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 * escape a string according to the local platform's escape character
164 * @return escaped file
166 public static String escapeString(String file)
168 StringBuffer f = new StringBuffer();
169 int p = 0, lastp = 0;
170 while ((p = file.indexOf('\\', lastp)) > -1)
172 f.append(file.subSequence(lastp, p));
176 f.append(file.substring(lastp));
181 * Answers true if the mouse event has Meta-down (Command key on Mac) or
182 * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
183 * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
184 * Mac, you can use e.isPopupTrigger().
189 public static boolean isControlDown(MouseEvent e)
191 return isControlDown(e, isMac());
195 * Overloaded version of method (to allow unit testing)
201 protected static boolean isControlDown(MouseEvent e, boolean aMac)
205 return e.isControlDown();
207 // answer false for right mouse button
208 // shortcut key will be META for a Mac
209 return !e.isPopupTrigger()
210 && (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
211 & e.getModifiers()) != 0;
212 // could we use e.isMetaDown() here?
215 // BH: I don't know about that previous method. Here is what SwingJS uses.
216 // Notice the distinction in mouse events. (BUTTON3_MASK == META)
218 // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
219 // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
221 // if (id != MouseEvent.MOUSE_RELEASED)
224 //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
225 //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
227 //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
229 //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
233 // // mac, linux, unix
234 // if (id != MouseEvent.MOUSE_PRESSED)
236 // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
237 // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
238 // return rt || (ctrl && lt);
244 * Windows (not Mac, Linux, or Unix) and right button to test for the
245 * right-mouse pressed event in Windows that would have opened a menu or a
251 public static boolean isWinRightButton(MouseEvent e)
253 // was !isAMac(), but that is true also for Linux and Unix and JS,
255 return isWin() && SwingUtilities.isRightMouseButton(e);
259 * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
260 * without pressing the button.
265 public static boolean isWinMiddleButton(MouseEvent e)
267 // was !isAMac(), but that is true also for Linux and Unix and JS
268 return isWin() && SwingUtilities.isMiddleMouseButton(e);
271 public static boolean allowMnemonics()
276 public final static int TIME_RESET = 0;
278 public final static int TIME_MARK = 1;
280 public static final int TIME_SET = 2;
282 public static final int TIME_GET = 3;
284 public static long time, mark, set, duration;
289 * Platform.timeCheck(null, Platform.TIME_MARK);
293 * Platform.timeCheck("some message", Platform.TIME_MARK);
295 * reset...[set/mark]n...get
300 public static void timeCheck(String msg, int mode)
302 long t = System.currentTimeMillis();
310 System.err.println("Platform: timer reset\t\t\t" + msg);
316 // total time between set/mark points
317 duration += (t - set);
327 System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
328 + "\t" + ((t - mark) / 1000f) + "\t" + msg);
339 System.err.println("Platform: timer get\t" + ((t - time) / 1000f)
340 + "\t" + ((duration) / 1000f) + "\t" + msg);
348 * Dump the input stream to an output file.
352 * @throws IOException
353 * if the file cannot be created or there is a problem reading the
356 public static void streamToFile(InputStream is, File outFile)
362 jsutil.setFileBytes(outFile, is);
366 FileOutputStream fio = new FileOutputStream(outFile);
369 byte[] bb = new byte[32 * 1024];
371 while ((l = is.read(bb)) > 0)
382 * Encode the URI using JavaScript encodeURIComponent
385 * @return encoded value
387 public static String encodeURI(String value)
390 * @j2sNative value = encodeURIComponent(value);
396 * Open the URL using a simple window call if this is JavaScript
399 * @return true if window has been opened
401 public static boolean openURL(String url) throws IOException
405 BrowserLauncher.openURL(url);
417 public static Object parseJSON(InputStream response)
418 throws IOException, ParseException
422 return JSON.parse(response);
425 BufferedReader br = null;
428 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
429 return new JSONParser().parse(br);
437 } catch (IOException e)
445 public static Object parseJSON(String json) throws ParseException
447 return (isJS ? JSON.parse(json) : new JSONParser().parse(json));
450 public static Object parseJSON(Reader r)
451 throws IOException, ParseException
460 return new JSONParser().parse(r);
462 // Using a file reader is not currently supported in SwingJS JavaScript
464 if (r instanceof FileReader)
466 throw new IOException(
467 "StringJS does not support FileReader parsing for JSON -- but it could...");
469 return JSON.parse(r);
474 * Retrieve the object's embedded size from a div's style on a page if
475 * embedded in SwingJS.
478 * JFrame or JInternalFrame
479 * @param defaultWidth
480 * use -1 to return null (no default size)
481 * @param defaultHeight
482 * @return the embedded dimensions or null (no default size or not embedded)
484 public static Dimension getDimIfEmbedded(Component frame,
485 int defaultWidth, int defaultHeight)
490 d = (Dimension) getEmbeddedAttribute(frame, "dim");
492 return (d == null && defaultWidth >= 0
493 ? new Dimension(defaultWidth, defaultHeight)
498 public static Regex newRegex(String searchString, String replaceString)
501 return (replaceString == null ? new Regex(searchString)
502 : new Regex(searchString, replaceString));
505 public static Regex newRegexPerl(String code)
508 return Regex.perlCode(code);
512 * Initialize Java debug logging. A representative sample -- adapt as desired.
