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 java.awt.Component;
24 import java.awt.Dimension;
25 import java.awt.Toolkit;
26 import java.awt.event.MouseEvent;
27 import java.io.BufferedReader;
29 import java.io.FileOutputStream;
30 import java.io.FileReader;
31 import java.io.IOException;
32 import java.io.InputStream;
33 import java.io.InputStreamReader;
34 import java.io.Reader;
36 import java.nio.file.Files;
37 import java.nio.file.Path;
38 import java.nio.file.attribute.BasicFileAttributes;
39 import java.util.Date;
41 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 jalview.bin.Jalview;
54 import jalview.javascript.json.JSON;
55 import swingjs.api.JSUtilI;
58 * System platform information used by Applet and Application
65 private static boolean isJS = /** @j2sNative true || */
68 private static Boolean isNoJSMac = null, isNoJSWin = null, isMac = null,
71 private static Boolean isHeadless = null;
73 private static swingjs.api.JSUtilI jsutil;
81 // this is ok - it's a highly embedded method in Java; the deprecation
83 // really a recommended best practice.
84 jsutil = ((JSUtilI) Class.forName("swingjs.JSUtil").newInstance());
85 } catch (InstantiationException | IllegalAccessException
86 | ClassNotFoundException e)
92 // private static Boolean isHeadless = null;
95 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
99 public static boolean isMac()
101 return (isMac == null
102 ? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0))
107 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
111 public static boolean isWin()
113 return (isWin == null
114 ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0))
120 * @return true if HTML5 JavaScript
122 public static boolean isJS()
128 * sorry folks - Macs really are different
130 * BH: disabled for SwingJS -- will need to check key-press issues
132 * @return true if we do things in a special way.
134 public static boolean isAMacAndNotJS()
136 return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac);
140 * Check if we are on a Microsoft plaform...
142 * @return true if we have to cope with another platform variation
144 public static boolean isWindowsAndNotJS()
146 return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
151 * @return true if we are running in non-interactive no UI mode
153 public static boolean isHeadless()
155 if (isHeadless == null)
157 isHeadless = "true".equals(System.getProperty("java.awt.headless"));
164 * @return nominal maximum command line length for this platform
166 public static int getMaxCommandLineLength()
168 // TODO: determine nominal limits for most platforms.
169 return 2046; // this is the max length for a windows NT system.
173 * Answers the input with every backslash replaced with a double backslash (an
174 * 'escaped' single backslash)
179 public static String escapeBackslashes(String s)
181 return s == null ? null : s.replace("\\", "\\\\");
185 * Answers true if the mouse event has Meta-down (Command key on Mac) or
186 * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
187 * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
188 * Mac, you can use e.isPopupTrigger().
193 public static boolean isControlDown(MouseEvent e)
195 return isControlDown(e, isMac());
199 * Overloaded version of method (to allow unit testing)
205 protected static boolean isControlDown(MouseEvent e, boolean aMac)
209 return e.isControlDown();
211 // Jalview 2.11 code below: above is as amended for JalviewJS
213 // * answer false for right mouse button
215 // if (e.isPopupTrigger())
220 // (jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() //
221 // .getMenuShortcutKeyMaskEx()
222 // & jalview.util.ShortcutKeyMaskExWrapper
223 // .getModifiersEx(e)) != 0; // getModifiers()) != 0;
225 // answer false for right mouse button
226 // shortcut key will be META for a Mac
227 return !e.isPopupTrigger()
228 && (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
229 & e.getModifiers()) != 0;
230 // could we use e.isMetaDown() here?
233 // BH: I don't know about that previous method. Here is what SwingJS uses.
234 // Notice the distinction in mouse events. (BUTTON3_MASK == META)
236 // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
237 // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
239 // if (id != MouseEvent.MOUSE_RELEASED)
242 //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
243 //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
245 //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
247 //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
251 // // mac, linux, unix
252 // if (id != MouseEvent.MOUSE_PRESSED)
254 // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
255 // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
256 // return rt || (ctrl && lt);
262 * Windows (not Mac, Linux, or Unix) and right button to test for the
263 * right-mouse pressed event in Windows that would have opened a menu or a
269 public static boolean isWinRightButton(MouseEvent e)
271 // was !isAMac(), but that is true also for Linux and Unix and JS,
273 return isWin() && SwingUtilities.isRightMouseButton(e);
277 * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
278 * without pressing the button.
