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.channels.Channels;
37 import java.nio.channels.ReadableByteChannel;
38 import java.nio.file.Files;
39 import java.nio.file.Path;
40 import java.nio.file.Paths;
41 import java.nio.file.StandardCopyOption;
42 import java.nio.file.attribute.BasicFileAttributes;
43 import java.util.Date;
44 import java.util.Locale;
46 import java.util.Properties;
47 import java.util.logging.ConsoleHandler;
48 import java.util.logging.Level;
49 import java.util.logging.Logger;
51 import javax.swing.SwingUtilities;
53 import org.json.simple.parser.JSONParser;
54 import org.json.simple.parser.ParseException;
56 import com.stevesoft.pat.Regex;
58 import jalview.bin.Jalview;
59 import jalview.javascript.json.JSON;
60 import swingjs.api.JSUtilI;
63 * System platform information used by Applet and Application
70 private static boolean isJS = /** @j2sNative true || */
73 private static Boolean isNoJSMac = null, isNoJSWin = null, isMac = null,
76 private static Boolean isHeadless = null;
78 private static swingjs.api.JSUtilI jsutil;
86 // this is ok - it's a highly embedded method in Java; the deprecation
88 // really a recommended best practice.
89 jsutil = ((JSUtilI) Class.forName("swingjs.JSUtil").newInstance());
90 } catch (InstantiationException | IllegalAccessException
91 | ClassNotFoundException e)
97 // private static Boolean isHeadless = null;
100 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
104 public static boolean isMac()
106 return (isMac == null
107 ? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0))
112 * added to group mouse events into Windows and nonWindows (mac, unix, linux)
116 public static boolean isWin()
118 return (isWin == null
119 ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0))
125 * @return true if HTML5 JavaScript
127 public static boolean isJS()
133 * sorry folks - Macs really are different
135 * BH: disabled for SwingJS -- will need to check key-press issues
137 * @return true if we do things in a special way.
139 public static boolean isAMacAndNotJS()
141 return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac);
145 * Check if we are on a Microsoft plaform...
147 * @return true if we have to cope with another platform variation
149 public static boolean isWindowsAndNotJS()
151 return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
156 * @return true if we are running in non-interactive no UI mode
158 public static boolean isHeadless()
160 if (isHeadless == null)
162 isHeadless = "true".equals(System.getProperty("java.awt.headless"));
169 * @return nominal maximum command line length for this platform
171 public static int getMaxCommandLineLength()
173 // TODO: determine nominal limits for most platforms.
174 return 2046; // this is the max length for a windows NT system.
178 * Answers the input with every backslash replaced with a double backslash (an
179 * 'escaped' single backslash)
184 public static String escapeBackslashes(String s)
186 return s == null ? null : s.replace("\\", "\\\\");
190 * Answers true if the mouse event has Meta-down (Command key on Mac) or
191 * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
192 * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
193 * Mac, you can use e.isPopupTrigger().
198 public static boolean isControlDown(MouseEvent e)
200 return isControlDown(e, isMac());
204 * Overloaded version of method (to allow unit testing)
210 protected static boolean isControlDown(MouseEvent e, boolean aMac)
214 return e.isControlDown();
216 // Jalview 2.11 code below: above is as amended for JalviewJS
218 // * answer false for right mouse button
220 // if (e.isPopupTrigger())
225 // (jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() //
226 // .getMenuShortcutKeyMaskEx()
227 // & jalview.util.ShortcutKeyMaskExWrapper
228 // .getModifiersEx(e)) != 0; // getModifiers()) != 0;
230 // answer false for right mouse button
231 // shortcut key will be META for a Mac
232 return !e.isPopupTrigger()
233 && (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
234 & e.getModifiers()) != 0;
235 // could we use e.isMetaDown() here?
238 // BH: I don't know about that previous method. Here is what SwingJS uses.
