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.Dimension;
27 import java.awt.Toolkit;
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.net.MalformedURLException;
39 import java.util.Properties;
40 import java.util.logging.ConsoleHandler;
41 import java.util.logging.Level;
42 import java.util.logging.Logger;
44 import javax.swing.JComponent;
45 import javax.swing.SwingUtilities;
47 import org.json.simple.parser.JSONParser;
48 import org.json.simple.parser.ParseException;
50 import com.stevesoft.pat.Regex;
53 * System platform information used by Applet and Application
60 private static boolean isJS = /** @j2sNative true || */
63 private static Boolean isNoJSMac = null, isNoJSWin = null, isMac = null,
66 // private static Boolean isHeadless = null;
69 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
73 public static boolean isMac()
76 ? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0))
81 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
85 public static boolean isWin()
88 ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0))
94 * @return true if HTML5 JavaScript
96 public static boolean isJS()
102 * sorry folks - Macs really are different
104 * BH: disabled for SwingJS -- will need to check key-press issues
106 * @return true if we do things in a special way.
108 public static boolean isAMacAndNotJS()
110 return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac);
114 * Check if we are on a Microsoft plaform...
116 * @return true if we have to cope with another platform variation
118 public static boolean isWindowsAndNotJS()
120 return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
125 // * @return true if we are running in non-interactive no UI mode
127 // public static boolean isHeadless()
129 // if (isHeadless == null)
131 // isHeadless = "true".equals(System.getProperty("java.awt.headless"));
133 // return isHeadless;
138 * @return nominal maximum command line length for this platform
140 public static int getMaxCommandLineLength()
142 // TODO: determine nominal limits for most platforms.
143 return 2046; // this is the max length for a windows NT system.
147 * escape a string according to the local platform's escape character
150 * @return escaped file
152 public static String escapeString(String file)
154 StringBuffer f = new StringBuffer();
155 int p = 0, lastp = 0;
156 while ((p = file.indexOf('\\', lastp)) > -1)
158 f.append(file.subSequence(lastp, p));
162 f.append(file.substring(lastp));
167 * Answers true if the mouse event has Meta-down (Command key on Mac) or
168 * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
169 * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
170 * Mac, you can use e.isPopupTrigger().
175 public static boolean isControlDown(MouseEvent e)
177 return isControlDown(e, isMac());
181 * Overloaded version of method (to allow unit testing)
187 protected static boolean isControlDown(MouseEvent e, boolean aMac)
191 return e.isControlDown();
193 // answer false for right mouse button
194 // shortcut key will be META for a Mac
195 return !e.isPopupTrigger()
196 && (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
197 & e.getModifiers()) != 0;
198 // could we use e.isMetaDown() here?
201 // BH: I don't know about that previous method. Here is what SwingJS uses.
202 // Notice the distinction in mouse events. (BUTTON3_MASK == META)
204 // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
205 // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
207 // if (id != MouseEvent.MOUSE_RELEASED)
210 //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
211 //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
213 //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
215 //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
219 // // mac, linux, unix
220 // if (id != MouseEvent.MOUSE_PRESSED)
222 // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
223 // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
224 // return rt || (ctrl && lt);
230 * Windows (not Mac, Linux, or Unix) and right button to test for the
231 * right-mouse pressed event in Windows that would have opened a menu or a
237 public static boolean isWinRightButton(MouseEvent e)
239 // was !isAMac(), but that is true also for Linux and Unix and JS,
241 return isWin() && SwingUtilities.isRightMouseButton(e);
245 * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
246 * without pressing the button.
251 public static boolean isWinMiddleButton(MouseEvent e)
253 // was !isAMac(), but that is true also for Linux and Unix and JS
254 return isWin() && SwingUtilities.isMiddleMouseButton(e);
257 public static boolean allowMnemonics()
262 public final static int TIME_RESET = 0;
264 public final static int TIME_MARK = 1;
266 public static final int TIME_SET = 2;
268 public static final int TIME_GET = 3;
270 public static long time, mark, set, duration;
275 * Platform.timeCheck(null, Platform.TIME_MARK);
279 * Platform.timeCheck("some message", Platform.TIME_MARK);
281 * reset...[set/mark]n...get
286 public static void timeCheck(String msg, int mode)
288 long t = System.currentTimeMillis();
296 System.err.println("Platform: timer reset\t\t\t" + msg);
302 // total time between set/mark points
303 duration += (t - set);
313 System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
314 + "\t" + ((t - mark) / 1000f) + "\t" + msg);
325 System.err.println("Platform: timer get\t" + ((t - time) / 1000f)
326 + "\t" + ((duration) / 1000f) + "\t" + msg);
333 public static void cacheFileData(String path, Object data)
335 if (!isJS() || data == null)
342 * swingjs.JSUtil.cacheFileData$S$O(path, data);
347 public static void cacheFileData(File file)
350 if (!isJS() || (data = Platform.getFileBytes(file)) == null)
354 cacheFileData(file.toString(), data);
357 public static byte[] getFileBytes(File f)
359 // TODO temporary doubling of 秘bytes and _bytes;
360 // just remove _bytes when new transpiler has been installed
361 return /** @j2sNative f && (f.秘bytes || f._bytes) || */
365 public static byte[] getFileAsBytes(String fileStr)
368 // BH 2018 hack for no support for access-origin
370 * @j2sNative bytes = swingjs.JSUtil.getFileAsBytes$O(fileStr)
372 cacheFileData(fileStr, bytes);
376 @SuppressWarnings("unused")
377 public static String getFileAsString(String url)
383 * ret = swingjs.JSUtil.getFileAsString$S(url);
387 cacheFileData(url, ret);
391 public static boolean setFileBytes(File f, String urlstring)
397 @SuppressWarnings("unused")
398 byte[] bytes = getFileAsBytes(urlstring);
399 // TODO temporary doubling of 秘bytes and _bytes;
400 // just remove _bytes when new transpiler has been installed
402 * @j2sNative f.秘bytes = f._bytes = bytes;
407 public static void addJ2SBinaryType(String ext)
412 * J2S._binaryTypes.push("." + ext + "?");
418 * Encode the URI using JavaScript encodeURIComponent
421 * @return encoded value
423 public static String encodeURI(String value)
426 * @j2sNative value = encodeURIComponent(value);
432 * Open the URL using a simple window call if this is JavaScript
435 * @return true if window has been opened
437 public static boolean openURL(String url) throws IOException
441 BrowserLauncher.openURL(url);
453 public static String getUniqueAppletID()
455 @SuppressWarnings("unused")
456 ThreadGroup g = Thread.currentThread().getThreadGroup();
458 * @j2sNative return g.秘html5Applet._uniqueId;
466 * Read the Info block for this applet.
