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 jalview.javascript.json.JSON;
25 import java.awt.Dimension;
26 import java.awt.Toolkit;
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.net.MalformedURLException;
38 import java.util.Properties;
39 import java.util.logging.ConsoleHandler;
40 import java.util.logging.Level;
41 import java.util.logging.Logger;
43 import javax.swing.JComponent;
44 import javax.swing.SwingUtilities;
46 import org.json.simple.parser.JSONParser;
47 import org.json.simple.parser.ParseException;
49 import com.stevesoft.pat.Regex;
51 import swingjs.api.JSUtilI;
54 * System platform information used by Applet and Application
61 private static boolean isJS = /** @j2sNative true || */
64 private static Boolean isNoJSMac = null, isNoJSWin = null, isMac = null,
67 private static swingjs.api.JSUtilI jsutil;
73 jsutil = ((JSUtilI) Class.forName("swingjs.JSUtil").newInstance());
74 } catch (InstantiationException | IllegalAccessException
75 | ClassNotFoundException e)
81 // private static Boolean isHeadless = null;
84 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
88 public static boolean isMac()
91 ? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0))
96 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
100 public static boolean isWin()
102 return (isWin == null
103 ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0))
109 * @return true if HTML5 JavaScript
111 public static boolean isJS()
117 * sorry folks - Macs really are different
119 * BH: disabled for SwingJS -- will need to check key-press issues
121 * @return true if we do things in a special way.
123 public static boolean isAMacAndNotJS()
125 return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac);
129 * Check if we are on a Microsoft plaform...
131 * @return true if we have to cope with another platform variation
133 public static boolean isWindowsAndNotJS()
135 return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
140 // * @return true if we are running in non-interactive no UI mode
142 // public static boolean isHeadless()
144 // if (isHeadless == null)
146 // isHeadless = "true".equals(System.getProperty("java.awt.headless"));
148 // return isHeadless;
153 * @return nominal maximum command line length for this platform
155 public static int getMaxCommandLineLength()
157 // TODO: determine nominal limits for most platforms.
158 return 2046; // this is the max length for a windows NT system.
162 * escape a string according to the local platform's escape character
165 * @return escaped file
167 public static String escapeString(String file)
169 StringBuffer f = new StringBuffer();
170 int p = 0, lastp = 0;
171 while ((p = file.indexOf('\\', lastp)) > -1)
173 f.append(file.subSequence(lastp, p));
177 f.append(file.substring(lastp));
182 * Answers true if the mouse event has Meta-down (Command key on Mac) or
183 * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
184 * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
185 * Mac, you can use e.isPopupTrigger().
190 public static boolean isControlDown(MouseEvent e)
192 return isControlDown(e, isMac());
196 * Overloaded version of method (to allow unit testing)
202 protected static boolean isControlDown(MouseEvent e, boolean aMac)
206 return e.isControlDown();
208 // answer false for right mouse button
209 // shortcut key will be META for a Mac
210 return !e.isPopupTrigger()
211 && (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
212 & e.getModifiers()) != 0;
213 // could we use e.isMetaDown() here?
216 // BH: I don't know about that previous method. Here is what SwingJS uses.
217 // Notice the distinction in mouse events. (BUTTON3_MASK == META)
219 // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
220 // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
222 // if (id != MouseEvent.MOUSE_RELEASED)
225 //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
226 //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
228 //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
230 //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
234 // // mac, linux, unix
235 // if (id != MouseEvent.MOUSE_PRESSED)
237 // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
238 // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
239 // return rt || (ctrl && lt);
245 * Windows (not Mac, Linux, or Unix) and right button to test for the
246 * right-mouse pressed event in Windows that would have opened a menu or a
252 public static boolean isWinRightButton(MouseEvent e)
254 // was !isAMac(), but that is true also for Linux and Unix and JS,
256 return isWin() && SwingUtilities.isRightMouseButton(e);
260 * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
261 * without pressing the button.