239 // Notice the distinction in mouse events. (BUTTON3_MASK == META)
241 // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
242 // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
244 // if (id != MouseEvent.MOUSE_RELEASED)
247 //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
248 //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
250 //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
252 //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
256 // // mac, linux, unix
257 // if (id != MouseEvent.MOUSE_PRESSED)
259 // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
260 // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
261 // return rt || (ctrl && lt);
267 * Windows (not Mac, Linux, or Unix) and right button to test for the
268 * right-mouse pressed event in Windows that would have opened a menu or a
274 public static boolean isWinRightButton(MouseEvent e)
276 // was !isAMac(), but that is true also for Linux and Unix and JS,
278 return isWin() && SwingUtilities.isRightMouseButton(e);
282 * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
283 * without pressing the button.
288 public static boolean isWinMiddleButton(MouseEvent e)
290 // was !isAMac(), but that is true also for Linux and Unix and JS
291 return isWin() && SwingUtilities.isMiddleMouseButton(e);
294 public static boolean allowMnemonics()
299 public final static int TIME_RESET = 0;
301 public final static int TIME_MARK = 1;
303 public static final int TIME_SET = 2;
305 public static final int TIME_GET = 3;
307 public static long time, mark, set, duration;
312 * Platform.timeCheck(null, Platform.TIME_MARK);
316 * Platform.timeCheck("some message", Platform.TIME_MARK);
318 * reset...[set/mark]n...get
323 public static void timeCheck(String msg, int mode)
325 long t = System.currentTimeMillis();
333 System.err.println("Platform: timer reset\t\t\t" + msg);
339 // total time between set/mark points
340 duration += (t - set);
350 System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
351 + "\t" + ((t - mark) / 1000f) + "\t" + msg);
362 System.err.println("Platform: timer dur\t" + ((t - time) / 1000f)
363 + "\t" + ((duration) / 1000f) + "\t" + msg);
370 public static void cacheFileData(String path, Object data)
372 if (isJS && data != null)
374 jsutil.cachePathData(path, data);
378 public static void cacheFileData(File file)
382 byte[] data = Platform.getFileBytes(file);
386 cacheFileData(file.toString(), data);
392 public static byte[] getFileBytes(File f)
394 return (isJS && f != null ? jsutil.getBytes(f) : null);
397 public static byte[] getFileAsBytes(String fileStr)
399 if (isJS && fileStr != null)
401 byte[] bytes = (byte[]) jsutil.getFile(fileStr, false);
402 cacheFileData(fileStr, bytes);
408 public static String getFileAsString(String url)
410 if (isJS && url != null)
412 String ret = (String) jsutil.getFile(url, true);
413 cacheFileData(url, ret);
419 public static boolean setFileBytes(File f, String urlstring)
421 if (isJS && f != null && urlstring != null)
423 @SuppressWarnings("unused")
424 byte[] bytes = getFileAsBytes(urlstring);
425 jsutil.setFileBytes(f, bytes);
431 public static void addJ2SBinaryType(String ext)
435 jsutil.addBinaryFileType(ext);
440 * Encode the URI using JavaScript encodeURIComponent
443 * @return encoded value
445 public static String encodeURI(String value)
448 * @j2sNative value = encodeURIComponent(value);
454 * Open the URL using a simple window call if this is JavaScript
457 * @return true if window has been opened
459 public static boolean openURL(String url) throws IOException
474 public static String getUniqueAppletID()
476 return (isJS ? (String) jsutil.getAppletAttribute("_uniqueId") : null);
480 * Read the Info block for this applet.
485 * @return unique id for this applet
487 public static void readInfoProperties(String prefix, Properties p)
491 String id = getUniqueAppletID();
495 @SuppressWarnings("unused")
496 Object info = jsutil.getAppletAttribute("__Info");
498 * @j2sNative for (key in info) { value = info[key];
501 if (key.indexOf(prefix) == 0)
503 System.out.println("Platform id=" + id + " reading Info." + key
515 public static void setAjaxJSON(URL url)
523 public static Object parseJSON(InputStream response)
524 throws IOException, ParseException
528 return JSON.parse(response);
531 BufferedReader br = null;
534 br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
535 return new JSONParser().parse(br);
543 } catch (IOException e)
551 public static Object parseJSON(String json) throws ParseException
553 return (isJS() ? JSON.parse(json) : new JSONParser().parse(json));
556 public static Object parseJSON(Reader r)
557 throws IOException, ParseException
566 return new JSONParser().parse(r);
568 // Using a file reader is not currently supported in SwingJS JavaScript
570 if (r instanceof FileReader)
572 throw new IOException(
573 "StringJS does not support FileReader parsing for JSON -- but it could...");
575 return JSON.parse(r);
579 * Dump the input stream to an output file.