514 public static void startJavaLogging()
520 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
521 "java.awt.Component", "java.awt.focus.Component",
522 "java.awt.event.Component",
523 "java.awt.focus.DefaultKeyboardFocusManager");
528 * Initiate Java logging for a given class. Only for Java, not JavaScript;
529 * Allows debugging of complex event processing.
533 public static void logClass(String... classNames)
541 Logger rootLogger = Logger.getLogger("");
542 rootLogger.setLevel(Level.ALL);
543 ConsoleHandler consoleHandler = new ConsoleHandler();
544 consoleHandler.setLevel(Level.ALL);
545 for (int i = classNames.length; --i >= 0;)
547 Logger logger = Logger.getLogger(classNames[i]);
548 logger.setLevel(Level.ALL);
549 logger.addHandler(consoleHandler);
554 /// JavaScript-only methods ///
556 public static void cacheFileData(String path, Object data)
558 if (isJS && data != null)
560 jsutil.cachePathData(path, data);
564 public static void cacheFileData(File file)
568 byte[] data = Platform.getFileBytes(file);
572 cacheFileData(file.toString(), data);
578 public static byte[] getFileBytes(File f)
580 return (isJS && f != null ? jsutil.getBytes(f) : null);
583 public static byte[] getFileAsBytes(String fileStr)
585 if (isJS && fileStr != null)
587 byte[] bytes = (byte[]) jsutil.getFile(fileStr, false);
588 cacheFileData(fileStr, bytes);
594 @SuppressWarnings("unused")
595 public static String getFileAsString(String url)
597 if (isJS && url != null)
599 String ret = (String) jsutil.getFile(url, true);
600 cacheFileData(url, ret);
606 public static boolean setFileBytes(File f, String urlstring)
608 if (isJS && f != null && urlstring != null)
610 @SuppressWarnings("unused")
611 byte[] bytes = getFileAsBytes(urlstring);
612 jsutil.setFileBytes(f, bytes);
618 public static void addJ2SBinaryType(String ext)
622 jsutil.addBinaryFileType(ext);
626 public static String getUniqueAppletID()
628 return (isJS ? (String) jsutil.getAppletAttribute("_uniqueId") : null);
632 * Read the Info block for this applet.
637 * @return unique id for this applet
639 public static void readInfoProperties(String prefix, Properties p)
643 String id = getUniqueAppletID();
647 @SuppressWarnings("unused")
648 Object info = jsutil.getAppletAttribute("__Info");
650 * @j2sNative for (key in info) { value = info[key];
653 if (key.indexOf(prefix) == 0)
655 System.out.println("Platform id=" + id + " reading Info." + key
667 public static void setAjaxJSON(URL url)
677 * Add a known domain that implements access-control-allow-origin:*
679 * These should be reviewed periodically.
682 * for a service that is not allowing ajax
684 * @author hansonr@stolaf.edu
687 public static void addJ2SDirectDatabaseCall(String domain)
692 jsutil.addDirectDatabaseCall(domain);
695 "Platform adding known access-control-allow-origin * for domain "
701 public static void getURLCommandArguments()
705 * Retrieve the first query field as command arguments to Jalview. Include
706 * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
707 * element to this value.
710 * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
711 * + "?").split("?")[1].split("#")[0]); a &&
712 * (J2S.thisApplet.__Info.args = a.split(" "));
717 public static URL getDocumentBase()
719 return (isJS ? jsutil.getDocumentBase() : null);
722 public static URL getCodeBase()
724 return (isJS ? jsutil.getCodeBase() : null);
728 * load a resource -- probably a core file -- if and only if a particular
729 * class has not been instantialized. We use a String here because if we used
730 * a .class object, that reference itself would simply load the class, and we
731 * want the core package to include that as well.
733 * @param resourcePath
736 public static void loadStaticResource(String resourcePath,
741 jsutil.loadResourceIfClassUnknown(resourcePath, className);
745 public static void ensureRegex()
749 loadStaticResource("core/core_stevesoft.z.js",
750 "com.stevesoft.pat.Regex");
755 * Set the "app" property of the HTML5 applet object, for example,
756 * "testApplet.app", to point to the Jalview instance. This will be the object
757 * that page developers use that is similar to the original Java applet object
758 * that was accessed via LiveConnect.
762 public static void setAppClass(Object j)
766 jsutil.setAppletAttribute("app", j);
772 * If this frame ia embedded in a web page, return a known type.
775 * a JFrame or JInternalFrame
777 * @return null if frame is not embedded.
779 public static Object getEmbeddedAttribute(Component frame, String type)
781 return (isJS ? jsutil.getEmbeddedAttribute(frame, type) : null);
784 public static void stackTrace()
788 throw new NullPointerException();
789 } catch (Exception e)