266 public static boolean isWinMiddleButton(MouseEvent e)
268 // was !isAMac(), but that is true also for Linux and Unix and JS
269 return isWin() && SwingUtilities.isMiddleMouseButton(e);
272 public static boolean allowMnemonics()
277 public final static int TIME_RESET = 0;
279 public final static int TIME_MARK = 1;
281 public static final int TIME_SET = 2;
283 public static final int TIME_GET = 3;
285 public static long time, mark, set, duration;
290 * Platform.timeCheck(null, Platform.TIME_MARK);
294 * Platform.timeCheck("some message", Platform.TIME_MARK);
296 * reset...[set/mark]n...get
301 public static void timeCheck(String msg, int mode)
303 long t = System.currentTimeMillis();
311 System.err.println("Platform: timer reset\t\t\t" + msg);
317 // total time between set/mark points
318 duration += (t - set);
328 System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
329 + "\t" + ((t - mark) / 1000f) + "\t" + msg);
340 System.err.println("Platform: timer get\t" + ((t - time) / 1000f)
341 + "\t" + ((duration) / 1000f) + "\t" + msg);
348 public static void cacheFileData(String path, Object data)
350 if (!isJS() || data == null)
354 jsutil.cachePathData(path, data);
357 public static void cacheFileData(File file)
360 if (!isJS() || (data = Platform.getFileBytes(file)) == null)
364 cacheFileData(file.toString(), data);
367 public static byte[] getFileBytes(File f)
370 return jsutil.getBytes(f);
373 public static byte[] getFileAsBytes(String fileStr)
375 byte[] bytes = (byte[]) jsutil.getFile(fileStr, false);
376 cacheFileData(fileStr, bytes);
380 @SuppressWarnings("unused")
381 public static String getFileAsString(String url)
383 String ret = (String) jsutil.getFile(url, true);
384 cacheFileData(url, ret);
388 public static boolean setFileBytes(File f, String urlstring)
394 @SuppressWarnings("unused")
395 byte[] bytes = getFileAsBytes(urlstring);
396 jsutil.setFileBytes(f, bytes);
400 public static void addJ2SBinaryType(String ext)
406 * J2S._binaryTypes.push("." + ext + "?");
412 * Encode the URI using JavaScript encodeURIComponent
415 * @return encoded value
417 public static String encodeURI(String value)
420 * @j2sNative value = encodeURIComponent(value);
426 * Open the URL using a simple window call if this is JavaScript
429 * @return true if window has been opened
431 public static boolean openURL(String url) throws IOException
435 BrowserLauncher.openURL(url);
447 public static String getUniqueAppletID()
449 @SuppressWarnings("unused")
450 ThreadGroup g = Thread.currentThread().getThreadGroup();
452 * @j2sNative return g.秘html5Applet._uniqueId;
460 * Read the Info block for this applet.
465 * @return unique id for this applet
467 public static void readInfoProperties(String prefix, Properties p)
473 @SuppressWarnings("unused")
474 ThreadGroup g = Thread.currentThread().getThreadGroup();
475 String id = getUniqueAppletID();
476 String key = "", value = "";
478 * @j2sNative var info = g.秘html5Applet.__Info || {}; for (var key in info)
479 * { if (key.indexOf(prefix) == 0) { value = "" + info[key];
483 "Platform id=" + id + " reading Info." + key + " = " + value);
494 public static void setAjaxJSON(URL url)
502 public static Object parseJSON(InputStream response)
503 throws IOException, ParseException
507 return JSON.parse(response);
510 BufferedReader br = null;
513 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
514 return new JSONParser().parse(br);
522 } catch (IOException e)
530 public static Object parseJSON(String json) throws ParseException
532 return (isJS() ? JSON.parse(json)
533 : new JSONParser().parse(json));
536 public static Object parseJSON(Reader r)
537 throws IOException, ParseException
546 return new JSONParser().parse(r);
548 // Using a file reader is not currently supported in SwingJS JavaScript
550 if (r instanceof FileReader)
552 throw new IOException(
553 "StringJS does not support FileReader parsing for JSON -- but it could...");
555 return JSON.parse(r);
560 * Dump the input stream to an output file.
564 * @throws IOException
565 * if the file cannot be created or there is a problem reading the
568 public static void streamToFile(InputStream is, File outFile)
571 FileOutputStream fio = new FileOutputStream(outFile);
576 * @j2sNative outFile.setBytes$O && outFile.setBytes$O(is) &&
582 byte[] bb = new byte[32 * 1024];
584 while ((l = is.read(bb)) > 0)
595 * Add a known domain that implements access-control-allow-origin:*
597 * These should be reviewed periodically.
