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;
52 * System platform information used by Applet and Application
59 private static boolean isJS = /** @j2sNative true || */
62 private static Boolean isNoJSMac = null, isNoJSWin = null, isMac = null,
65 // private static Boolean isHeadless = null;
68 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
72 public static boolean isMac()
75 ? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0))
80 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
84 public static boolean isWin()
87 ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0))
93 * @return true if HTML5 JavaScript
95 public static boolean isJS()
101 * sorry folks - Macs really are different
103 * BH: disabled for SwingJS -- will need to check key-press issues
105 * @return true if we do things in a special way.
107 public static boolean isAMacAndNotJS()
109 return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac);
113 * Check if we are on a Microsoft plaform...
115 * @return true if we have to cope with another platform variation
117 public static boolean isWindowsAndNotJS()
119 return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
124 // * @return true if we are running in non-interactive no UI mode
126 // public static boolean isHeadless()
128 // if (isHeadless == null)
130 // isHeadless = "true".equals(System.getProperty("java.awt.headless"));
132 // return isHeadless;
137 * @return nominal maximum command line length for this platform
139 public static int getMaxCommandLineLength()
141 // TODO: determine nominal limits for most platforms.
142 return 2046; // this is the max length for a windows NT system.
146 * escape a string according to the local platform's escape character
149 * @return escaped file
151 public static String escapeString(String file)
153 StringBuffer f = new StringBuffer();
154 int p = 0, lastp = 0;
155 while ((p = file.indexOf('\\', lastp)) > -1)
157 f.append(file.subSequence(lastp, p));
161 f.append(file.substring(lastp));
166 * Answers true if the mouse event has Meta-down (Command key on Mac) or
167 * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
168 * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
169 * Mac, you can use e.isPopupTrigger().
174 public static boolean isControlDown(MouseEvent e)
176 return isControlDown(e, isMac());
180 * Overloaded version of method (to allow unit testing)
186 protected static boolean isControlDown(MouseEvent e, boolean aMac)
190 return e.isControlDown();
192 // answer false for right mouse button
193 // shortcut key will be META for a Mac
194 return !e.isPopupTrigger()
195 && (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
196 & e.getModifiers()) != 0;
197 // could we use e.isMetaDown() here?
200 // BH: I don't know about that previous method. Here is what SwingJS uses.
201 // Notice the distinction in mouse events. (BUTTON3_MASK == META)
203 // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
204 // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
206 // if (id != MouseEvent.MOUSE_RELEASED)
209 //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
210 //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
212 //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
214 //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
218 // // mac, linux, unix
219 // if (id != MouseEvent.MOUSE_PRESSED)
221 // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
222 // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
223 // return rt || (ctrl && lt);
229 * Windows (not Mac, Linux, or Unix) and right button to test for the
230 * right-mouse pressed event in Windows that would have opened a menu or a
236 public static boolean isWinRightButton(MouseEvent e)
238 // was !isAMac(), but that is true also for Linux and Unix and JS,
240 return isWin() && SwingUtilities.isRightMouseButton(e);
244 * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
245 * without pressing the button.
