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.Locale;
40 import java.util.Properties;
41 import java.util.logging.ConsoleHandler;
42 import java.util.logging.Level;
43 import java.util.logging.Logger;
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;
52 import swingjs.api.JSUtilI;
54 ////////THIS FILE IS NOW OUTDATED /////////////
57 * System platform information used by Applet and Application
64 private static boolean isJS = /** @j2sNative true || */
67 private static Boolean isNoJSMac = null, isNoJSWin = null, isMac = null,
70 private static swingjs.api.JSUtilI jsutil;
76 jsutil = ((JSUtilI) Class.forName("swingjs.JSUtil").newInstance());
77 } catch (InstantiationException | IllegalAccessException
78 | ClassNotFoundException e)
84 // private static Boolean isHeadless = null;
87 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
91 public static boolean isMac()
94 ? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0))
99 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
103 public static boolean isWin()
105 return (isWin == null
106 ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0))
112 * @return true if HTML5 JavaScript
114 public static boolean isJS()
120 * sorry folks - Macs really are different
122 * BH: disabled for SwingJS -- will need to check key-press issues
124 * @return true if we do things in a special way.
126 public static boolean isAMacAndNotJS()
128 return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac);
132 * Check if we are on a Microsoft plaform...
134 * @return true if we have to cope with another platform variation
136 public static boolean isWindowsAndNotJS()
138 return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
143 // * @return true if we are running in non-interactive no UI mode
145 // public static boolean isHeadless()
147 // if (isHeadless == null)
149 // isHeadless = "true".equals(System.getProperty("java.awt.headless"));
151 // return isHeadless;
156 * @return nominal maximum command line length for this platform
158 public static int getMaxCommandLineLength()
160 // TODO: determine nominal limits for most platforms.
161 return 2046; // this is the max length for a windows NT system.
165 * An earlier version of escapeString()? Looks fine to me -- BH
167 * Answers the input with every backslash replaced with a double backslash (an
168 * 'escaped' single backslash)
173 public static String escapeBackslashes(String s)
175 return s == null ? null : s.replace("\\", "\\\\");
179 * Answers true if the mouse event has Meta-down (Command key on Mac) or
180 * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
181 * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
182 * Mac, you can use e.isPopupTrigger().
187 public static boolean isControlDown(MouseEvent e)
189 return isControlDown(e, isMac());
193 * Overloaded version of method (to allow unit testing)
199 protected static boolean isControlDown(MouseEvent e, boolean aMac)
203 return e.isControlDown();
205 // answer false for right mouse button
206 // shortcut key will be META for a Mac
207 return !e.isPopupTrigger()
208 && (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
209 & e.getModifiers()) != 0;
210 // could we use e.isMetaDown() here?
213 // BH: I don't know about that previous method. Here is what SwingJS uses.
214 // Notice the distinction in mouse events. (BUTTON3_MASK == META)
216 // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
217 // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
219 // if (id != MouseEvent.MOUSE_RELEASED)
222 //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
223 //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
225 //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
227 //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
231 // // mac, linux, unix
232 // if (id != MouseEvent.MOUSE_PRESSED)
234 // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
235 // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
236 // return rt || (ctrl && lt);
242 * Windows (not Mac, Linux, or Unix) and right button to test for the
243 * right-mouse pressed event in Windows that would have opened a menu or a
249 public static boolean isWinRightButton(MouseEvent e)
251 // was !isAMac(), but that is true also for Linux and Unix and JS,
253 return isWin() && SwingUtilities.isRightMouseButton(e);
257 * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
258 * without pressing the button.
263 public static boolean isWinMiddleButton(MouseEvent e)
265 // was !isAMac(), but that is true also for Linux and Unix and JS
266 return isWin() && SwingUtilities.isMiddleMouseButton(e);
269 public static boolean allowMnemonics()
274 public final static int TIME_RESET = 0;
276 public final static int TIME_MARK = 1;
278 public static final int TIME_SET = 2;
280 public static final int TIME_GET = 3;
282 public static long time, mark, set, duration;
287 * Platform.timeCheck(null, Platform.TIME_MARK);
291 * Platform.timeCheck("some message", Platform.TIME_MARK);
293 * reset...[set/mark]n...get
298 public static void timeCheck(String msg, int mode)
300 long t = System.currentTimeMillis();
308 System.err.println("Platform: timer reset\t\t\t" + msg);
314 // total time between set/mark points
315 duration += (t - set);
325 System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
326 + "\t" + ((t - mark) / 1000f) + "\t" + msg);
337 System.err.println("Platform: timer get\t" + ((t - time) / 1000f)
338 + "\t" + ((duration) / 1000f) + "\t" + msg);
346 * Dump the input stream to an output file.
