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;
40 import javax.swing.SwingUtilities;
42 import org.json.simple.parser.JSONParser;
43 import org.json.simple.parser.ParseException;
45 import java.util.HashMap;
46 import java.util.HashSet;
48 import java.util.logging.ConsoleHandler;
49 import java.util.logging.Level;
50 import java.util.logging.Logger;
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
136 * based on System.getProperty("java.awt.headless")
138 public static boolean isHeadless()
140 if (isHeadless == null)
142 isHeadless = "true".equals(System.getProperty("java.awt.headless"));
149 * @return nominal maximum command line length for this platform
151 public static int getMaxCommandLineLength()
153 // TODO: determine nominal limits for most platforms.
154 return 2046; // this is the max length for a windows NT system.
158 * Answers the input with every backslash replaced with a double backslash (an
159 * 'escaped' single backslash)
164 public static String escapeBackslashes(String s)
166 return s == null ? null : s.replace("\\", "\\\\");
170 * Answers true if the mouse event has Meta-down (Command key on Mac) or
171 * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
172 * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
173 * Mac, you can use e.isPopupTrigger().
178 public static boolean isControlDown(MouseEvent e)
180 return isControlDown(e, isMac());
184 * Overloaded version of method (to allow unit testing)
190 protected static boolean isControlDown(MouseEvent e, boolean aMac)
194 return e.isControlDown();
196 // answer false for right mouse button
197 // shortcut key will be META for a Mac
198 return !e.isPopupTrigger()
199 && (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
200 & e.getModifiers()) != 0;
201 // could we use e.isMetaDown() here?
204 // BH: I don't know about that previous method. Here is what SwingJS uses.
205 // Notice the distinction in mouse events. (BUTTON3_MASK == META)
207 // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
208 // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
210 // if (id != MouseEvent.MOUSE_RELEASED)
213 //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
214 //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
216 //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
218 //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
222 // // mac, linux, unix
223 // if (id != MouseEvent.MOUSE_PRESSED)
225 // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
226 // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
227 // return rt || (ctrl && lt);
233 * Windows (not Mac, Linux, or Unix) and right button to test for the
234 * right-mouse pressed event in Windows that would have opened a menu or a
240 public static boolean isWinRightButton(MouseEvent e)
242 // was !isAMac(), but that is true also for Linux and Unix and JS,
244 return isWin() && SwingUtilities.isRightMouseButton(e);
248 * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
249 * without pressing the button.
254 public static boolean isWinMiddleButton(MouseEvent e)
256 // was !isAMac(), but that is true also for Linux and Unix and JS
257 return isWin() && SwingUtilities.isMiddleMouseButton(e);
260 public static boolean allowMnemonics()
265 public final static int TIME_RESET = 0;
267 public final static int TIME_MARK = 1;
269 public static final int TIME_SET = 2;
271 public static final int TIME_GET = 3;
273 public static long time, mark, set, duration;
278 * Platform.timeCheck(null, Platform.TIME_MARK);
282 * Platform.timeCheck("some message", Platform.TIME_MARK);
284 * reset...[set/mark]n...get
289 public static void timeCheck(String msg, int mode)
291 long t = System.currentTimeMillis();
299 System.err.println("Platform: timer reset\t\t\t" + msg);
305 // total time between set/mark points
306 duration += (t - set);
316 System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
317 + "\t" + ((t - mark) / 1000f) + "\t" + msg);
328 System.err.println("Platform: timer get\t" + ((t - time) / 1000f)
329 + "\t" + ((duration) / 1000f) + "\t" + msg);
336 ////// jsutil additions, simplifications
338 public static void cacheFileData(String path, Object data)
342 jsutil.cachePathData(path, data);
346 public static void cacheFileData(File file)
350 byte[] bytes = getFileBytes(file);
353 cacheFileData(file.toString(), bytes);
358 public static byte[] getFileBytes(File f)
360 return (isJS() && f != null ? jsutil.getBytes(f) : null);
363 public static byte[] getFileAsBytes(String fileStr)
365 byte[] bytes = (isJS() && fileStr != null
366 ? (byte[]) jsutil.getFile(fileStr, false)
370 cacheFileData(fileStr, bytes);
375 public static String getFileAsString(String url)
380 ret = (String) jsutil.getFile(url, true);
383 cacheFileData(url, ret);
389 public static boolean setFileBytes(File f, String urlstring)
395 byte[] bytes = getFileAsBytes(urlstring);
399 jsutil.setFileBytes(f, bytes);
400 } catch (Throwable t)
402 System.out.println("Platform.setFileBytes failed: " + t);
407 public static void addJ2SBinaryType(String ext)
411 jsutil.addBinaryFileType(ext);
416 * Encode the URI using JavaScript encodeURIComponent
419 * @return encoded value
421 public static String encodeURI(String value)
424 * @j2sNative value = encodeURIComponent(value);
430 * Open the URL using a simple window call if this is JavaScript
433 * @return true if window has been opened
435 public static boolean openURL(String url) throws IOException
439 BrowserLauncher.openURL(url);
451 public static String getUniqueAppletID()
453 // Caution -- null here means using current thread instead of a known component.