283 public static boolean isWinMiddleButton(MouseEvent e)
285 // was !isAMac(), but that is true also for Linux and Unix and JS
286 return isWin() && SwingUtilities.isMiddleMouseButton(e);
289 public static boolean allowMnemonics()
294 public final static int TIME_RESET = 0;
296 public final static int TIME_MARK = 1;
298 public static final int TIME_SET = 2;
300 public static final int TIME_GET = 3;
302 public static long time, mark, set, duration;
307 * Platform.timeCheck(null, Platform.TIME_MARK);
311 * Platform.timeCheck("some message", Platform.TIME_MARK);
313 * reset...[set/mark]n...get
318 public static void timeCheck(String msg, int mode)
320 long t = System.currentTimeMillis();
328 System.err.println("Platform: timer reset\t\t\t" + msg);
334 // total time between set/mark points
335 duration += (t - set);
345 System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
346 + "\t" + ((t - mark) / 1000f) + "\t" + msg);
357 System.err.println("Platform: timer dur\t" + ((t - time) / 1000f)
358 + "\t" + ((duration) / 1000f) + "\t" + msg);
365 public static void cacheFileData(String path, Object data)
367 if (isJS && data != null)
369 jsutil.cachePathData(path, data);
373 public static void cacheFileData(File file)
377 byte[] data = Platform.getFileBytes(file);
381 cacheFileData(file.toString(), data);
387 public static byte[] getFileBytes(File f)
389 return (isJS && f != null ? jsutil.getBytes(f) : null);
392 public static byte[] getFileAsBytes(String fileStr)
394 if (isJS && fileStr != null)
396 byte[] bytes = (byte[]) jsutil.getFile(fileStr, false);
397 cacheFileData(fileStr, bytes);
403 public static String getFileAsString(String url)
405 if (isJS && url != null)
407 String ret = (String) jsutil.getFile(url, true);
408 cacheFileData(url, ret);
414 public static boolean setFileBytes(File f, String urlstring)
416 if (isJS && f != null && urlstring != null)
418 @SuppressWarnings("unused")
419 byte[] bytes = getFileAsBytes(urlstring);
420 jsutil.setFileBytes(f, bytes);
426 public static void addJ2SBinaryType(String ext)
430 jsutil.addBinaryFileType(ext);
435 * Encode the URI using JavaScript encodeURIComponent
438 * @return encoded value
440 public static String encodeURI(String value)
443 * @j2sNative value = encodeURIComponent(value);
449 * Open the URL using a simple window call if this is JavaScript
452 * @return true if window has been opened
454 public static boolean openURL(String url) throws IOException
469 public static String getUniqueAppletID()
471 return (isJS ? (String) jsutil.getAppletAttribute("_uniqueId") : null);
475 * Read the Info block for this applet.
480 * @return unique id for this applet
482 public static void readInfoProperties(String prefix, Properties p)
486 String id = getUniqueAppletID();
490 @SuppressWarnings("unused")
491 Object info = jsutil.getAppletAttribute("__Info");
493 * @j2sNative for (key in info) { value = info[key];
496 if (key.indexOf(prefix) == 0)
498 System.out.println("Platform id=" + id + " reading Info." + key
510 public static void setAjaxJSON(URL url)
518 public static Object parseJSON(InputStream response)
519 throws IOException, ParseException
523 return JSON.parse(response);
526 BufferedReader br = null;
529 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
530 return new JSONParser().parse(br);
538 } catch (IOException e)
546 public static Object parseJSON(String json) throws ParseException
548 return (isJS() ? JSON.parse(json) : new JSONParser().parse(json));
551 public static Object parseJSON(Reader r)
552 throws IOException, ParseException
561 return new JSONParser().parse(r);
563 // Using a file reader is not currently supported in SwingJS JavaScript
565 if (r instanceof FileReader)
567 throw new IOException(
568 "StringJS does not support FileReader parsing for JSON -- but it could...");
570 return JSON.parse(r);
574 * Dump the input stream to an output file.
578 * @throws IOException
579 * if the file cannot be created or there is a problem reading the
582 public static void streamToFile(InputStream is, File outFile)
588 jsutil.setFileBytes(outFile, is);
592 FileOutputStream fio = new FileOutputStream(outFile);
595 byte[] bb = new byte[32 * 1024];
597 while ((l = is.read(bb)) > 0)
608 * Add a known domain that implements access-control-allow-origin:*
610 * These should be reviewed periodically.
613 * for a service that is not allowing ajax
615 * @author hansonr@stolaf.edu
618 public static void addJ2SDirectDatabaseCall(String domain)
623 jsutil.addDirectDatabaseCall(domain);
626 "Platform adding known access-control-allow-origin * for domain "
633 * Allow for URL-line command arguments. Untested.
636 public static void getURLCommandArguments()
641 * Retrieve the first query field as command arguments to Jalview. Include
642 * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
643 * element to this value.
646 * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
647 * + "?").split("?")[1].split("#")[0]); a &&
648 * (J2S.thisApplet.__Info.args = a.split(" "));
650 * System.out.println("URL arguments: " + a);
652 } catch (Throwable t) {
657 * A (case sensitive) file path comparator that ignores the difference between
664 public static boolean pathEquals(String path1, String path2)
668 return path2 == null;
674 String p1 = path1.replace('\\', '/');
675 String p2 = path2.replace('\\', '/');
676 return p1.equals(p2);
679 ///////////// JAL-3253 Applet additions //////////////
682 * Retrieve the object's embedded size from a div's style on a page if
683 * embedded in SwingJS.
