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 swingjs.api.JSUtilI jsutil;
72 jsutil = ((JSUtilI) Class.forName("swingjs.JSUtil").newInstance());
73 } catch (InstantiationException | IllegalAccessException
74 | ClassNotFoundException e)
80 // private static Boolean isHeadless = null;
83 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
87 public static boolean isMac()
90 ? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0))
95 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
99 public static boolean isWin()
101 return (isWin == null
102 ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0))
108 * @return true if HTML5 JavaScript
110 public static boolean isJS()
116 * sorry folks - Macs really are different
118 * BH: disabled for SwingJS -- will need to check key-press issues
120 * @return true if we do things in a special way.
122 public static boolean isAMacAndNotJS()
124 return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac);
128 * Check if we are on a Microsoft plaform...
130 * @return true if we have to cope with another platform variation
132 public static boolean isWindowsAndNotJS()
134 return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
139 // * @return true if we are running in non-interactive no UI mode
141 // public static boolean isHeadless()
143 // if (isHeadless == null)
145 // isHeadless = "true".equals(System.getProperty("java.awt.headless"));
147 // return isHeadless;
152 * @return nominal maximum command line length for this platform
154 public static int getMaxCommandLineLength()
156 // TODO: determine nominal limits for most platforms.
157 return 2046; // this is the max length for a windows NT system.
161 * An earlier version of escapeString()? Looks fine to me -- BH
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 // answer false for right mouse button
202 // shortcut key will be META for a Mac
203 return !e.isPopupTrigger()
204 && (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
205 & e.getModifiers()) != 0;
206 // could we use e.isMetaDown() here?
209 // BH: I don't know about that previous method. Here is what SwingJS uses.
210 // Notice the distinction in mouse events. (BUTTON3_MASK == META)
212 // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
213 // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
215 // if (id != MouseEvent.MOUSE_RELEASED)
218 //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
219 //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
221 //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
223 //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
227 // // mac, linux, unix
228 // if (id != MouseEvent.MOUSE_PRESSED)
230 // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
231 // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
232 // return rt || (ctrl && lt);
238 * Windows (not Mac, Linux, or Unix) and right button to test for the
239 * right-mouse pressed event in Windows that would have opened a menu or a
245 public static boolean isWinRightButton(MouseEvent e)
247 // was !isAMac(), but that is true also for Linux and Unix and JS,
249 return isWin() && SwingUtilities.isRightMouseButton(e);
253 * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
254 * without pressing the button.
259 public static boolean isWinMiddleButton(MouseEvent e)
261 // was !isAMac(), but that is true also for Linux and Unix and JS
262 return isWin() && SwingUtilities.isMiddleMouseButton(e);
265 public static boolean allowMnemonics()
270 public final static int TIME_RESET = 0;
272 public final static int TIME_MARK = 1;
274 public static final int TIME_SET = 2;
276 public static final int TIME_GET = 3;
278 public static long time, mark, set, duration;
283 * Platform.timeCheck(null, Platform.TIME_MARK);
287 * Platform.timeCheck("some message", Platform.TIME_MARK);
289 * reset...[set/mark]n...get
294 public static void timeCheck(String msg, int mode)
296 long t = System.currentTimeMillis();
304 System.err.println("Platform: timer reset\t\t\t" + msg);
310 // total time between set/mark points
311 duration += (t - set);
321 System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
322 + "\t" + ((t - mark) / 1000f) + "\t" + msg);
333 System.err.println("Platform: timer get\t" + ((t - time) / 1000f)
334 + "\t" + ((duration) / 1000f) + "\t" + msg);
342 * Dump the input stream to an output file.
346 * @throws IOException
347 * if the file cannot be created or there is a problem reading the
350 public static void streamToFile(InputStream is, File outFile)
356 jsutil.setFileBytes(outFile, is);
360 FileOutputStream fio = new FileOutputStream(outFile);
363 byte[] bb = new byte[32 * 1024];
365 while ((l = is.read(bb)) > 0)
376 * Encode the URI using JavaScript encodeURIComponent
379 * @return encoded value
381 public static String encodeURI(String value)
384 * @j2sNative value = encodeURIComponent(value);
390 * Open the URL using a simple window call if this is JavaScript
393 * @return true if window has been opened
395 public static boolean openURL(String url) throws IOException
399 BrowserLauncher.openURL(url);
411 public static Object parseJSON(InputStream response)
412 throws IOException, ParseException
416 return JSON.parse(response);
419 BufferedReader br = null;
422 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
423 return new JSONParser().parse(br);
431 } catch (IOException e)
439 public static Object parseJSON(String json) throws ParseException
441 return (isJS ? JSON.parse(json) : new JSONParser().parse(json));
444 public static Object parseJSON(Reader r)
445 throws IOException, ParseException
454 return new JSONParser().parse(r);
456 // Using a file reader is not currently supported in SwingJS JavaScript
458 if (r instanceof FileReader)
460 throw new IOException(
461 "StringJS does not support FileReader parsing for JSON -- but it could...");
463 return JSON.parse(r);
468 * Retrieve the object's embedded size from a div's style on a page if
469 * embedded in SwingJS.