455 return jsutil.getAppletForComponent(null)._getID();
459 * Read the Info block for this applet.
464 * @return unique id for this applet
466 public static void readInfoProperties(String prefix, Properties p)
470 jsutil.readInfoProperties(prefix, p);
474 public static void setAjaxJSON(URL url)
482 public static Object parseJSON(InputStream response)
483 throws IOException, ParseException
487 return JSON.parse(response);
490 BufferedReader br = null;
493 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
494 return new JSONParser().parse(br);
502 } catch (IOException e)
510 public static Object parseJSON(String json) throws ParseException
512 return (isJS() ? JSON.parse(json)
513 : new JSONParser().parse(json));
516 public static Object parseJSON(Reader r)
517 throws IOException, ParseException
526 return new JSONParser().parse(r);
528 // Using a file reader is not currently supported in SwingJS JavaScript
530 if (r instanceof FileReader)
532 throw new IOException(
533 "StringJS does not support FileReader parsing for JSON -- but it could...");
535 return JSON.parse(r);
540 * Dump the input stream to an output file.
544 * @throws IOException
545 * if the file cannot be created or there is a problem reading the
548 public static void streamToFile(InputStream is, File outFile)
551 if (isJS() && jsutil.streamToFile(is, outFile))
555 FileOutputStream fio = new FileOutputStream(outFile);
558 byte[] bb = new byte[32 * 1024];
560 while ((l = is.read(bb)) > 0)
571 * Add a known domain that implements access-control-allow-origin:*
573 * These should be reviewed periodically.
576 * for a service that is not allowing ajax
578 * @author hansonr@stolaf.edu
581 public static void addJ2SDirectDatabaseCall(String domain)
586 jsutil.addDirectDatabaseCall(domain);
591 * Retrieve the first query field as command arguments to Jalview. Include
592 * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
593 * element to this value.
596 @SuppressWarnings("unused")
597 public static void getURLCommandArguments()
603 String[] args = null;
606 * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
607 * + "?").split("?")[1].split("#")[0]); args && (args =
612 jsutil.setAppletInfo("args", args);
619 * A (case sensitive) file path comparator that ignores the difference between /
627 public static boolean pathEquals(String path1, String path2)
631 return path2 == null;
637 String p1 = path1.replace('\\', '/');
638 String p2 = path2.replace('\\', '/');
639 return p1.equals(p2);
642 ///// new methods from applet branch only
645 public static URL getDocumentBase()
647 return (isJS() ? jsutil.getDocumentBase() : null);
650 public static URL getCodeBase()
652 return (isJS() ? jsutil.getCodeBase() : null);
655 public static void ensureJmol()
659 jsutil.loadResourceIfClassUnknown("core/core_jvjmol.z.js",
660 "org.jmol.viewer.Viewer");
664 public static void ensureRegex()
668 jsutil.loadResourceIfClassUnknown("core/core_stevesoft.z.js",
669 "com.stevesoft.pat.Regex");
673 public static Regex newRegex(String searchString, String replaceString)
676 return (replaceString == null ? new Regex(searchString)
677 : new Regex(searchString, replaceString));
680 public static Regex newRegexPerl(String code)
683 return Regex.perlCode(code);
687 * Initialize Java debug logging. A representative sample -- adapt as desired.