686 * JFrame or JInternalFrame
687 * @param defaultWidth
688 * use -1 to return null (no default size)
689 * @param defaultHeight
690 * @return the embedded dimensions or null (no default size or not embedded)
692 public static Dimension getDimIfEmbedded(Component frame,
693 int defaultWidth, int defaultHeight)
698 d = (Dimension) getEmbeddedAttribute(frame, "dim");
700 return (d == null && defaultWidth >= 0
701 ? new Dimension(defaultWidth, defaultHeight)
706 public static Regex newRegex(String regex)
708 return newRegex(regex, null);
711 public static Regex newRegex(String searchString, String replaceString)
714 return (replaceString == null ? new Regex(searchString)
715 : new Regex(searchString, replaceString));
718 public static Regex newRegexPerl(String code)
721 return Regex.perlCode(code);
725 * Initialize Java debug logging. A representative sample -- adapt as desired.
727 public static void startJavaLogging()
733 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
734 "java.awt.Component", "java.awt.focus.Component",
735 "java.awt.event.Component",
736 "java.awt.focus.DefaultKeyboardFocusManager");
741 * Initiate Java logging for a given class. Only for Java, not JavaScript;
742 * Allows debugging of complex event processing.
746 public static void logClass(String... classNames)
754 Logger rootLogger = Logger.getLogger("");
755 rootLogger.setLevel(Level.ALL);
756 ConsoleHandler consoleHandler = new ConsoleHandler();
757 consoleHandler.setLevel(Level.ALL);
758 for (int i = classNames.length; --i >= 0;)
760 Logger logger = Logger.getLogger(classNames[i]);
761 logger.setLevel(Level.ALL);
762 logger.addHandler(consoleHandler);
768 * load a resource -- probably a core file -- if and only if a particular
769 * class has not been instantialized. We use a String here because if we used
770 * a .class object, that reference itself would simply load the class, and we
771 * want the core package to include that as well.
773 * @param resourcePath
776 public static void loadStaticResource(String resourcePath,
781 jsutil.loadResourceIfClassUnknown(resourcePath, className);
785 public static void ensureRegex()
789 loadStaticResource("core/core_stevesoft.z.js",
790 "com.stevesoft.pat.Regex");
795 * Set the "app" property of the HTML5 applet object, for example,
796 * "testApplet.app", to point to the Jalview instance. This will be the object
797 * that page developers use that is similar to the original Java applet object
798 * that was accessed via LiveConnect.
802 public static void setAppClass(Object j)
806 jsutil.setAppletAttribute("app", j);
812 * If this frame ia embedded in a web page, return a known type.
815 * a JFrame or JInternalFrame
817 * @return null if frame is not embedded.
819 public static Object getEmbeddedAttribute(Component frame, String type)
821 return (isJS ? jsutil.getEmbeddedAttribute(frame, type) : null);
824 public static void stackTrace()
828 throw new NullPointerException();
829 } catch (Exception e)
836 public static URL getDocumentBase()
838 return (isJS ? jsutil.getDocumentBase() : null);
841 public static URL getCodeBase()
843 return (isJS ? jsutil.getCodeBase() : null);
846 public static String getUserPath(String subpath)
848 char sep = File.separatorChar;
849 return System.getProperty("user.home") + sep
850 + subpath.replace('/', sep);
854 * This method enables checking if a cached file has exceeded a certain
860 * the threshold in days
863 public static boolean isFileOlderThanThreshold(File file, int noOfDays)
867 // not meaningful in SwingJS -- this is a session-specific temp file. It
868 // doesn't have a timestamp.
871 Path filePath = file.toPath();
872 BasicFileAttributes attr;
876 attr = Files.readAttributes(filePath, BasicFileAttributes.class);
877 diffInDays = (int) ((new Date().getTime()
878 - attr.lastModifiedTime().toMillis())
879 / (1000 * 60 * 60 * 24));
880 // System.out.println("Diff in days : " + diffInDays);
881 } catch (IOException e)
885 return noOfDays <= diffInDays;
889 * Get the leading integer part of a string that begins with an integer.
892 * - the string input to process
894 * - value returned if unsuccessful
897 public static int getLeadingIntegerValue(String input, int failValue)
905 int val = /** @j2sNative 1 ? parseInt(input) : */
907 return (val == val + 0 ? val : failValue);
909 // JavaScript does not support Regex ? lookahead
910 String[] parts = input.split("(?=\\D)(?<=\\d)");
911 if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+"))
913 return Integer.valueOf(parts[0]);
918 public static Map<String, Object> getAppletInfoAsMap()
920 return (isJS ? jsutil.getAppletInfoAsMap() : null);
924 * Get the SwingJS applet ID and combine that with the frameType
927 * "alignment", "desktop", etc., or null
930 public static String getAppID(String frameType)
932 String id = Jalview.getInstance().j2sAppletID;
935 Jalview.getInstance().j2sAppletID = id = (String) jsutil
936 .getAppletAttribute("_id");
938 return id + (frameType == null ? "" : "-" + frameType);