471 * @return unique id for this applet
473 public static void readInfoProperties(String prefix, Properties p)
479 @SuppressWarnings("unused")
480 ThreadGroup g = Thread.currentThread().getThreadGroup();
481 String id = getUniqueAppletID();
482 String key = "", value = "";
484 * @j2sNative var info = g.秘html5Applet.__Info || {}; for (var key in info)
485 * { if (key.indexOf(prefix) == 0) { value = "" + info[key];
489 "Platform id=" + id + " reading Info." + key + " = " + value);
500 public static void setAjaxJSON(URL url)
508 public static Object parseJSON(InputStream response)
509 throws IOException, ParseException
513 return JSON.parse(response);
516 BufferedReader br = null;
519 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
520 return new JSONParser().parse(br);
528 } catch (IOException e)
536 public static Object parseJSON(String json) throws ParseException
538 return (isJS() ? JSON.parse(json)
539 : new JSONParser().parse(json));
542 public static Object parseJSON(Reader r)
543 throws IOException, ParseException
552 return new JSONParser().parse(r);
554 // Using a file reader is not currently supported in SwingJS JavaScript
556 if (r instanceof FileReader)
558 throw new IOException(
559 "StringJS does not support FileReader parsing for JSON -- but it could...");
561 return JSON.parse(r);
566 * Dump the input stream to an output file.
570 * @throws IOException
571 * if the file cannot be created or there is a problem reading the
574 public static void streamToFile(InputStream is, File outFile)
577 FileOutputStream fio = new FileOutputStream(outFile);
582 * @j2sNative outFile.setBytes$O && outFile.setBytes$O(is) &&
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 ensureRegex()
705 loadStaticResource("core/core_stevesoft.z.js",
706 "com.stevesoft.pat.Regex");
709 public static Regex newRegex(String searchString, String replaceString)
712 return (replaceString == null ? new Regex(searchString)
713 : new Regex(searchString, replaceString));
716 public static Regex newRegexPerl(String code)
719 return Regex.perlCode(code);
723 * Initialize Java debug logging. A representative sample -- adapt as desired.
725 public static void startJavaLogging()
731 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
732 "java.awt.Component", "java.awt.focus.Component",
733 "java.awt.event.Component",
734 "java.awt.focus.DefaultKeyboardFocusManager");
739 * Initiate Java logging for a given class. Only for Java, not JavaScript;
740 * Allows debugging of complex event processing.
744 public static void logClass(String... classNames)
752 Logger rootLogger = Logger.getLogger("");
753 rootLogger.setLevel(Level.ALL);
754 ConsoleHandler consoleHandler = new ConsoleHandler();
755 consoleHandler.setLevel(Level.ALL);
756 for (int i = classNames.length; --i >= 0;)
758 Logger logger = Logger.getLogger(classNames[i]);
759 logger.setLevel(Level.ALL);
760 logger.addHandler(consoleHandler);
766 * Set the "app" property of the HTML5 applet object, for example,
767 * "testApplet.app", to point to the Jalview instance. This will be the object
768 * that page developers use that is similar to the original Java applet object
769 * that was accessed via LiveConnect.
773 public static void setAppClass(Object j)
779 @SuppressWarnings("unused")
780 Thread t = Thread.currentThread();
782 * Set up "testApplet.app" to be this instance
786 * try {self[t.name].app = j}catch(e){}
791 * Retrieve the object's embedded size from a div's style on a page if
792 * embedded in SwingJS.
795 * JFrame or JInternalFrame
796 * @param defaultWidth
797 * use -1 to return null (no default size)
798 * @param defaultHeight
799 * @return the embedded dimensions or null (no default size or not embedded)
801 public static Dimension getDimIfEmbedded(JComponent frame,
802 int defaultWidth, int defaultHeight)
804 Dimension d = /** @j2sNative frame.ui.getEmbedded$S("dim") || */
806 return (d == null && defaultWidth >= 0
807 ? new Dimension(defaultWidth, defaultHeight)
813 * If this frame Is this frame embedded in a web page, return a known type.
816 * a JFrame or JInternalFrame
818 * @return null if frame is not embedded.
820 public static Object getEmbeddedAttribute(Object frame, String type)
826 return (/** @j2sNative frame.ui.getEmbedded$S(type) || */
830 public static void stackTrace()
834 throw new NullPointerException();
835 } catch (Exception e)