250 public static boolean isWinMiddleButton(MouseEvent e)
252 // was !isAMac(), but that is true also for Linux and Unix and JS
253 return isWin() && SwingUtilities.isMiddleMouseButton(e);
256 public static boolean allowMnemonics()
261 public final static int TIME_RESET = 0;
263 public final static int TIME_MARK = 1;
265 public static final int TIME_SET = 2;
267 public static final int TIME_GET = 3;
269 public static long time, mark, set, duration;
274 * Platform.timeCheck(null, Platform.TIME_MARK);
278 * Platform.timeCheck("some message", Platform.TIME_MARK);
280 * reset...[set/mark]n...get
285 public static void timeCheck(String msg, int mode)
287 long t = System.currentTimeMillis();
295 System.err.println("Platform: timer reset\t\t\t" + msg);
301 // total time between set/mark points
302 duration += (t - set);
312 System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
313 + "\t" + ((t - mark) / 1000f) + "\t" + msg);
324 System.err.println("Platform: timer get\t" + ((t - time) / 1000f)
325 + "\t" + ((duration) / 1000f) + "\t" + msg);
332 public static void cacheFileData(String path, Object data)
334 if (!isJS() || data == null)
341 * swingjs.JSUtil.cacheFileData$S$O(path, data);
346 public static void cacheFileData(File file)
349 if (!isJS() || (data = Platform.getFileBytes(file)) == null)
353 cacheFileData(file.toString(), data);
356 public static byte[] getFileBytes(File f)
358 // TODO temporary doubling of 秘bytes and _bytes;
359 // just remove _bytes when new transpiler has been installed
360 return /** @j2sNative f && (f.秘bytes || f._bytes) || */
364 public static byte[] getFileAsBytes(String fileStr)
367 // BH 2018 hack for no support for access-origin
369 * @j2sNative bytes = swingjs.JSUtil.getFileAsBytes$O(fileStr)
371 cacheFileData(fileStr, bytes);
375 @SuppressWarnings("unused")
376 public static String getFileAsString(String url)
382 * ret = swingjs.JSUtil.getFileAsString$S(url);
386 cacheFileData(url, ret);
390 public static boolean setFileBytes(File f, String urlstring)
396 @SuppressWarnings("unused")
397 byte[] bytes = getFileAsBytes(urlstring);
398 // TODO temporary doubling of 秘bytes and _bytes;
399 // just remove _bytes when new transpiler has been installed
401 * @j2sNative f.秘bytes = f._bytes = bytes;
406 public static void addJ2SBinaryType(String ext)
411 * J2S._binaryTypes.push("." + ext + "?");
417 * Encode the URI using JavaScript encodeURIComponent
420 * @return encoded value
422 public static String encodeURI(String value)
425 * @j2sNative value = encodeURIComponent(value);
431 * Open the URL using a simple window call if this is JavaScript
434 * @return true if window has been opened
436 public static boolean openURL(String url) throws IOException
440 BrowserLauncher.openURL(url);
452 public static String getUniqueAppletID()
454 @SuppressWarnings("unused")
455 ThreadGroup g = Thread.currentThread().getThreadGroup();
457 * @j2sNative return g.秘html5Applet._uniqueId;
465 * Read the Info block for this applet.
470 * @return unique id for this applet
472 public static void readInfoProperties(String prefix, Properties p)
478 @SuppressWarnings("unused")
479 ThreadGroup g = Thread.currentThread().getThreadGroup();
480 String id = getUniqueAppletID();
481 String key = "", value = "";
483 * @j2sNative var info = g.秘html5Applet.__Info || {}; for (var key in info)
484 * { if (key.indexOf(prefix) == 0) { value = "" + info[key];
488 "Platform id=" + id + " reading Info." + key + " = " + value);
499 public static void setAjaxJSON(URL url)
507 public static Object parseJSON(InputStream response)
508 throws IOException, ParseException
512 return JSON.parse(response);
515 BufferedReader br = null;
518 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
519 return new JSONParser().parse(br);
527 } catch (IOException e)
535 public static Object parseJSON(String json) throws ParseException
537 return (isJS() ? JSON.parse(json)
538 : new JSONParser().parse(json));
541 public static Object parseJSON(Reader r)
542 throws IOException, ParseException
551 return new JSONParser().parse(r);
553 // Using a file reader is not currently supported in SwingJS JavaScript
555 if (r instanceof FileReader)
557 throw new IOException(
558 "StringJS does not support FileReader parsing for JSON -- but it could...");
560 return JSON.parse(r);
565 * Dump the input stream to an output file.
569 * @throws IOException
570 * if the file cannot be created or there is a problem reading the
573 public static void streamToFile(InputStream is, File outFile)
577 * JSTempFile direct transfer
579 * @j2sNative outFile.setBytes$O && outFile.setBytes$O(is) &&
585 FileOutputStream fio = new FileOutputStream(outFile);
588 byte[] bb = new byte[32 * 1024];
590 while ((l = is.read(bb)) > 0)
601 * Add a known domain that implements access-control-allow-origin:*
603 * These should be reviewed periodically.
606 * for a service that is not allowing ajax
608 * @author hansonr@stolaf.edu
611 public static void addJ2SDirectDatabaseCall(String domain)
617 "Platform adding known access-control-allow-origin * for domain "
622 * J2S.addDirectDatabaseCall(domain);
628 public static void getURLCommandArguments()
632 * Retrieve the first query field as command arguments to Jalview. Include
633 * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
634 * element to this value.
637 * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
638 * + "?").split("?")[1].split("#")[0]); a &&
639 * (J2S.thisApplet.__Info.args = a.split(" "));
644 public static URL getDocumentBase()
650 @SuppressWarnings("unused")
651 Object g = Thread.currentThread().getThreadGroup();
653 * @j2sNative g.秘html5Applet._appletPanel.appletDocumentBase
658 } catch (MalformedURLException e)
664 public static URL getCodeBase()
670 @SuppressWarnings("unused")
671 Object g = Thread.currentThread().getThreadGroup();
673 * @j2sNative g.秘html5Applet._appletPanel.appletCodeBase
678 } catch (MalformedURLException e)
685 * load a resource -- probably a core file -- if and only if a particular
686 * class has not been instantialized. We use a String here because if we used
687 * a .class object, that reference itself would simply load the class, and we
688 * want the core package to include that as well.
690 * @param resourcePath
693 public static void loadStaticResource(Object resourcePath,
698 * @j2sNative if (!swingjs.JSUtil.isClassLoaded$S(className))
699 * swingjs.JSUtil.loadStaticResource$S(resourcePath);
703 public static void ensureJmol()
705 loadStaticResource("core/core_jvjmol.z.js", "org.jmol.viewer.Viewer");
708 public static void ensureRegex()
710 loadStaticResource("core/core_stevesoft.z.js",
711 "com.stevesoft.pat.Regex");
714 public static Regex newRegex(String searchString, String replaceString)
717 return (replaceString == null ? new Regex(searchString)
718 : new Regex(searchString, replaceString));
721 public static Regex newRegexPerl(String code)
724 return Regex.perlCode(code);
728 * Initialize Java debug logging. A representative sample -- adapt as desired.
730 public static void startJavaLogging()
736 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
737 "java.awt.Component", "java.awt.focus.Component",
738 "java.awt.event.Component",
739 "java.awt.focus.DefaultKeyboardFocusManager");
744 * Initiate Java logging for a given class. Only for Java, not JavaScript;
745 * Allows debugging of complex event processing.
749 public static void logClass(String... classNames)
757 Logger rootLogger = Logger.getLogger("");
758 rootLogger.setLevel(Level.ALL);
759 ConsoleHandler consoleHandler = new ConsoleHandler();
760 consoleHandler.setLevel(Level.ALL);
761 for (int i = classNames.length; --i >= 0;)
763 Logger logger = Logger.getLogger(classNames[i]);
764 logger.setLevel(Level.ALL);
765 logger.addHandler(consoleHandler);
771 * Set the "app" property of the HTML5 applet object, for example,
772 * "testApplet.app", to point to the Jalview instance. This will be the object
773 * that page developers use that is similar to the original Java applet object
774 * that was accessed via LiveConnect.
778 public static void setAppClass(Object j)
784 @SuppressWarnings("unused")
785 Thread t = Thread.currentThread();
787 * Set up "testApplet.app" to be this instance
791 * try {self[t.name].app = j}catch(e){}
796 * Retrieve the object's embedded size from a div's style on a page if
797 * embedded in SwingJS.
800 * JFrame or JInternalFrame
801 * @param defaultWidth
802 * use -1 to return null (no default size)
803 * @param defaultHeight
804 * @return the embedded dimensions or null (no default size or not embedded)
806 public static Dimension getDimIfEmbedded(JComponent frame,
807 int defaultWidth, int defaultHeight)
809 Dimension d = /** @j2sNative frame.ui.getEmbedded$S("dim") || */
811 return (d == null && defaultWidth >= 0
812 ? new Dimension(defaultWidth, defaultHeight)
818 * If this frame Is this frame embedded in a web page, return a known type.
821 * a JFrame or JInternalFrame
823 * @return null if frame is not embedded.
825 public static Object getEmbeddedAttribute(Object frame, String type)
831 return (/** @j2sNative frame.ui.getEmbedded$S(type) || */
835 public static void stackTrace()
839 throw new NullPointerException();
840 } catch (Exception e)