350 * @throws IOException
351 * if the file cannot be created or there is a problem reading the
354 public static void streamToFile(InputStream is, File outFile)
360 jsutil.setFileBytes(outFile, is);
364 FileOutputStream fio = new FileOutputStream(outFile);
367 byte[] bb = new byte[32 * 1024];
369 while ((l = is.read(bb)) > 0)
380 * Encode the URI using JavaScript encodeURIComponent
383 * @return encoded value
385 public static String encodeURI(String value)
388 * @j2sNative value = encodeURIComponent(value);
394 * Open the URL using a simple window call if this is JavaScript
397 * @return true if window has been opened
399 public static boolean openURL(String url) throws IOException
403 BrowserLauncher.openURL(url);
415 public static Object parseJSON(InputStream response)
416 throws IOException, ParseException
420 return JSON.parse(response);
423 BufferedReader br = null;
426 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
427 return new JSONParser().parse(br);
435 } catch (IOException e)
443 public static Object parseJSON(String json) throws ParseException
445 return (isJS ? JSON.parse(json) : new JSONParser().parse(json));
448 public static Object parseJSON(Reader r)
449 throws IOException, ParseException
458 return new JSONParser().parse(r);
460 // Using a file reader is not currently supported in SwingJS JavaScript
462 if (r instanceof FileReader)
464 throw new IOException(
465 "StringJS does not support FileReader parsing for JSON -- but it could...");
467 return JSON.parse(r);
472 * Retrieve the object's embedded size from a div's style on a page if
473 * embedded in SwingJS.
476 * JFrame or JInternalFrame
477 * @param defaultWidth
478 * use -1 to return null (no default size)
479 * @param defaultHeight
480 * @return the embedded dimensions or null (no default size or not embedded)
482 public static Dimension getDimIfEmbedded(Component frame,
483 int defaultWidth, int defaultHeight)
488 d = (Dimension) getEmbeddedAttribute(frame, "dim");
490 return (d == null && defaultWidth >= 0
491 ? new Dimension(defaultWidth, defaultHeight)
496 public static Regex newRegex(String searchString, String replaceString)
499 return (replaceString == null ? new Regex(searchString)
500 : new Regex(searchString, replaceString));
503 public static Regex newRegexPerl(String code)
506 return Regex.perlCode(code);
510 * Initialize Java debug logging. A representative sample -- adapt as desired.
512 public static void startJavaLogging()
518 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
519 "java.awt.Component", "java.awt.focus.Component",
520 "java.awt.event.Component",
521 "java.awt.focus.DefaultKeyboardFocusManager");
526 * Initiate Java logging for a given class. Only for Java, not JavaScript;
527 * Allows debugging of complex event processing.
531 public static void logClass(String... classNames)
539 Logger rootLogger = Logger.getLogger("");
540 rootLogger.setLevel(Level.ALL);
541 ConsoleHandler consoleHandler = new ConsoleHandler();
542 consoleHandler.setLevel(Level.ALL);
543 for (int i = classNames.length; --i >= 0;)
545 Logger logger = Logger.getLogger(classNames[i]);
546 logger.setLevel(Level.ALL);
547 logger.addHandler(consoleHandler);
552 /// JavaScript-only methods ///
554 public static void cacheFileData(String path, Object data)
556 if (isJS && data != null)
558 jsutil.cachePathData(path, data);
562 public static void cacheFileData(File file)
566 byte[] data = Platform.getFileBytes(file);
570 cacheFileData(file.toString(), data);
576 public static byte[] getFileBytes(File f)
578 return (isJS && f != null ? jsutil.getBytes(f) : null);
581 public static byte[] getFileAsBytes(String fileStr)
583 if (isJS && fileStr != null)
585 byte[] bytes = (byte[]) jsutil.getFile(fileStr, false);
586 cacheFileData(fileStr, bytes);
592 @SuppressWarnings("unused")
593 public static String getFileAsString(String url)
595 if (isJS && url != null)
597 String ret = (String) jsutil.getFile(url, true);
598 cacheFileData(url, ret);
604 public static boolean setFileBytes(File f, String urlstring)
606 if (isJS && f != null && urlstring != null)
608 @SuppressWarnings("unused")
609 byte[] bytes = getFileAsBytes(urlstring);
610 jsutil.setFileBytes(f, bytes);
616 public static void addJ2SBinaryType(String ext)
620 jsutil.addBinaryFileType(ext);
624 public static String getUniqueAppletID()
626 return (isJS ? (String) jsutil.getAppletAttribute("_uniqueId") : null);
630 * Read the Info block for this applet.