472 * JFrame or JInternalFrame
473 * @param defaultWidth
474 * use -1 to return null (no default size)
475 * @param defaultHeight
476 * @return the embedded dimensions or null (no default size or not embedded)
478 public static Dimension getDimIfEmbedded(Component frame,
479 int defaultWidth, int defaultHeight)
484 d = (Dimension) getEmbeddedAttribute(frame, "dim");
486 return (d == null && defaultWidth >= 0
487 ? new Dimension(defaultWidth, defaultHeight)
492 public static Regex newRegex(String searchString, String replaceString)
495 return (replaceString == null ? new Regex(searchString)
496 : new Regex(searchString, replaceString));
499 public static Regex newRegexPerl(String code)
502 return Regex.perlCode(code);
506 * Initialize Java debug logging. A representative sample -- adapt as desired.
508 public static void startJavaLogging()
514 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
515 "java.awt.Component", "java.awt.focus.Component",
516 "java.awt.event.Component",
517 "java.awt.focus.DefaultKeyboardFocusManager");
522 * Initiate Java logging for a given class. Only for Java, not JavaScript;
523 * Allows debugging of complex event processing.
527 public static void logClass(String... classNames)
535 Logger rootLogger = Logger.getLogger("");
536 rootLogger.setLevel(Level.ALL);
537 ConsoleHandler consoleHandler = new ConsoleHandler();
538 consoleHandler.setLevel(Level.ALL);
539 for (int i = classNames.length; --i >= 0;)
541 Logger logger = Logger.getLogger(classNames[i]);
542 logger.setLevel(Level.ALL);
543 logger.addHandler(consoleHandler);
548 /// JavaScript-only methods ///
550 public static void cacheFileData(String path, Object data)
552 if (isJS && data != null)
554 jsutil.cachePathData(path, data);
558 public static void cacheFileData(File file)
562 byte[] data = Platform.getFileBytes(file);
566 cacheFileData(file.toString(), data);
572 public static byte[] getFileBytes(File f)
574 return (isJS && f != null ? jsutil.getBytes(f) : null);
577 public static byte[] getFileAsBytes(String fileStr)
579 if (isJS && fileStr != null)
581 byte[] bytes = (byte[]) jsutil.getFile(fileStr, false);
582 cacheFileData(fileStr, bytes);
588 @SuppressWarnings("unused")
589 public static String getFileAsString(String url)
591 if (isJS && url != null)
593 String ret = (String) jsutil.getFile(url, true);
594 cacheFileData(url, ret);
600 public static boolean setFileBytes(File f, String urlstring)
602 if (isJS && f != null && urlstring != null)
604 @SuppressWarnings("unused")
605 byte[] bytes = getFileAsBytes(urlstring);
606 jsutil.setFileBytes(f, bytes);
612 public static void addJ2SBinaryType(String ext)
616 jsutil.addBinaryFileType(ext);
620 public static String getUniqueAppletID()
622 return (isJS ? (String) jsutil.getAppletAttribute("_uniqueId") : null);
626 * Read the Info block for this applet.
631 * @return unique id for this applet
633 public static void readInfoProperties(String prefix, Properties p)
637 String id = getUniqueAppletID();
641 @SuppressWarnings("unused")
642 Object info = jsutil.getAppletAttribute("__Info");
644 * @j2sNative for (key in info) { value = info[key];
647 if (key.indexOf(prefix) == 0)
649 System.out.println("Platform id=" + id + " reading Info." + key
661 public static void setAjaxJSON(URL url)
671 * Add a known domain that implements access-control-allow-origin:*
673 * These should be reviewed periodically.
676 * for a service that is not allowing ajax
678 * @author hansonr@stolaf.edu
681 public static void addJ2SDirectDatabaseCall(String domain)
686 jsutil.addDirectDatabaseCall(domain);
689 "Platform adding known access-control-allow-origin * for domain "
695 public static void getURLCommandArguments()
699 * Retrieve the first query field as command arguments to Jalview. Include
700 * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
701 * element to this value.
704 * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
705 * + "?").split("?")[1].split("#")[0]); a &&
706 * (J2S.thisApplet.__Info.args = a.split(" "));
712 * A (case sensitive) file path comparator that ignores the difference between
719 public static boolean pathEquals(String path1, String path2)
723 return path2 == null;
729 String p1 = path1.replace('\\', '/');
730 String p2 = path2.replace('\\', '/');
731 return p1.equals(p2);
734 public static URL getDocumentBase()
736 return (isJS ? jsutil.getDocumentBase() : null);
739 public static URL getCodeBase()
741 return (isJS ? jsutil.getCodeBase() : null);
745 * load a resource -- probably a core file -- if and only if a particular
746 * class has not been instantialized. We use a String here because if we used
747 * a .class object, that reference itself would simply load the class, and we
748 * want the core package to include that as well.
750 * @param resourcePath
753 public static void loadStaticResource(String resourcePath,
758 jsutil.loadResourceIfClassUnknown(resourcePath, className);
762 public static void ensureRegex()
766 loadStaticResource("core/core_stevesoft.z.js",
767 "com.stevesoft.pat.Regex");
772 * Set the "app" property of the HTML5 applet object, for example,
773 * "testApplet.app", to point to the Jalview instance. This will be the object
774 * that page developers use that is similar to the original Java applet object
775 * that was accessed via LiveConnect.
779 public static void setAppClass(Object j)
783 jsutil.setAppletAttribute("app", j);
789 * If this frame ia embedded in a web page, return a known type.
792 * a JFrame or JInternalFrame
794 * @return null if frame is not embedded.
796 public static Object getEmbeddedAttribute(Component frame, String type)
798 return (isJS ? jsutil.getEmbeddedAttribute(frame, type) : null);
801 public static void stackTrace()
805 throw new NullPointerException();
806 } catch (Exception e)