*/
package jalview.util;
-import jalview.javascript.json.JSON;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.GraphicsEnvironment;
import java.awt.Toolkit;
+import java.awt.event.KeyEvent;
import java.awt.event.MouseEvent;
import java.io.BufferedReader;
import java.io.File;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
+import java.lang.reflect.Method;
import java.net.URL;
+import java.nio.channels.Channels;
+import java.nio.channels.ReadableByteChannel;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.StandardCopyOption;
+import java.nio.file.attribute.BasicFileAttributes;
+import java.util.Date;
+import java.util.Locale;
+import java.util.Map;
import java.util.Properties;
+import java.util.logging.ConsoleHandler;
+import java.util.logging.Level;
+import java.util.logging.Logger;
import javax.swing.SwingUtilities;
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
+import com.stevesoft.pat.Regex;
+
+import jalview.bin.Jalview;
+import jalview.javascript.json.JSON;
+import swingjs.api.JSUtilI;
/**
* System platform information used by Applet and Application
*
private static Boolean isHeadless = null;
+ private static swingjs.api.JSUtilI jsutil;
+
+ static
+ {
+ if (isJS)
+ {
+ try
+ {
+ // this is ok - it's a highly embedded method in Java; the deprecation
+ // is
+ // really a recommended best practice.
+ jsutil = ((JSUtilI) Class.forName("swingjs.JSUtil").newInstance());
+ } catch (InstantiationException | IllegalAccessException
+ | ClassNotFoundException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ }
/**
* added to group mouse events into Windows and nonWindows (mac, unix, linux)
*
: isMac);
}
+ public static int SHORTCUT_KEY_MASK = (Platform.isMac()
+ ? KeyEvent.META_DOWN_MASK
+ : KeyEvent.CTRL_DOWN_MASK);
+
+ static
+ {
+ if (!GraphicsEnvironment.isHeadless())
+ {
+ // Using non-deprecated Extended key mask modifiers, but Java 8 has no
+ // getMenuShortcutKeyMaskEx method
+ Toolkit tk = Toolkit.getDefaultToolkit();
+ Method method = null;
+ try
+ {
+ method = tk.getClass().getMethod("getMenuShortcutKeyMaskEx");
+ } catch (Exception e)
+ {
+ System.err.println(
+ "Could not find Toolkit method getMenuShortcutKeyMaskEx. Trying getMenuShortcutKeyMask.");
+ }
+ if (method == null)
+ {
+ try
+ {
+ method = tk.getClass().getMethod("getMenuShortcutKeyMask");
+ } catch (Exception e)
+ {
+ System.err.println(
+ "Could not find Toolkit method getMenuShortcutKeyMaskEx or getMenuShortcutKeyMask.");
+ e.printStackTrace();
+ }
+ }
+ if (method != null)
+ {
+ try
+ {
+ method.setAccessible(true);
+ SHORTCUT_KEY_MASK = ((int) method.invoke(tk, new Object[0]));
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+ if (SHORTCUT_KEY_MASK <= 0xF)
+ {
+ // shift this into the extended region (was Java 8)
+ SHORTCUT_KEY_MASK = SHORTCUT_KEY_MASK << 6;
+ }
+ }
+ }
/**
* added to group mouse events into Windows and nonWindows (mac, unix, linux)
*
}
/**
- * Check if we are on a Microsoft plaform...
+ * Check if we are on a Microsoft platform...
*
* @return true if we have to cope with another platform variation
*/
*/
protected static boolean isControlDown(MouseEvent e, boolean aMac)
{
- if (!aMac)
- {
- return e.isControlDown();
-
- // Jalview 2.11 code below: above is as amended for JalviewJS
- // /*
- // * answer false for right mouse button
- // */
- // if (e.isPopupTrigger())
- // {
- // return false;
- // }
- // return
- // (jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() //
- // .getMenuShortcutKeyMaskEx()
- // & jalview.util.ShortcutKeyMaskExWrapper
- // .getModifiersEx(e)) != 0; // getModifiers()) != 0;
- }
- // answer false for right mouse button
- // shortcut key will be META for a Mac
- return !e.isPopupTrigger()
- && (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
- & e.getModifiers()) != 0;
- // could we use e.isMetaDown() here?
