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
461 public static String getUniqueAppletID()
463 return (isJS ? (String) jsutil.getAppletAttribute("_uniqueId") : null);
468 * Read the Info block for this applet.
473 * @return unique id for this applet
475 public static void readInfoProperties(String prefix, Properties p)
479 String id = getUniqueAppletID();
483 @SuppressWarnings("unused")
484 Object info = jsutil.getAppletAttribute("__Info");
486 * @j2sNative for (key in info) { value = info[key];
489 if (key.indexOf(prefix) == 0)
491 System.out.println("Platform id=" + id + " reading Info." + key
503 public static void setAjaxJSON(URL url)
511 public static Object parseJSON(InputStream response)
512 throws IOException, ParseException
516 return JSON.parse(response);
519 BufferedReader br = null;
522 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
523 return new JSONParser().parse(br);
531 } catch (IOException e)
539 public static Object parseJSON(String json) throws ParseException
541 return (isJS() ? JSON.parse(json)
542 : new JSONParser().parse(json));
545 public static Object parseJSON(Reader r)
546 throws IOException, ParseException
555 return new JSONParser().parse(r);
557 // Using a file reader is not currently supported in SwingJS JavaScript
559 if (r instanceof FileReader)
561 throw new IOException(
562 "StringJS does not support FileReader parsing for JSON -- but it could...");
564 return JSON.parse(r);
568 * Dump the input stream to an output file.
572 * @throws IOException
573 * if the file cannot be created or there is a problem
574 * reading the input stream.
576 public static void streamToFile(InputStream is, File outFile)
582 jsutil.setFileBytes(outFile, is);
586 FileOutputStream fio = new FileOutputStream(outFile);
589 byte[] bb = new byte[32 * 1024];
591 while ((l = is.read(bb)) > 0)
602 * Add a known domain that implements access-control-allow-origin:*
604 * These should be reviewed periodically.
607 * for a service that is not allowing ajax
609 * @author hansonr@stolaf.edu
612 public static void addJ2SDirectDatabaseCall(String domain)
617 jsutil.addDirectDatabaseCall(domain);
620 "Platform adding known access-control-allow-origin * for domain "
626 public static void getURLCommandArguments()
630 * Retrieve the first query field as command arguments to Jalview. Include
631 * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
632 * element to this value.
635 * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
636 * + "?").split("?")[1].split("#")[0]); a &&
637 * (J2S.thisApplet.__Info.args = a.split(" "));
643 * A (case sensitive) file path comparator that ignores the difference between /
650 public static boolean pathEquals(String path1, String path2)
654 return path2 == null;
660 String p1 = path1.replace('\\', '/');
661 String p2 = path2.replace('\\', '/');
662 return p1.equals(p2);
667 ///////////// JAL-3253 Applet additions //////////////
671 * Retrieve the object's embedded size from a div's style on a page if
672 * embedded in SwingJS.
675 * JFrame or JInternalFrame
676 * @param defaultWidth
677 * use -1 to return null (no default size)
678 * @param defaultHeight
679 * @return the embedded dimensions or null (no default size or not embedded)
681 public static Dimension getDimIfEmbedded(Component frame,
682 int defaultWidth, int defaultHeight)
687 d = (Dimension) getEmbeddedAttribute(frame, "dim");
689 return (d == null && defaultWidth >= 0
690 ? new Dimension(defaultWidth, defaultHeight)
695 public static Regex newRegex(String regex)
697 return newRegex(regex, null);
700 public static Regex newRegex(String searchString, String replaceString)
703 return (replaceString == null ? new Regex(searchString)
704 : new Regex(searchString, replaceString));
707 public static Regex newRegexPerl(String code)
710 return Regex.perlCode(code);
714 * Initialize Java debug logging. A representative sample -- adapt as desired.
716 public static void startJavaLogging()
722 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
723 "java.awt.Component", "java.awt.focus.Component",
724 "java.awt.event.Component",
725 "java.awt.focus.DefaultKeyboardFocusManager");
730 * Initiate Java logging for a given class. Only for Java, not JavaScript;
731 * Allows debugging of complex event processing.
735 public static void logClass(String... classNames)
743 Logger rootLogger = Logger.getLogger("");
744 rootLogger.setLevel(Level.ALL);
745 ConsoleHandler consoleHandler = new ConsoleHandler();
746 consoleHandler.setLevel(Level.ALL);
747 for (int i = classNames.length; --i >= 0;)
749 Logger logger = Logger.getLogger(classNames[i]);
750 logger.setLevel(Level.ALL);
751 logger.addHandler(consoleHandler);
758 * load a resource -- probably a core file -- if and only if a particular
759 * class has not been instantialized. We use a String here because if we used
760 * a .class object, that reference itself would simply load the class, and we
761 * want the core package to include that as well.
763 * @param resourcePath
766 public static void loadStaticResource(String resourcePath,
771 jsutil.loadResourceIfClassUnknown(resourcePath, className);
775 public static void ensureRegex()
779 loadStaticResource("core/core_stevesoft.z.js",
780 "com.stevesoft.pat.Regex");
785 * Set the "app" property of the HTML5 applet object, for example,
786 * "testApplet.app", to point to the Jalview instance. This will be the object
787 * that page developers use that is similar to the original Java applet object
788 * that was accessed via LiveConnect.
792 public static void setAppClass(Object j)
796 jsutil.setAppletAttribute("app", j);
802 * If this frame ia embedded in a web page, return a known type.
805 * a JFrame or JInternalFrame
807 * @return null if frame is not embedded.
809 public static Object getEmbeddedAttribute(Component frame, String type)
811 return (isJS ? jsutil.getEmbeddedAttribute(frame, type) : null);
814 public static void stackTrace()
818 throw new NullPointerException();
819 } catch (Exception e)
826 public static URL getDocumentBase()
828 return (isJS ? jsutil.getDocumentBase() : null);
831 public static URL getCodeBase()
833 return (isJS ? jsutil.getCodeBase() : null);