600 * for a service that is not allowing ajax
602 * @author hansonr@stolaf.edu
605 public static void addJ2SDirectDatabaseCall(String domain)
611 "Platform adding known access-control-allow-origin * for domain "
616 * J2S.addDirectDatabaseCall(domain);
622 public static void getURLCommandArguments()
626 * Retrieve the first query field as command arguments to Jalview. Include
627 * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
628 * element to this value.
631 * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
632 * + "?").split("?")[1].split("#")[0]); a &&
633 * (J2S.thisApplet.__Info.args = a.split(" "));
638 public static URL getDocumentBase()
644 @SuppressWarnings("unused")
645 Object g = Thread.currentThread().getThreadGroup();
647 * @j2sNative g.秘html5Applet._appletPanel.appletDocumentBase
652 } catch (MalformedURLException e)
658 public static URL getCodeBase()
664 @SuppressWarnings("unused")
665 Object g = Thread.currentThread().getThreadGroup();
667 * @j2sNative g.秘html5Applet._appletPanel.appletCodeBase
672 } catch (MalformedURLException e)
679 * load a resource -- probably a core file -- if and only if a particular
680 * class has not been instantialized. We use a String here because if we used
681 * a .class object, that reference itself would simply load the class, and we
682 * want the core package to include that as well.
684 * @param resourcePath
687 public static void loadStaticResource(Object resourcePath,
692 * @j2sNative if (!swingjs.JSUtil.isClassLoaded$S(className))
693 * swingjs.JSUtil.loadStaticResource$S(resourcePath);
697 public static void ensureRegex()
699 loadStaticResource("core/core_stevesoft.z.js",
700 "com.stevesoft.pat.Regex");
703 public static Regex newRegex(String searchString, String replaceString)
706 return (replaceString == null ? new Regex(searchString)
707 : new Regex(searchString, replaceString));
710 public static Regex newRegexPerl(String code)
713 return Regex.perlCode(code);
717 * Initialize Java debug logging. A representative sample -- adapt as desired.
719 public static void startJavaLogging()
725 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
726 "java.awt.Component", "java.awt.focus.Component",
727 "java.awt.event.Component",
728 "java.awt.focus.DefaultKeyboardFocusManager");
733 * Initiate Java logging for a given class. Only for Java, not JavaScript;
734 * Allows debugging of complex event processing.
738 public static void logClass(String... classNames)
746 Logger rootLogger = Logger.getLogger("");
747 rootLogger.setLevel(Level.ALL);
748 ConsoleHandler consoleHandler = new ConsoleHandler();
749 consoleHandler.setLevel(Level.ALL);
750 for (int i = classNames.length; --i >= 0;)
752 Logger logger = Logger.getLogger(classNames[i]);
753 logger.setLevel(Level.ALL);
754 logger.addHandler(consoleHandler);
760 * Set the "app" property of the HTML5 applet object, for example,
761 * "testApplet.app", to point to the Jalview instance. This will be the object
762 * that page developers use that is similar to the original Java applet object
763 * that was accessed via LiveConnect.
767 public static void setAppClass(Object j)
773 @SuppressWarnings("unused")
774 Thread t = Thread.currentThread();
776 * Set up "testApplet.app" to be this instance
780 * try {self[t.name].app = j}catch(e){}
785 * Retrieve the object's embedded size from a div's style on a page if
786 * embedded in SwingJS.
789 * JFrame or JInternalFrame
790 * @param defaultWidth
791 * use -1 to return null (no default size)
792 * @param defaultHeight
793 * @return the embedded dimensions or null (no default size or not embedded)
795 public static Dimension getDimIfEmbedded(JComponent frame,
796 int defaultWidth, int defaultHeight)
798 Dimension d = /** @j2sNative frame.ui.getEmbedded$S("dim") || */
800 return (d == null && defaultWidth >= 0
801 ? new Dimension(defaultWidth, defaultHeight)
807 * If this frame Is this frame embedded in a web page, return a known type.
810 * a JFrame or JInternalFrame
812 * @return null if frame is not embedded.
814 public static Object getEmbeddedAttribute(Object frame, String type)
820 return (/** @j2sNative frame.ui.getEmbedded$S(type) || */
824 public static void stackTrace()
828 throw new NullPointerException();
829 } catch (Exception e)