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.Component;
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;
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;
50 import swingjs.api.JSUtilI;
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;
68 private static swingjs.api.JSUtilI jsutil;
74 jsutil = ((JSUtilI) Class.forName("swingjs.JSUtil").newInstance());
75 } catch (InstantiationException | IllegalAccessException
76 | ClassNotFoundException e)
82 // private static Boolean isHeadless = null;
85 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
89 public static boolean isMac()
92 ? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0))
97 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
101 public static boolean isWin()
103 return (isWin == null
104 ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0))
110 * @return true if HTML5 JavaScript
112 public static boolean isJS()
118 * sorry folks - Macs really are different
120 * BH: disabled for SwingJS -- will need to check key-press issues
122 * @return true if we do things in a special way.
124 public static boolean isAMacAndNotJS()
126 return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac);
130 * Check if we are on a Microsoft plaform...
132 * @return true if we have to cope with another platform variation
134 public static boolean isWindowsAndNotJS()
136 return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
141 * @return true if we are running in non-interactive no UI mode
143 public static boolean isHeadless()
145 if (isHeadless == null)
147 isHeadless = "true".equals(System.getProperty("java.awt.headless"));
154 * @return nominal maximum command line length for this platform
156 public static int getMaxCommandLineLength()
158 // TODO: determine nominal limits for most platforms.
159 return 2046; // this is the max length for a windows NT system.
163 * Answers the input with every backslash replaced with a double backslash (an
164 * 'escaped' single backslash)
169 public static String escapeBackslashes(String s)
171 return s == null ? null : s.replace("\\", "\\\\");
175 * Answers true if the mouse event has Meta-down (Command key on Mac) or
176 * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
177 * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
178 * Mac, you can use e.isPopupTrigger().
183 public static boolean isControlDown(MouseEvent e)
185 return isControlDown(e, isMac());
189 * Overloaded version of method (to allow unit testing)
195 protected static boolean isControlDown(MouseEvent e, boolean aMac)
199 return e.isControlDown();
201 // Jalview 2.11 code below: above is as amended for JalviewJS
203 // * answer false for right mouse button
205 // if (e.isPopupTrigger())
210 // (jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() //
211 // .getMenuShortcutKeyMaskEx()
212 // & jalview.util.ShortcutKeyMaskExWrapper
213 // .getModifiersEx(e)) != 0; // getModifiers()) != 0;
215 // answer false for right mouse button
216 // shortcut key will be META for a Mac
217 return !e.isPopupTrigger()
218 && (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
219 & e.getModifiers()) != 0;
220 // could we use e.isMetaDown() here?
223 // BH: I don't know about that previous method. Here is what SwingJS uses.
224 // Notice the distinction in mouse events. (BUTTON3_MASK == META)
226 // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
227 // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
229 // if (id != MouseEvent.MOUSE_RELEASED)
232 //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
233 //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
235 //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
237 //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
241 // // mac, linux, unix
242 // if (id != MouseEvent.MOUSE_PRESSED)
244 // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
245 // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
246 // return rt || (ctrl && lt);
252 * Windows (not Mac, Linux, or Unix) and right button to test for the
253 * right-mouse pressed event in Windows that would have opened a menu or a
259 public static boolean isWinRightButton(MouseEvent e)
261 // was !isAMac(), but that is true also for Linux and Unix and JS,
263 return isWin() && SwingUtilities.isRightMouseButton(e);
267 * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
268 * without pressing the button.
273 public static boolean isWinMiddleButton(MouseEvent e)
275 // was !isAMac(), but that is true also for Linux and Unix and JS
276 return isWin() && SwingUtilities.isMiddleMouseButton(e);
279 public static boolean allowMnemonics()
284 public final static int TIME_RESET = 0;
286 public final static int TIME_MARK = 1;
288 public static final int TIME_SET = 2;
290 public static final int TIME_GET = 3;
292 public static long time, mark, set, duration;
297 * Platform.timeCheck(null, Platform.TIME_MARK);
301 * Platform.timeCheck("some message", Platform.TIME_MARK);
303 * reset...[set/mark]n...get
308 public static void timeCheck(String msg, int mode)
310 long t = System.currentTimeMillis();
318 System.err.println("Platform: timer reset\t\t\t" + msg);
324 // total time between set/mark points
325 duration += (t - set);
335 System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
336 + "\t" + ((t - mark) / 1000f) + "\t" + msg);
347 System.err.println("Platform: timer dur\t" + ((t - time) / 1000f)
348 + "\t" + ((duration) / 1000f) + "\t" + msg);
355 public static void cacheFileData(String path, Object data)
357 if (isJS && data != null)
359 jsutil.cachePathData(path, data);
364 public static void cacheFileData(File file)
368 byte[] data = Platform.getFileBytes(file);
372 cacheFileData(file.toString(), data);
378 public static byte[] getFileBytes(File f)
380 return (isJS && f != null ? jsutil.getBytes(f) : null);
383 public static byte[] getFileAsBytes(String fileStr)
385 if (isJS && fileStr != null)
387 byte[] bytes = (byte[]) jsutil.getFile(fileStr, false);
388 cacheFileData(fileStr, bytes);
394 public static String getFileAsString(String url)
396 if (isJS && url != null)
398 String ret = (String) jsutil.getFile(url, true);
399 cacheFileData(url, ret);
405 public static boolean setFileBytes(File f, String urlstring)
407 if (isJS && f != null && urlstring != null)
409 @SuppressWarnings("unused")
410 byte[] bytes = getFileAsBytes(urlstring);
411 jsutil.setFileBytes(f, bytes);
418 public static void addJ2SBinaryType(String ext)
422 jsutil.addBinaryFileType(ext);
427 * Encode the URI using JavaScript encodeURIComponent
430 * @return encoded value
432 public static String encodeURI(String value)
435 * @j2sNative value = encodeURIComponent(value);
441 * Open the URL using a simple window call if this is JavaScript
444 * @return true if window has been opened
446 public static boolean openURL(String url) throws IOException
450 // BH note -- this next line is brought into Platform, as it is Java-only.