+ //
+ // System.out.println(e.isPopupTrigger()
+ // + " " + ((SHORTCUT_KEY_MASK & e.getModifiersEx()) != 0)
+ // + " " + e.isControlDown());
+ return (aMac
+ ? !e.isPopupTrigger()
+ && (SHORTCUT_KEY_MASK & e.getModifiersEx()) != 0
+ : e.isControlDown());
}
// BH: I don't know about that previous method. Here is what SwingJS uses.
public static long time, mark, set, duration;
+ /**
+ * typical usage:
+ *
+ * Platform.timeCheck(null, Platform.TIME_MARK);
+ *
+ * ...
+ *
+ * Platform.timeCheck("some message", Platform.TIME_MARK);
+ *
+ * reset...[set/mark]n...get
+ *
+ * @param msg
+ * @param mode
+ */
public static void timeCheck(String msg, int mode)
{
long t = System.currentTimeMillis();
{
case TIME_RESET:
time = mark = t;
+ duration = 0;
if (msg != null)
{
System.err.println("Platform: timer reset\t\t\t" + msg);
case TIME_MARK:
if (set > 0)
{
+ // total time between set/mark points
duration += (t - set);
}
else
public static void cacheFileData(String path, Object data)
{
- if (!isJS() || data == null)
+ if (isJS && data != null)
{
- return;
+ jsutil.cachePathData(path, data);
}
- /**
- * @j2sNative
- *
- * swingjs.JSUtil.cacheFileData$S$O(path, data);
- *
- */
}
public static void cacheFileData(File file)
{
- byte[] data;
- if (!isJS() || (data = Platform.getFileBytes(file)) == null)
+ if (isJS)
{
- return;
+ byte[] data = Platform.getFileBytes(file);
+ {
+ if (data != null)
+ {
+ cacheFileData(file.toString(), data);
+ }
+ }
}
- cacheFileData(file.toString(), data);
}
public static byte[] getFileBytes(File f)
{
- return /** @j2sNative f && swingjs.JSUtil.getFileAsBytes$O(f) || */
- null;
+ return (isJS && f != null ? jsutil.getBytes(f) : null);
}
public static byte[] getFileAsBytes(String fileStr)
{
- byte[] bytes = null;
- // BH 2018 hack for no support for access-origin
- /**
- * @j2sNative bytes = swingjs.JSUtil.getFileAsBytes$O(fileStr)
- */
- cacheFileData(fileStr, bytes);
- return bytes;
+ if (isJS && fileStr != null)
+ {
+ byte[] bytes = (byte[]) jsutil.getFile(fileStr, false);
+ cacheFileData(fileStr, bytes);
+ return bytes;
+ }
+ return null;
}
- @SuppressWarnings("unused")
public static String getFileAsString(String url)
{
- String ret = null;
- /**
- * @j2sNative
- *
- * ret = swingjs.JSUtil.getFileAsString$S(url);
- *
- *
- */
- cacheFileData(url, ret);
- return ret;
+ if (isJS && url != null)
+ {
+ String ret = (String) jsutil.getFile(url, true);
+ cacheFileData(url, ret);
+ return ret;
+ }
+ return null;
}
public static boolean setFileBytes(File f, String urlstring)
{
- if (!isJS())
+ if (isJS && f != null && urlstring != null)
{
- return false;
+ @SuppressWarnings("unused")
+ byte[] bytes = getFileAsBytes(urlstring);
+ jsutil.setFileBytes(f, bytes);
+ return true;
}
- @SuppressWarnings("unused")
- byte[] bytes = getFileAsBytes(urlstring);
- // TODO temporary doubling of 秘bytes and _bytes;
- // just remove _bytes when new transpiler has been installed
- /**
- * @j2sNative f.\u79d8bytes = f._bytes = bytes;
- */
- return true;
+ return false;
}
public static void addJ2SBinaryType(String ext)
{
- /**
- * @j2sNative
- *
- * J2S._binaryTypes.push("." + ext + "?");
- *
- */
+ if (isJS)
+ {
+ jsutil.addBinaryFileType(ext);
+ }
}
/**
* @param url
* @return true if window has been opened
*/