635 * @return unique id for this applet
637 public static void readInfoProperties(String prefix, Properties p)
641 String id = getUniqueAppletID();
645 @SuppressWarnings("unused")
646 Object info = getAppletInfo(null);
648 * @j2sNative for (key in info) { value = info[key];
651 if (key.indexOf(prefix) == 0)
653 System.out.println("Platform id=" + id + " reading Info." + key
665 public static void setAjaxJSON(URL url)
675 * Add a known domain that implements access-control-allow-origin:*
677 * These should be reviewed periodically.
680 * for a service that is not allowing ajax
682 * @author hansonr@stolaf.edu
685 public static void addJ2SDirectDatabaseCall(String domain)
690 jsutil.addDirectDatabaseCall(domain);
693 "Platform adding known access-control-allow-origin * for domain "
699 public static void getURLCommandArguments()
703 * Retrieve the first query field as command arguments to Jalview. Include
704 * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
705 * element to this value.
708 * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
709 * + "?").split("?")[1].split("#")[0]); a &&
710 * (J2S.thisApplet.__Info.args = a.split(" "));
716 * A (case sensitive) file path comparator that ignores the difference between
723 public static boolean pathEquals(String path1, String path2)
727 return path2 == null;
733 String p1 = path1.replace('\\', '/');
734 String p2 = path2.replace('\\', '/');
735 return p1.equals(p2);
738 public static URL getDocumentBase()
740 return (isJS ? jsutil.getDocumentBase() : null);
743 public static URL getCodeBase()
745 return (isJS ? jsutil.getCodeBase() : null);
749 * load a resource -- probably a core file -- if and only if a particular
750 * class has not been instantialized. We use a String here because if we used
751 * a .class object, that reference itself would simply load the class, and we
752 * want the core package to include that as well.
754 * @param resourcePath
757 public static void loadStaticResource(String resourcePath,
762 jsutil.loadResourceIfClassUnknown(resourcePath, className);
766 public static void ensureRegex()
770 loadStaticResource("core/core_stevesoft.z.js",
771 "com.stevesoft.pat.Regex");
776 * Set the "app" property of the HTML5 applet object, for example,
777 * "testApplet.app", to point to the Jalview instance. This will be the object
778 * that page developers use that is similar to the original Java applet object
779 * that was accessed via LiveConnect.
783 public static void setAppClass(Object j)
787 jsutil.setAppletAttribute("app", j);
793 * If this frame ia embedded in a web page, return a known type.
796 * a JFrame or JInternalFrame
798 * @return null if frame is not embedded.
800 public static Object getEmbeddedAttribute(Component frame, String type)
802 return (isJS ? jsutil.getEmbeddedAttribute(frame, type) : null);
805 public static void stackTrace()
809 throw new NullPointerException();
810 } catch (Exception e)
817 @SuppressWarnings("unchecked")
818 public static Object getAppletInfo(String key)
820 return (isJS ? (Map<String, Object>) jsutil.getAppletInfo(key) : null);
824 * Option to avoid unnecessary seeking of nonexistent resources in JavaScript.
825 * Works in Java as well.
830 public static Locale getLocaleOrNone(Locale loc)
832 return (isJS && loc.getCountry() == "en" ? new Locale("") : loc);