case sensitive) file path comparator that ignores the difference between /
656 public static boolean pathEquals(String path1, String path2)
660 return path2 == null;
666 String p1 = path1.replace('\\', '/');
667 String p2 = path2.replace('\\', '/');
668 return p1.equals(p2);
673 ///////////// JAL-3253 Applet additions //////////////
677 * Retrieve the object's embedded size from a div's style on a page if
678 * embedded in SwingJS.
681 * JFrame or JInternalFrame
682 * @param defaultWidth
683 * use -1 to return null (no default size)
684 * @param defaultHeight
685 * @return the embedded dimensions or null (no default size or not embedded)
687 public static Dimension getDimIfEmbedded(Component frame,
688 int defaultWidth, int defaultHeight)
693 d = (Dimension) getEmbeddedAttribute(frame, "dim");
695 return (d == null && defaultWidth >= 0
696 ? new Dimension(defaultWidth, defaultHeight)
701 public static Regex newRegex(String regex)
703 return newRegex(regex, null);
706 public static Regex newRegex(String searchString, String replaceString)
709 return (replaceString == null ? new Regex(searchString)
710 : new Regex(searchString, replaceString));
713 public static Regex newRegexPerl(String code)
716 return Regex.perlCode(code);
720 * Initialize Java debug logging. A representative sample -- adapt as desired.
722 public static void startJavaLogging()
728 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
729 "java.awt.Component", "java.awt.focus.Component",
730 "java.awt.event.Component",
731 "java.awt.focus.DefaultKeyboardFocusManager");
736 * Initiate Java logging for a given class. Only for Java, not JavaScript;
737 * Allows debugging of complex event processing.
741 public static void logClass(String... classNames)
749 Logger rootLogger = Logger.getLogger("");
750 rootLogger.setLevel(Level.ALL);
751 ConsoleHandler consoleHandler = new ConsoleHandler();
752 consoleHandler.setLevel(Level.ALL);
753 for (int i = classNames.length; --i >= 0;)
755 Logger logger = Logger.getLogger(classNames[i]);
756 logger.setLevel(Level.ALL);
757 logger.addHandler(consoleHandler);
764 * load a resource -- probably a core file -- if and only if a particular
765 * class has not been instantialized. We use a String here because if we used
766 * a .class object, that reference itself would simply load the class, and we
767 * want the core package to include that as well.
769 * @param resourcePath
772 public static void loadStaticResource(String resourcePath,
777 jsutil.loadResourceIfClassUnknown(resourcePath, className);
781 public static void ensureRegex()
785 loadStaticResource("core/core_stevesoft.z.js",
786 "com.stevesoft.pat.Regex");
791 * Set the "app" property of the HTML5 applet object, for example,
792 * "testApplet.app", to point to the Jalview instance. This will be the object
793 * that page developers use that is similar to the original Java applet object
794 * that was accessed via LiveConnect.
798 public static void setAppClass(Object j)
802 jsutil.setAppletAttribute("app", j);
808 * If this frame ia embedded in a web page, return a known type.
811 * a JFrame or JInternalFrame
813 * @return null if frame is not embedded.
815 public static Object getEmbeddedAttribute(Component frame, String type)
817 return (isJS ? jsutil.getEmbeddedAttribute(frame, type) : null);
820 public static void stackTrace()
824 throw new NullPointerException();
825 } catch (Exception e)
832 public static URL getDocumentBase()
834 return (isJS ? jsutil.getDocumentBase() : null);
837 public static URL getCodeBase()
839 return (isJS ? jsutil.getCodeBase() : null);
842 public static String getUserPath(String subpath)
844 char sep = File.separatorChar;
845 return System.getProperty("user.home") + sep + subpath.replace('/', sep);
849 * This method enables checking if a cached file has exceeded a certain
855 * the threshold in days
858 public static boolean isFileOlderThanThreshold(File file, int noOfDays)
861 // not meaningful in SwingJS -- this is a session-specific temp file. It doesn't have a timestamp.
864 Path filePath = file.toPath();
865 BasicFileAttributes attr;
869 attr = Files.readAttributes(filePath, BasicFileAttributes.class);
870 diffInDays = (int) ((new Date().getTime()
871 - attr.lastModifiedTime().toMillis())
872 / (1000 * 60 * 60 * 24));
873 // System.out.println("Diff in days : " + diffInDays);
874 } catch (IOException e)
878 return noOfDays <= diffInDays;
882 * Get the leading integer part of a string that begins with an integer.
885 * - the string input to process
887 * - value returned if unsuccessful
890 public static int getLeadingIntegerValue(String input, int failValue)
897 int val = /** @j2sNative 1 ? parseInt(input) : */ 0;
898 return (val == val + 0 ? val : failValue);
900 // JavaScript does not support Regex ? lookahead
901 String[] parts = input.split("(?=\\D)(?<=\\d)");
902 if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+"))
904 return Integer.valueOf(parts[0]);
909 public static Map<String, Object> getAppletInfoAsMap()
911 return (isJS ? jsutil.getAppletInfoAsMap() : null);