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.Color;
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.SwingUtilities;
45 import org.json.simple.parser.JSONParser;
46 import org.json.simple.parser.ParseException;
48 import com.stevesoft.pat.Regex;
51 * System platform information used by Applet and Application
58 private static boolean isJS = /** @j2sNative true || */
61 private static Boolean isNoJSMac = null, isNoJSWin = null, isMac = null,
64 // private static Boolean isHeadless = null;
67 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
71 public static boolean isMac()
74 ? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0))
79 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
83 public static boolean isWin()
86 ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0))
92 * @return true if HTML5 JavaScript
94 public static boolean isJS()
100 * sorry folks - Macs really are different
102 * BH: disabled for SwingJS -- will need to check key-press issues
104 * @return true if we do things in a special way.
106 public static boolean isAMacAndNotJS()
108 return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac);
112 * Check if we are on a Microsoft plaform...
114 * @return true if we have to cope with another platform variation
116 public static boolean isWindowsAndNotJS()
118 return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
123 // * @return true if we are running in non-interactive no UI mode
125 // public static boolean isHeadless()
127 // if (isHeadless == null)
129 // isHeadless = "true".equals(System.getProperty("java.awt.headless"));
131 // return isHeadless;
136 * @return nominal maximum command line length for this platform
138 public static int getMaxCommandLineLength()
140 // TODO: determine nominal limits for most platforms.
141 return 2046; // this is the max length for a windows NT system.
145 * escape a string according to the local platform's escape character
148 * @return escaped file
150 public static String escapeString(String file)
152 StringBuffer f = new StringBuffer();
153 int p = 0, lastp = 0;
154 while ((p = file.indexOf('\\', lastp)) > -1)
156 f.append(file.subSequence(lastp, p));
160 f.append(file.substring(lastp));
165 * Answers true if the mouse event has Meta-down (Command key on Mac) or
166 * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
167 * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
168 * Mac, you can use e.isPopupTrigger().
173 public static boolean isControlDown(MouseEvent e)
175 return isControlDown(e, isMac());
179 * Overloaded version of method (to allow unit testing)
185 protected static boolean isControlDown(MouseEvent e, boolean aMac)
189 return e.isControlDown();
191 // answer false for right mouse button
192 // shortcut key will be META for a Mac
193 return !e.isPopupTrigger()
194 && (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
195 & e.getModifiers()) != 0;
196 // could we use e.isMetaDown() here?
199 // BH: I don't know about that previous method. Here is what SwingJS uses.
200 // Notice the distinction in mouse events. (BUTTON3_MASK == META)
202 // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
203 // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
205 // if (id != MouseEvent.MOUSE_RELEASED)
208 //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
209 //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
211 //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
213 //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
217 // // mac, linux, unix
218 // if (id != MouseEvent.MOUSE_PRESSED)
220 // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
221 // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
222 // return rt || (ctrl && lt);
228 * Windows (not Mac, Linux, or Unix) and right button to test for the
229 * right-mouse pressed event in Windows that would have opened a menu or a
235 public static boolean isWinRightButton(MouseEvent e)
237 // was !isAMac(), but that is true also for Linux and Unix and JS,
239 return isWin() && SwingUtilities.isRightMouseButton(e);
243 * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
244 * without pressing the button.
