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.HashMap;
39 import java.util.HashSet;
40 import java.util.Properties;
42 import java.util.logging.ConsoleHandler;
43 import java.util.logging.Level;
44 import java.util.logging.Logger;
46 import javax.swing.SwingUtilities;
48 import org.json.simple.parser.JSONParser;
49 import org.json.simple.parser.ParseException;
51 import com.stevesoft.pat.Regex;
53 import swingjs.api.JSUtilI;
56 * System platform information used by Applet and Application
63 private static boolean isJS = /** @j2sNative true || */
66 private static JSUtilI jsutil = /**
67 * @j2sNative new Clazz.new_("swingjs.JSUtil")
73 private static Boolean isNoJSMac = null, isNoJSWin = null, isMac = null,
76 // private static Boolean isHeadless = null;
79 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
83 public static boolean isMac()
86 ? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0))
91 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
95 public static boolean isWin()
98 ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0))
104 * @return true if HTML5 JavaScript
106 public static boolean isJS()
112 * sorry folks - Macs really are different
114 * BH: disabled for SwingJS -- will need to check key-press issues
116 * @return true if we do things in a special way.
118 public static boolean isAMacAndNotJS()
120 return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac);
124 * Check if we are on a Microsoft plaform...
126 * @return true if we have to cope with another platform variation
128 public static boolean isWindowsAndNotJS()
130 return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
135 // * @return true if we are running in non-interactive no UI mode
137 // public static boolean isHeadless()
139 // if (isHeadless == null)
141 // isHeadless = "true".equals(System.getProperty("java.awt.headless"));
143 // return isHeadless;
148 * @return nominal maximum command line length for this platform
150 public static int getMaxCommandLineLength()
152 // TODO: determine nominal limits for most platforms.
153 return 2046; // this is the max length for a windows NT system.
157 * escape a string according to the local platform's escape character
160 * @return escaped file
162 public static String escapeString(String file)
164 StringBuffer f = new StringBuffer();
165 int p = 0, lastp = 0;
166 while ((p = file.indexOf('\\', lastp)) > -1)
168 f.append(file.subSequence(lastp, p));
172 f.append(file.substring(lastp));
177 * Answers true if the mouse event has Meta-down (Command key on Mac) or
178 * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
179 * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
180 * Mac, you can use e.isPopupTrigger().
185 public static boolean isControlDown(MouseEvent e)
187 return isControlDown(e, isMac());
191 * Overloaded version of method (to allow unit testing)
197 protected static boolean isControlDown(MouseEvent e, boolean aMac)
201 return e.isControlDown();
203 // answer false for right mouse button
204 // shortcut key will be META for a Mac
205 return !e.isPopupTrigger()
206 && (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
207 & e.getModifiers()) != 0;
208 // could we use e.isMetaDown() here?
211 // BH: I don't know about that previous method. Here is what SwingJS uses.
212 // Notice the distinction in mouse events. (BUTTON3_MASK == META)
214 // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
215 // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
217 // if (id != MouseEvent.MOUSE_RELEASED)
220 //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
221 //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
223 //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
225 //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
229 // // mac, linux, unix
230 // if (id != MouseEvent.MOUSE_PRESSED)
232 // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
233 // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
234 // return rt || (ctrl && lt);
240 * Windows (not Mac, Linux, or Unix) and right button to test for the
241 * right-mouse pressed event in Windows that would have opened a menu or a
247 public static boolean isWinRightButton(MouseEvent e)
249 // was !isAMac(), but that is true also for Linux and Unix and JS,
251 return isWin() && SwingUtilities.isRightMouseButton(e);
255 * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
256 * without pressing the button.
261 public static boolean isWinMiddleButton(MouseEvent e)
263 // was !isAMac(), but that is true also for Linux and Unix and JS
264 return isWin() && SwingUtilities.isMiddleMouseButton(e);
267 public static boolean allowMnemonics()
272 public final static int TIME_RESET = 0;
274 public final static int TIME_MARK = 1;
276 public static final int TIME_SET = 2;
278 public static final int TIME_GET = 3;
280 public static long time, mark, set, duration;
285 * Platform.timeCheck(null, Platform.TIME_MARK);
289 * Platform.timeCheck("some message", Platform.TIME_MARK);
291 * reset...[set/mark]n...get
296 public static void timeCheck(String msg, int mode)
298 long t = System.currentTimeMillis();
306 System.err.println("Platform: timer reset\t\t\t" + msg);
312 // total time between set/mark points
313 duration += (t - set);
323 System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
324 + "\t" + ((t - mark) / 1000f) + "\t" + msg);
335 System.err.println("Platform: timer get\t" + ((t - time) / 1000f)
336 + "\t" + ((duration) / 1000f) + "\t" + msg);
344 * Encode the URI using JavaScript encodeURIComponent
347 * @return encoded value
349 public static String encodeURI(String value)
352 * @j2sNative value = encodeURIComponent(value);
358 * Open the URL using a simple window call if this is JavaScript
361 * @return true if window has been opened
363 public static boolean openURL(String url) throws IOException
367 BrowserLauncher.openURL(url);
379 public static void stackTrace()
381 new NullPointerException("testing only").printStackTrace();
384 public static void cacheFileData(String path, Object data)
388 jsutil.cachePathData(path, data);
392 public static void cacheFileData(File file)
396 byte[] bytes = getFileBytes(file);
399 cacheFileData(file.toString(), bytes);
404 public static byte[] getFileBytes(File f)
406 return (isJS() && f != null ? jsutil.getBytes(f) : null);
409 public static byte[] getFileAsBytes(String fileStr)
411 byte[] bytes = (isJS() && fileStr != null
412 ? (byte[]) jsutil.getFile(fileStr, false)
416 cacheFileData(fileStr, bytes);
421 public static String getFileAsString(String url)
426 ret = (String) jsutil.getFile(url, true);
429 cacheFileData(url, ret);
435 public static boolean setFileBytes(File f, String urlstring)
441 byte[] bytes = getFileAsBytes(urlstring);
445 jsutil.setFileBytes(f, bytes);
446 } catch (Throwable t)
448 System.out.println("Platform.setFileBytes failed: " + t);
453 public static void addJ2SBinaryType(String ext)
456 jsutil.addBinaryFileType(ext);
460 * Read the Info block for this applet.
465 * @return unique id for this applet
467 public static void readInfoProperties(String prefix, Properties p)
471 jsutil.readInfoProperties(prefix, p);
475 public static void setAjaxJSON(URL url)
483 public static Object parseJSON(InputStream response)
484 throws IOException, ParseException
488 return JSON.parse(response);
491 BufferedReader br = null;
494 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
495 return new JSONParser().parse(br);
503 } catch (IOException e)
511 public static Object parseJSON(String json) throws ParseException
513 return (isJS() ? JSON.parse(json)
514 : new JSONParser().parse(json));
517 public static Object parseJSON(Reader r)
518 throws IOException, ParseException
527 return new JSONParser().parse(r);
529 // Using a file reader is not currently supported in SwingJS JavaScript
531 if (r instanceof FileReader)
533 throw new IOException(
534 "StringJS does not support FileReader parsing for JSON -- but it could...");
536 return JSON.parse(r);
541 * Dump the input stream to an output file.
545 * @throws IOException
546 * if the file cannot be created or there is a problem reading the
549 public static void streamToFile(InputStream is, File outFile)
552 if (isJS() && jsutil.streamToFile(is, outFile))
556 FileOutputStream fio = new FileOutputStream(outFile);
559 byte[] bb = new byte[32 * 1024];
561 while ((l = is.read(bb)) > 0)
572 * Add a known domain that implements access-control-allow-origin:*
574 * These should be reviewed periodically.
577 * for a service that is not allowing ajax
579 * @author hansonr@stolaf.edu
582 public static void addJ2SDirectDatabaseCall(String domain)
587 jsutil.addDirectDatabaseCall(domain);
592 * Retrieve the first query field as command arguments to Jalview. Include
593 * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
594 * element to this value.