583 * @throws IOException
584 * if the file cannot be created or there is a problem reading the
587 public static void streamToFile(InputStream is, File outFile)
593 jsutil.setFileBytes(outFile, is);
597 FileOutputStream fio = new FileOutputStream(outFile);
600 byte[] bb = new byte[32 * 1024];
602 while ((l = is.read(bb)) > 0)
613 * Add a known domain that implements access-control-allow-origin:*
615 * These should be reviewed periodically.
618 * for a service that is not allowing ajax
620 * @author hansonr@stolaf.edu
623 public static void addJ2SDirectDatabaseCall(String domain)
628 jsutil.addDirectDatabaseCall(domain);
631 "Platform adding known access-control-allow-origin * for domain "
638 * Allow for URL-line command arguments. Untested.
641 public static void getURLCommandArguments()
646 * Retrieve the first query field as command arguments to Jalview. Include
647 * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
648 * element to this value.
651 * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
652 * + "?").split("?")[1].split("#")[0]); a &&
653 * (J2S.thisApplet.__Info.args = a.split(" "));
655 * System.out.println("URL arguments: " + a);
657 } catch (Throwable t) {
662 * A (case sensitive) file path comparator that ignores the difference between
669 public static boolean pathEquals(String path1, String path2)
673 return path2 == null;
679 String p1 = path1.replace('\\', '/');
680 String p2 = path2.replace('\\', '/');
681 return p1.equals(p2);
684 ///////////// JAL-3253 Applet additions //////////////
687 * Retrieve the object's embedded size from a div's style on a page if
688 * embedded in SwingJS.
691 * JFrame or JInternalFrame
692 * @param defaultWidth
693 * use -1 to return null (no default size)
694 * @param defaultHeight
695 * @return the embedded dimensions or null (no default size or not embedded)
697 public static Dimension getDimIfEmbedded(Component frame,
698 int defaultWidth, int defaultHeight)
703 d = (Dimension) getEmbeddedAttribute(frame, "dim");
705 return (d == null && defaultWidth >= 0
706 ? new Dimension(defaultWidth, defaultHeight)
711 public static Regex newRegex(String regex)
713 return newRegex(regex, null);
716 public static Regex newRegex(String searchString, String replaceString)
719 return (replaceString == null ? new Regex(searchString)
720 : new Regex(searchString, replaceString));
723 public static Regex newRegexPerl(String code)
726 return Regex.perlCode(code);
730 * Initialize Java debug logging. A representative sample -- adapt as desired.
732 public static void startJavaLogging()
738 logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
739 "java.awt.Component", "java.awt.focus.Component",
740 "java.awt.event.Component",
741 "java.awt.focus.DefaultKeyboardFocusManager");
746 * Initiate Java logging for a given class. Only for Java, not JavaScript;
747 * Allows debugging of complex event processing.
751 public static void logClass(String... classNames)
759 Logger rootLogger = Logger.getLogger("");
760 rootLogger.setLevel(Level.ALL);
761 ConsoleHandler consoleHandler = new ConsoleHandler();
762 consoleHandler.setLevel(Level.ALL);
763 for (int i = classNames.length; --i >= 0;)
765 Logger logger = Logger.getLogger(classNames[i]);
766 logger.setLevel(Level.ALL);
767 logger.addHandler(consoleHandler);
773 * load a resource -- probably a core file -- if and only if a particular
774 * class has not been instantialized. We use a String here because if we used
775 * a .class object, that reference itself would simply load the class, and we
776 * want the core package to include that as well.
778 * @param resourcePath
781 public static void loadStaticResource(String resourcePath,
786 jsutil.loadResourceIfClassUnknown(resourcePath, className);
790 public static void ensureRegex()
794 loadStaticResource("core/core_stevesoft.z.js",
795 "com.stevesoft.pat.Regex");
800 * Set the "app" property of the HTML5 applet object, for example,
801 * "testApplet.app", to point to the Jalview instance. This will be the object
802 * that page developers use that is similar to the original Java applet object
803 * that was accessed via LiveConnect.
807 public static void setAppClass(Object j)
811 jsutil.setAppClass(j);
817 * If this frame is embedded in a web page, return a known type.
820 * a JFrame or JInternalFrame
821 * @param type "name", "node", "init", "dim", or any DOM attribute, such as "id"
822 * @return null if frame is not embedded.
824 public static Object getEmbeddedAttribute(Component frame, String type)
826 return (isJS ? jsutil.getEmbeddedAttribute(frame, type) : null);
829 public static void stackTrace()
833 throw new NullPointerException();
834 } catch (Exception e)
841 public static URL getDocumentBase()
843 return (isJS ? jsutil.getDocumentBase() : null);
846 public static URL getCodeBase()
848 return (isJS ? jsutil.getCodeBase() : null);
851 public static String getUserPath(String subpath)
853 char sep = File.separatorChar;
854 return System.getProperty("user.home") + sep
855 + subpath.replace('/', sep);
859 * This method enables checking if a cached file has exceeded a certain
865 * the threshold in days
868 public static boolean isFileOlderThanThreshold(File file, int noOfDays)
872 // not meaningful in SwingJS -- this is a session-specific temp file. It
873 // doesn't have a timestamp.
876 Path filePath = file.toPath();
877 BasicFileAttributes attr;
881 attr = Files.readAttributes(filePath, BasicFileAttributes.class);
882 diffInDays = (int) ((new Date().getTime()
883 - attr.lastModifiedTime().toMillis())
884 / (1000 * 60 * 60 * 24));
885 // System.out.println("Diff in days : " + diffInDays);
886 } catch (IOException e)
890 return noOfDays <= diffInDays;
894 * Get the leading integer part of a string that begins with an integer.
897 * - the string input to process
899 * - value returned if unsuccessful
902 public static int getLeadingIntegerValue(String input, int failValue)
910 int val = /** @j2sNative 1 ? parseInt(input) : */
912 return (val == val + 0 ? val : failValue);
914 // JavaScript does not support Regex ? lookahead
915 String[] parts = input.split("(?=\\D)(?<=\\d)");
916 if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+"))
918 return Integer.valueOf(parts[0]);
923 public static Map<String, Object> getAppletInfoAsMap()
925 return (isJS ? jsutil.getAppletInfoAsMap() : null);
929 * Get the SwingJS applet ID and combine that with the frameType
932 * "alignment", "desktop", etc., or null
935 public static String getAppID(String frameType)
938 String id = Jalview.getInstance().j2sAppletID;
941 Jalview.getInstance().j2sAppletID = id = (isJS ? (String) jsutil
942 .getAppletAttribute("_id") : "jalview");
944 return id + (frameType == null ? "" : "-" + frameType);
949 * Option to avoid unnecessary seeking of nonexistent resources in JavaScript.
950 * Works in Java as well.
955 public static Locale getLocaleOrNone(Locale loc)
957 return (isJS && loc.getLanguage() == "en" ? new Locale("") : loc);
961 * From UrlDownloadClient; trivial in JavaScript; painful in Java.
965 * @throws IOException
967 public static void download(String urlstring, String outfile)
971 try (InputStream is = new URL(urlstring).openStream())
975 streamToFile(is, new File(outfile));
978 temp = Files.createTempFile(".jalview_", ".tmp");
979 try (FileOutputStream fos = new FileOutputStream(temp.toString());
980 ReadableByteChannel rbc = Channels.newChannel(is))
982 fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
983 // copy tempfile to outfile once our download completes
984 // incase something goes wrong
985 Files.copy(temp, Paths.get(outfile),
986 StandardCopyOption.REPLACE_EXISTING);
988 } catch (IOException e)
997 Files.deleteIfExists(temp);
999 } catch (IOException e)
1001 System.out.println("Exception while deleting download temp file: "