- public static boolean openURL(String url)
+ public static boolean openURL(String url) throws IOException
{
if (!isJS())
{
public static String getUniqueAppletID()
{
- /**
- * @j2sNative return swingjs.JSUtil.getApplet$()._uniqueId;
- *
- */
- return null;
+ return (isJS ? (String) jsutil.getAppletAttribute("_uniqueId") : null);
}
*/
public static void readInfoProperties(String prefix, Properties p)
{
- if (!isJS())
+ if (isJS)
{
- return;
- }
- String id = getUniqueAppletID();
- String key = "", value = "";
- /**
- * @j2sNative var info = swingjs.JSUtil.getApplet$().__Info || {}; for (var
- * key in info) { if (key.indexOf(prefix) == 0) { value = "" +
- * info[key];
- */
+ String id = getUniqueAppletID();
- System.out.println(
- "Platform id=" + id + " reading Info." + key + " = " + value);
- p.put(id + "_" + key, value);
+ String key = "";
+ String value = "";
+ @SuppressWarnings("unused")
+ Object info = jsutil.getAppletAttribute("__Info");
+ /**
+ * @j2sNative for (key in info) { value = info[key];
+ */
- /**
- * @j2sNative
- *
- *
- * } }
- */
+ if (key.indexOf(prefix) == 0)
+ {
+ System.out.println("Platform id=" + id + " reading Info." + key
+ + " = " + value);
+ p.put(key, value);
+
+ }
+
+ /**
+ * @j2sNative }
+ */
+ }
}
public static void setAjaxJSON(URL url)
public static void streamToFile(InputStream is, File outFile)
throws IOException
{
- if (isJS() && /**
- * @j2sNative outFile.setBytes$O && outFile.setBytes$O(is) &&
- */
- true)
+ if (isJS)
{
+ jsutil.setFileBytes(outFile, is);
return;
}
FileOutputStream fio = new FileOutputStream(outFile);
public static void addJ2SDirectDatabaseCall(String domain)
{
- if (isJS())
+ if (isJS)
{
+ jsutil.addDirectDatabaseCall(domain);
System.out.println(
- "Platform adding known access-control-allow-origin * for domain "
- + domain);
+ "Platform adding known access-control-allow-origin * for domain "
+ + domain);
/**
* @j2sNative
*
}
+ /**
+ * Allow for URL-line command arguments. Untested.
+ *
+ */
public static void getURLCommandArguments()
{
- try
- {
+ try {
/**
* Retrieve the first query field as command arguments to Jalview. Include
* only if prior to "?j2s" or "&j2s" or "#". Assign the applet's
*
* @j2sNative var a =
* decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
- * + "?").split("?")[1].split("#")[0]); a &&
- * (System.out.println("URL arguments detected were "+a)) &&
- * (J2S.thisApplet.__Info.urlargs = a.split(" "));
- * (!J2S.thisApplet.__Info.args || J2S.thisApplet.__Info.args
- * == "" || J2S.thisApplet.__Info.args == "??") &&
- * (J2S.thisApplet.__Info.args = a) && (System.out.println("URL
- * arguments were passed to J2S main."));
+ * + "?").split("?")[1].split("#")[0]); a && (System.out.println("URL arguments detected were "+a)) &&
+ * (J2S.thisApplet.__Info.urlargs = a.split(" "));
+ * (!J2S.thisApplet.__Info.args || J2S.thisApplet.__Info.args == "" || J2S.thisApplet.__Info.args == "??") && (J2S.thisApplet.__Info.args = a) && (System.out.println("URL arguments were passed to J2S main."));
*/
} catch (Throwable t)
{
String p2 = path2.replace('\\', '/');
return p1.equals(p2);
}
+ ///////////// JAL-3253 Applet additions //////////////
+
+ /**
+ * Retrieve the object's embedded size from a div's style on a page if
+ * embedded in SwingJS.