689 public static void startJavaLogging()
695 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
696 "java.awt.Component", "java.awt.focus.Component",
697 "java.awt.event.Component",
698 "java.awt.focus.DefaultKeyboardFocusManager");
703 * Initiate Java logging for a given class. Only for Java, not JavaScript;
704 * Allows debugging of complex event processing.
708 public static void logClass(String... classNames)
716 Logger rootLogger = Logger.getLogger("");
717 rootLogger.setLevel(Level.ALL);
718 ConsoleHandler consoleHandler = new ConsoleHandler();
719 consoleHandler.setLevel(Level.ALL);
720 for (int i = classNames.length; --i >= 0;)
722 Logger logger = Logger.getLogger(classNames[i]);
723 logger.setLevel(Level.ALL);
724 logger.addHandler(consoleHandler);
730 * Set the "app" property of the HTML5 applet object, for example,
731 * "testApplet.app", to point to the Jalview instance. This will be the object
732 * that page developers use that is similar to the original Java applet object
733 * that was accessed via LiveConnect.
737 public static void setAppClass(Object app)
741 jsutil.setAppletAttribute("app", app);
746 * Retrieve the object's embedded size from a div's style on a page if
747 * embedded in SwingJS.
750 * JFrame or JInternalFrame
751 * @param defaultWidth
752 * use -1 to return null (no default size)
753 * @param defaultHeight
754 * @return the embedded dimensions or null (no default size or not embedded)
756 public static Dimension getDimIfEmbedded(Component frame,
757 int defaultWidth, int defaultHeight)
759 Dimension d = (Dimension) getEmbeddedAttribute(frame, "dim");
760 return (d == null && defaultWidth >= 0
761 ? new Dimension(defaultWidth, defaultHeight)
767 * If this frame Is this frame embedded in a web page, return a known type.
770 * a JFrame or JInternalFrame
772 * @return null if frame is not embedded.
774 public static Object getEmbeddedAttribute(Component frame, String type)
776 return (isJS() ? jsutil.getEmbeddedAttribute(frame, type) : null);
780 * Only called for JavaScript.
782 * @return Map for static singleton classes unique to a given applet
784 public static HashMap<?, ?> getJSSingletons()
786 return (isJS() ? jsutil.getJSContext("jssingletons") : null);
790 * By designating initialCapacity and loadFactor, we tell SwingJS to use a
791 * standard (slower) Java HashMap to back this HashSet, thus providing exactly
792 * the same iterator order (until a new Java version changes it!)
794 * @return a standard Java HashSet
796 public static Set<String> getJavaOrderedHashSet()
798 return new HashSet<>(16, 0.75f);
802 * Switch the flag in SwingJS to use or not use the JavaScript Map object in
803 * any Hashtable, HashMap, or HashSet. Default is enabled.
805 * For testing purposes only.
808 public static boolean setJavaScriptMapObjectEnabled(boolean enabled)
814 jsutil.setJavaScriptMapObjectEnabled(enabled);
815 HashSet<String> hs = new HashSet<>();
816 // Java hash table iterator in HashMap will return "one" before "two"
817 // because of its hash code;
818 // JavaScript Map object will return "two" first because it was added first.
821 return (hs.iterator().next() == (enabled ? "two" : "one"));
825 public static void stackTrace()
827 new NullPointerException("testing only").printStackTrace();
832 * escape a string according to the local platform's escape character
835 * @return escaped file
837 public static String escapeString(String file)
839 StringBuffer f = new StringBuffer();
840 int p = 0, lastp = 0;
841 while ((p = file.indexOf('\\', lastp)) > -1)
843 f.append(file.subSequence(lastp, p));
847 f.append(file.substring(lastp));
851 private static float javaVersion;
853 public static float getJavaVersion()
855 if (javaVersion == 0)
859 return javaVersion = Float.parseFloat(
860 System.getProperty("java.specification.version"));
861 } catch (Exception e)