451 BrowserLauncher.openURL(url);
463 public static String getUniqueAppletID()
465 return (isJS ? (String) jsutil.getAppletAttribute("_uniqueId") : null);
470 * Read the Info block for this applet.
475 * @return unique id for this applet
477 public static void readInfoProperties(String prefix, Properties p)
481 String id = getUniqueAppletID();
485 @SuppressWarnings("unused")
486 Object info = jsutil.getAppletAttribute("__Info");
488 * @j2sNative for (key in info) { value = info[key];
491 if (key.indexOf(prefix) == 0)
493 System.out.println("Platform id=" + id + " reading Info." + key
505 public static void setAjaxJSON(URL url)
513 public static Object parseJSON(InputStream response)
514 throws IOException, ParseException
518 return JSON.parse(response);
521 BufferedReader br = null;
524 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
525 return new JSONParser().parse(br);
533 } catch (IOException e)
541 public static Object parseJSON(String json) throws ParseException
543 return (isJS() ? JSON.parse(json)
544 : new JSONParser().parse(json));
547 public static Object parseJSON(Reader r)
548 throws IOException, ParseException
557 return new JSONParser().parse(r);
559 // Using a file reader is not currently supported in SwingJS JavaScript
561 if (r instanceof FileReader)
563 throw new IOException(
564 "StringJS does not support FileReader parsing for JSON -- but it could...");
566 return JSON.parse(r);
570 * Dump the input stream to an output file.
574 * @throws IOException
575 * if the file cannot be created or there is a problem
576 * reading the input stream.
578 public static void streamToFile(InputStream is, File outFile)
584 jsutil.setFileBytes(outFile, is);
588 FileOutputStream fio = new FileOutputStream(outFile);
591 byte[] bb = new byte[32 * 1024];
593 while ((l = is.read(bb)) > 0)
604 * Add a known domain that implements access-control-allow-origin:*
606 * These should be reviewed periodically.
609 * for a service that is not allowing ajax
611 * @author hansonr@stolaf.edu
614 public static void addJ2SDirectDatabaseCall(String domain)
619 jsutil.addDirectDatabaseCall(domain);
622 "Platform adding known access-control-allow-origin * for 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(" "));
645 * A (case sensitive) file path comparator that ignores the difference between /
652 public static boolean pathEquals(String path1, String path2)
656 return path2 == null;
662 String p1 = path1.replace('\\', '/');
663 String p2 = path2.replace('\\', '/');
664 return p1.equals(p2);
669 ///////////// JAL-3253 Applet additions //////////////
673 * Retrieve the object's embedded size from a div's style on a page if
674 * embedded in SwingJS.
677 * JFrame or JInternalFrame
678 * @param defaultWidth
679 * use -1 to return null (no default size)
680 * @param defaultHeight
681 * @return the embedded dimensions or null (no default size or not embedded)
683 public static Dimension getDimIfEmbedded(Component frame,
684 int defaultWidth, int defaultHeight)
689 d = (Dimension) getEmbeddedAttribute(frame, "dim");
691 return (d == null && defaultWidth >= 0
692 ? new Dimension(defaultWidth, defaultHeight)
697 public static Regex newRegex(String searchString, String replaceString)
700 return (replaceString == null ? new Regex(searchString)
701 : new Regex(searchString, replaceString));
704 public static Regex newRegexPerl(String code)
707 return Regex.perlCode(code);
711 * Initialize Java debug logging. A representative sample -- adapt as desired.
713 public static void startJavaLogging()
719 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
720 "java.awt.Component", "java.awt.focus.Component",
721 "java.awt.event.Component",
722 "java.awt.focus.DefaultKeyboardFocusManager");
727 * Initiate Java logging for a given class. Only for Java, not JavaScript;
728 * Allows debugging of complex event processing.
732 public static void logClass(String... classNames)
740 Logger rootLogger = Logger.getLogger("");
741 rootLogger.setLevel(Level.ALL);
742 ConsoleHandler consoleHandler = new ConsoleHandler();
743 consoleHandler.setLevel(Level.ALL);
744 for (int i = classNames.length; --i >= 0;)
746 Logger logger = Logger.getLogger(classNames[i]);
747 logger.setLevel(Level.ALL);
748 logger.addHandler(consoleHandler);
755 * load a resource -- probably a core file -- if and only if a particular
756 * class has not been instantialized. We use a String here because if we used
757 * a .class object, that reference itself would simply load the class, and we
758 * want the core package to include that as well.
760 * @param resourcePath
763 public static void loadStaticResource(String resourcePath,
768 jsutil.loadResourceIfClassUnknown(resourcePath, className);
772 public static void ensureRegex()
776 loadStaticResource("core/core_stevesoft.z.js",
777 "com.stevesoft.pat.Regex");
782 * Set the "app" property of the HTML5 applet object, for example,
783 * "testApplet.app", to point to the Jalview instance. This will be the object
784 * that page developers use that is similar to the original Java applet object
785 * that was accessed via LiveConnect.
789 public static void setAppClass(Object j)
793 jsutil.setAppletAttribute("app", j);
799 * If this frame ia embedded in a web page, return a known type.
802 * a JFrame or JInternalFrame
804 * @return null if frame is not embedded.
806 public static Object getEmbeddedAttribute(Component frame, String type)
808 return (isJS ? jsutil.getEmbeddedAttribute(frame, type) : null);
811 public static void stackTrace()
815 throw new NullPointerException();
816 } catch (Exception e)