+ *
+ * @param frame
+ * JFrame or JInternalFrame
+ * @param defaultWidth
+ * use -1 to return null (no default size)
+ * @param defaultHeight
+ * @return the embedded dimensions or null (no default size or not embedded)
+ */
+ public static Dimension getDimIfEmbedded(Component frame,
+ int defaultWidth, int defaultHeight)
+ {
+ Dimension d = null;
+ if (isJS)
+ {
+ d = (Dimension) getEmbeddedAttribute(frame, "dim");
+ }
+ return (d == null && defaultWidth >= 0
+ ? new Dimension(defaultWidth, defaultHeight)
+ : d);
+
+ }
+
+ public static Regex newRegex(String regex)
+ {
+ return newRegex(regex, null);
+ }
+
+ public static Regex newRegex(String searchString, String replaceString)
+ {
+ ensureRegex();
+ return (replaceString == null ? new Regex(searchString)
+ : new Regex(searchString, replaceString));
+ }
+
+ public static Regex newRegexPerl(String code)
+ {
+ ensureRegex();
+ return Regex.perlCode(code);
+ }
+
+ /**
+ * Initialize Java debug logging. A representative sample -- adapt as desired.
+ */
+ public static void startJavaLogging()
+ {
+ /**
+ * @j2sIgnore
+ */
+ {
+ logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
+ "java.awt.Component", "java.awt.focus.Component",
+ "java.awt.event.Component",
+ "java.awt.focus.DefaultKeyboardFocusManager");
+ }
+ }
+
+ /**
+ * Initiate Java logging for a given class. Only for Java, not JavaScript;
+ * Allows debugging of complex event processing.
+ *
+ * @param className
+ */
+ public static void logClass(String... classNames)
+ {
+ /**
+ * @j2sIgnore
+ *
+ *
+ */
+ {
+ Logger rootLogger = Logger.getLogger("");
+ rootLogger.setLevel(Level.ALL);
+ ConsoleHandler consoleHandler = new ConsoleHandler();
+ consoleHandler.setLevel(Level.ALL);
+ for (int i = classNames.length; --i >= 0;)
+ {
+ Logger logger = Logger.getLogger(classNames[i]);
+ logger.setLevel(Level.ALL);
+ logger.addHandler(consoleHandler);
+ }
+ }
+ }
+
+ /**
+ * load a resource -- probably a core file -- if and only if a particular
+ * class has not been instantialized. We use a String here because if we used
+ * a .class object, that reference itself would simply load the class, and we
+ * want the core package to include that as well.
+ *
+ * @param resourcePath
+ * @param className
+ */
+ public static void loadStaticResource(String resourcePath,
+ String className)
+ {
+ if (isJS)
+ {
+ jsutil.loadResourceIfClassUnknown(resourcePath, className);
+ }
+ }
+
+ public static void ensureRegex()
+ {
+ if (isJS)
+ {
+ loadStaticResource("core/core_stevesoft.z.js",
+ "com.stevesoft.pat.Regex");
+ }
+ }
+
+ /**
+ * Set the "app" property of the HTML5 applet object, for example,
+ * "testApplet.app", to point to the Jalview instance. This will be the object
+ * that page developers use that is similar to the original Java applet object
+ * that was accessed via LiveConnect.
+ *
+ * @param j
+ */
+ public static void setAppClass(Object j)
+ {
+ if (isJS)
+ {
+ jsutil.setAppClass(j);
+ }
+ }
+
+ /**
+ *
+ * If this frame is embedded in a web page, return a known type.
+ *
+ * @param frame
+ * a JFrame or JInternalFrame
+ * @param type
+ * "name", "node", "init", "dim", or any DOM attribute, such as "id"
+ * @return null if frame is not embedded.
+ */
+ public static Object getEmbeddedAttribute(Component frame, String type)
+ {
+ return (isJS ? jsutil.getEmbeddedAttribute(frame, type) : null);
+ }
+
+ public static void stackTrace()
+ {
+ try
+ {
+ throw new NullPointerException();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ }
+
+ public static URL getDocumentBase()
+ {
+ return (isJS ? jsutil.getDocumentBase() : null);
+ }
+
+ public static URL getCodeBase()
+ {
+ return (isJS ? jsutil.getCodeBase() : null);
+ }
+
+ public static String getUserPath(String subpath)
+ {
+ char sep = File.separatorChar;
+ return System.getProperty("user.home") + sep
+ + subpath.replace('/', sep);
+ }
+
+ /**
+ * This method enables checking if a cached file has exceeded a certain
+ * threshold(in days)
+ *
+ * @param file
+ * the cached file
+ * @param noOfDays
+ * the threshold in days
+ * @return
+ */
+ public static boolean isFileOlderThanThreshold(File file, int noOfDays)
+ {
+ if (isJS())
+ {
+ // not meaningful in SwingJS -- this is a session-specific temp file. It
+ // doesn't have a timestamp.