249 public static boolean isWinMiddleButton(MouseEvent e)
251 // was !isAMac(), but that is true also for Linux and Unix and JS
252 return isWin() && SwingUtilities.isMiddleMouseButton(e);
255 public static boolean allowMnemonics()
260 public final static int TIME_RESET = 0;
262 public final static int TIME_MARK = 1;
264 public static final int TIME_SET = 2;
266 public static final int TIME_GET = 3;
268 public static long time, mark, set, duration;
273 * Platform.timeCheck(null, Platform.TIME_MARK);
277 * Platform.timeCheck("some message", Platform.TIME_MARK);
279 * reset...[set/mark]n...get
284 public static void timeCheck(String msg, int mode)
286 long t = System.currentTimeMillis();
294 System.err.println("Platform: timer reset\t\t\t" + msg);
300 // total time between set/mark points
301 duration += (t - set);
311 System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
312 + "\t" + ((t - mark) / 1000f) + "\t" + msg);
323 System.err.println("Platform: timer get\t" + ((t - time) / 1000f)
324 + "\t" + ((duration) / 1000f) + "\t" + msg);
331 public static void cacheFileData(String path, Object data)
333 if (!isJS() || data == null)
340 * swingjs.JSUtil.cacheFileData$S$O(path, data);
345 public static void cacheFileData(File file)
348 if (!isJS() || (data = Platform.getFileBytes(file)) == null)
352 cacheFileData(file.toString(), data);
355 public static byte[] getFileBytes(File f)
357 // TODO temporary doubling of 秘bytes and _bytes;
358 // just remove _bytes when new transpiler has been installed
359 return /** @j2sNative f && (f.秘bytes || f._bytes) || */
363 public static byte[] getFileAsBytes(String fileStr)
366 // BH 2018 hack for no support for access-origin
368 * @j2sNative bytes = swingjs.JSUtil.getFileAsBytes$O(fileStr)
370 cacheFileData(fileStr, bytes);
374 @SuppressWarnings("unused")
375 public static String getFileAsString(String url)
381 * ret = swingjs.JSUtil.getFileAsString$S(url);
385 cacheFileData(url, ret);
389 public static boolean setFileBytes(File f, String urlstring)
395 @SuppressWarnings("unused")
396 byte[] bytes = getFileAsBytes(urlstring);
397 // TODO temporary doubling of 秘bytes and _bytes;
398 // just remove _bytes when new transpiler has been installed
400 * @j2sNative f.秘bytes = f._bytes = bytes;
405 public static void addJ2SBinaryType(String ext)
410 * J2S._binaryTypes.push("." + ext + "?");
416 * Encode the URI using JavaScript encodeURIComponent
419 * @return encoded value
421 public static String encodeURI(String value)
424 * @j2sNative value = encodeURIComponent(value);
430 * Open the URL using a simple window call if this is JavaScript
433 * @return true if window has been opened
435 public static boolean openURL(String url) throws IOException
439 BrowserLauncher.openURL(url);
451 public static String getUniqueAppletID()
453 @SuppressWarnings("unused")
454 ThreadGroup g = Thread.currentThread().getThreadGroup();
456 * @j2sNative return g.秘html5Applet._uniqueId;
464 * Read the Info block for this applet.
469 * @return unique id for this applet
471 public static void readInfoProperties(String prefix, Properties p)
477 @SuppressWarnings("unused")
478 ThreadGroup g = Thread.currentThread().getThreadGroup();
479 String id = getUniqueAppletID();
480 String key = "", value = "";
482 * @j2sNative var info = g.秘html5Applet.__Info || {}; for (var key in info)
483 * { if (key.indexOf(prefix) == 0) { value = "" + info[key];
487 "Platform id=" + id + " reading Info." + key + " = " + value);
498 public static void setAjaxJSON(URL url)
506 public static Object parseJSON(InputStream response)
507 throws IOException, ParseException
511 return JSON.parse(response);
514 BufferedReader br = null;
517 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
518 return new JSONParser().parse(br);
526 } catch (IOException e)
534 public static Object parseJSON(String json) throws ParseException
536 return (isJS() ? JSON.parse(json)
537 : new JSONParser().parse(json));
540 public static Object parseJSON(Reader r)
541 throws IOException, ParseException
550 return new JSONParser().parse(r);
552 // Using a file reader is not currently supported in SwingJS JavaScript
554 if (r instanceof FileReader)
556 throw new IOException(
557 "StringJS does not support FileReader parsing for JSON -- but it could...");
559 return JSON.parse(r);
564 * Dump the input stream to an output file.
568 * @throws IOException
569 * if the file cannot be created or there is a problem reading the
572 public static void streamToFile(InputStream is, File outFile)
575 FileOutputStream fio = new FileOutputStream(outFile);
580 * @j2sNative outFile.setBytes$O && outFile.setBytes$O(is) &&
586 byte[] bb = new byte[32 * 1024];
588 while ((l = is.read(bb)) > 0)
599 * Add a known domain that implements access-control-allow-origin:*
601 * These should be reviewed periodically.
604 * for a service that is not allowing ajax
606 * @author hansonr@stolaf.edu
609 public static void addJ2SDirectDatabaseCall(String domain)
615 "Platform adding known access-control-allow-origin * for domain "
620 * J2S.addDirectDatabaseCall(domain);
626 public static void getURLCommandArguments()
630 * Retrieve the first query field as command arguments to Jalview. Include
631 * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
632 * element to this value.
635 * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
636 * + "?").split("?")[1].split("#")[0]); a &&
637 * (J2S.thisApplet.__Info.args = a.split(" "));
642 public static URL getDocumentBase()
648 @SuppressWarnings("unused")
649 Object g = Thread.currentThread().getThreadGroup();
651 * @j2sNative g.秘html5Applet._appletPanel.appletDocumentBase
656 } catch (MalformedURLException e)
662 public static URL getCodeBase()
668 @SuppressWarnings("unused")
669 Object g = Thread.currentThread().getThreadGroup();
671 * @j2sNative g.秘html5Applet._appletPanel.appletCodeBase
676 } catch (MalformedURLException e)
683 * load a resource -- probably a core file -- if and only if a particular
684 * class has not been instantialized. We use a String here because if we used
685 * a .class object, that reference itself would simply load the class, and we
686 * want the core package to include that as well.
688 * @param resourcePath
691 public static void loadStaticResource(Object resourcePath,
696 * @j2sNative if (!swingjs.JSUtil.isClassLoaded$S(className))
697 * swingjs.JSUtil.loadStaticResource$S(resourcePath);
701 public static void ensureRegex()
703 loadStaticResource("core/core_stevesoft.z.js",
704 "com.stevesoft.pat.Regex");
707 public static Regex newRegex(String searchString, String replaceString)
710 return (replaceString == null ? new Regex(searchString)
711 : new Regex(searchString, replaceString));
714 public static Regex newRegexPerl(String code)
717 return Regex.perlCode(code);
723 public static Color getColorFromName(String name)
732 * return swingjs.JSUtil.getColorFromName$S(name);
735 // or make a static map; or use reflection on the field name
736 switch (name.toLowerCase())
745 return Color.darkGray;
751 return Color.lightGray;
753 return Color.magenta;
772 * Initialize Java debug logging. A representative sample -- adapt as desired.
774 public static void startJavaLogging()
780 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
781 "java.awt.Component", "java.awt.focus.Component",
782 "java.awt.event.Component",
783 "java.awt.focus.DefaultKeyboardFocusManager");
788 * Initiate Java logging for a given class. Only for Java, not JavaScript;
789 * Allows debugging of complex event processing.
793 public static void logClass(String... classNames)
801 Logger rootLogger = Logger.getLogger("");
802 rootLogger.setLevel(Level.ALL);
803 ConsoleHandler consoleHandler = new ConsoleHandler();
804 consoleHandler.setLevel(Level.ALL);
805 for (int i = classNames.length; --i >= 0;)
807 Logger logger = Logger.getLogger(classNames[i]);
808 logger.setLevel(Level.ALL);
809 logger.addHandler(consoleHandler);
815 * Set the "app" property of the HTML5 applet object, for example,
816 * "testApplet.app", to point to the Jalview instance. This will be the object
817 * that page developers use that is similar to the original Java applet object
818 * that was accessed via LiveConnect.
822 public static void setAppClass(Object j)
828 @SuppressWarnings("unused")
829 Thread t = Thread.currentThread();
831 * Set up "testApplet.app" to be this instance
835 * try {self[t.name].app = j}catch(e){}
839 public final static String EMBEDDED_DIM = "dim";
843 * If this frame Is this frame embedded in a web page, return a known type.
846 * a JFrame or JInternalFrame
848 * @return null if frame is not embedded.
850 public static Object getEmbeddedAttribute(Object frame, String type)
856 return (/** swingjs@j2sNative || frame.ui.getEmbedded(type) */
860 public static void stackTrace()
864 throw new NullPointerException();
865 } catch (Exception e)