597 @SuppressWarnings("unused")
598 public static void getURLCommandArguments()
605 String[] args = null;
608 * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
609 * + "?").split("?")[1].split("#")[0]); args && (args =
614 jsutil.setAppletInfo("args", args);
619 public static URL getDocumentBase()
621 return (isJS() ? jsutil.getDocumentBase() : null);
624 public static URL getCodeBase()
626 return (isJS() ? jsutil.getCodeBase() : null);
629 public static void ensureJmol()
631 jsutil.loadResourceIfClassUnknown("core/core_jvjmol.z.js",
632 "org.jmol.viewer.Viewer");
635 public static void ensureRegex()
637 jsutil.loadResourceIfClassUnknown("core/core_stevesoft.z.js",
638 "com.stevesoft.pat.Regex");
641 public static Regex newRegex(String searchString, String replaceString)
644 return (replaceString == null ? new Regex(searchString)
645 : new Regex(searchString, replaceString));
648 public static Regex newRegexPerl(String code)
651 return Regex.perlCode(code);
655 * Initialize Java debug logging. A representative sample -- adapt as desired.
657 public static void startJavaLogging()
663 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
664 "java.awt.Component", "java.awt.focus.Component",
665 "java.awt.event.Component",
666 "java.awt.focus.DefaultKeyboardFocusManager");
671 * Initiate Java logging for a given class. Only for Java, not JavaScript;
672 * Allows debugging of complex event processing.
676 public static void logClass(String... classNames)
684 Logger rootLogger = Logger.getLogger("");
685 rootLogger.setLevel(Level.ALL);
686 ConsoleHandler consoleHandler = new ConsoleHandler();
687 consoleHandler.setLevel(Level.ALL);
688 for (int i = classNames.length; --i >= 0;)
690 Logger logger = Logger.getLogger(classNames[i]);
691 logger.setLevel(Level.ALL);
692 logger.addHandler(consoleHandler);
698 * Set the "app" property of the HTML5 applet object, for example,
699 * "testApplet.app", to point to the Jalview instance. This will be the object
700 * that page developers use that is similar to the original Java applet object
701 * that was accessed via LiveConnect.
705 public static void setAppClass(Object app)
709 jsutil.setAppletAttribute("app", app);
714 * Retrieve the object's embedded size from a div's style on a page if
715 * embedded in SwingJS.
718 * JFrame or JInternalFrame
719 * @param defaultWidth
720 * use -1 to return null (no default size)
721 * @param defaultHeight
722 * @return the embedded dimensions or null (no default size or not embedded)
724 public static Dimension getDimIfEmbedded(Component frame,
725 int defaultWidth, int defaultHeight)
727 Dimension d = (Dimension) getEmbeddedAttribute(frame, "dim");
728 return (d == null && defaultWidth >= 0
729 ? new Dimension(defaultWidth, defaultHeight)
735 * If this frame Is this frame embedded in a web page, return a known type.
738 * a JFrame or JInternalFrame
740 * @return null if frame is not embedded.
742 public static Object getEmbeddedAttribute(Component frame, String type)
744 return (isJS() ? jsutil.getEmbeddedAttribute(frame, type) : null);
748 * Only called for JavaScript.
750 * @return Map for static singleton classes unique to a given applet
752 public static HashMap<?,?> getJSSingletons()
754 return (isJS() ? jsutil.getJSContext("jssingletons") : null);
758 * By designating initialCapacity and loadFactor, we tell SwingJS to use a
759 * standard (slower) Java HashMap to back this HashSet, thus providing exactly
760 * the same iterator order (until a new Java version changes it!)
762 * @return a standard Java HashSet
764 public static Set<String> getJavaOrderedHashSet()
766 return new HashSet<>(16, 0.75f);
770 * Switch the flag in SwingJS to use or not use the JavaScript Map object in
771 * any Hashtable, HashMap, or HashSet. Default is enabled.
773 * For testing purposes only.
776 public static boolean setJavaScriptMapObjectEnabled(boolean enabled)
782 jsutil.setJavaScriptMapObjectEnabled(enabled);
783 HashSet<String> hs = new HashSet<>();
784 // Java hash table iterator in HashMap will return "one" before "two"
785 // because of its hash code;
786 // JavaScript Map object will return "two" first because it was added first.
789 return (hs.iterator().next() == (enabled ? "two" : "one"));