+ return false;
+ }
+ Path filePath = file.toPath();
+ BasicFileAttributes attr;
+ int diffInDays = 0;
+ try
+ {
+ attr = Files.readAttributes(filePath, BasicFileAttributes.class);
+ diffInDays = (int) ((new Date().getTime()
+ - attr.lastModifiedTime().toMillis())
+ / (1000 * 60 * 60 * 24));
+ // System.out.println("Diff in days : " + diffInDays);
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ return noOfDays <= diffInDays;
+ }
+
+ /**
+ * Get the leading integer part of a string that begins with an integer.
+ *
+ * @param input
+ * - the string input to process
+ * @param failValue
+ * - value returned if unsuccessful
+ * @return
+ */
+ public static int getLeadingIntegerValue(String input, int failValue)
+ {
+ if (input == null)
+ {
+ return failValue;
+ }
+ if (isJS)
+ {
+ int val = /** @j2sNative 1 ? parseInt(input) : */
+ 0;
+ return (val == val + 0 ? val : failValue);
+ }
+ // JavaScript does not support Regex ? lookahead
+ String[] parts = input.split("(?=\\D)(?<=\\d)");
+ if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+"))
+ {
+ return Integer.valueOf(parts[0]);
+ }
+ return failValue;
+ }
+
+ public static Map<String, Object> getAppletInfoAsMap()
+ {
+ return (isJS ? jsutil.getAppletInfoAsMap() : null);
+ }
+
+ /**
+ * Get the SwingJS applet ID and combine that with the frameType
+ *
+ * @param frameType
+ * "alignment", "desktop", etc., or null
+ * @return
+ */
+ public static String getAppID(String frameType)
+ {
+
+ String id = Jalview.getInstance().j2sAppletID;
+ if (id == null)
+ {
+ Jalview.getInstance().j2sAppletID = id = (isJS
+ ? (String) jsutil.getAppletAttribute("_id")
+ : "jalview");
+ }
+ return id + (frameType == null ? "" : "-" + frameType);
+ }
+
+ /**
+ * Option to avoid unnecessary seeking of nonexistent resources in JavaScript.
+ * Works in Java as well.
+ *
+ * @param loc
+ * @return
+ */
+ public static Locale getLocaleOrNone(Locale loc)
+ {
+ return (isJS && loc.getLanguage() == "en" ? new Locale("") : loc);
+ }
+
+ /**
+ * From UrlDownloadClient; trivial in JavaScript; painful in Java.
+ *
+ * @param urlstring
+ * @param outfile
+ * @throws IOException
+ */
+ public static void download(String urlstring, String outfile)
+ throws IOException
+ {
+ Path temp = null;
+ try (InputStream is = new URL(urlstring).openStream())
+ {
+ if (isJS)
+ { // so much easier!
+ streamToFile(is, new File(outfile));
+ return;
+ }
+ temp = Files.createTempFile(".jalview_", ".tmp");
+ try (FileOutputStream fos = new FileOutputStream(temp.toString());
+ ReadableByteChannel rbc = Channels.newChannel(is))
+ {
+ fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
+ // copy tempfile to outfile once our download completes
+ // incase something goes wrong
+ Files.copy(temp, Paths.get(outfile),
+ StandardCopyOption.REPLACE_EXISTING);
+ }
+ } catch (IOException e)
+ {
+ throw e;
+ } finally
+ {
+ try
+ {
+ if (temp != null)
+ {
+ Files.deleteIfExists(temp);
+ }
+ } catch (IOException e)
+ {
+ System.out.println("Exception while deleting download temp file: "
+ + e.getMessage());
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff