-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \r
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- */\r
-package jalview.util;\r
-\r
-/**\r
- * System platform information used by Applet and Application\r
- * \r
- * @author Jim Procter\r
- */\r
-public class Platform\r
-{\r
- /**\r
- * sorry folks - Macs really are different\r
- * \r
- * @return true if we do things in a special way.\r
- */\r
- public boolean isAMac()\r
- {\r
- return java.lang.System.getProperty("os.name").indexOf("Mac") > -1;\r
-\r
- }\r
-\r
- public boolean isHeadless()\r
- {\r
- String hdls = java.lang.System.getProperty("java.awt.headless");\r
-\r
- return hdls != null && hdls.equals("true");\r
- }\r
-\r
- /**\r
- * \r
- * @return nominal maximum command line length for this platform\r
- */\r
- public static int getMaxCommandLineLength()\r
- {\r
- // TODO: determine nominal limits for most platforms.\r
- return 2046; // this is the max length for a windows NT system.\r
- }\r
-\r
- /**\r
- * escape a string according to the local platform's escape character\r
- * @param file\r
- * @return escaped file\r
- */\r
- public static String escapeString(String file)\r
- {\r
- StringBuffer f=new StringBuffer();\r
- int p=0,lastp=0;\r
- while ((p=file.indexOf('\\',lastp))>-1)\r
- {\r
- f.append(file.subSequence(lastp,p));\r
- f.append("\\\\");\r
- lastp=p+1;\r
- }\r
- f.append(file.substring(lastp));\r
- return f.toString();\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.util;
+
+import jalview.javascript.json.JSON;
+
+import java.awt.Color;
+import java.awt.Toolkit;
+import java.awt.event.MouseEvent;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.net.MalformedURLException;
+import java.net.URL;
+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;
+
+/**
+ * System platform information used by Applet and Application
+ *
+ * @author Jim Procter
+ */
+public class Platform
+{
+
+ private static boolean isJS = /** @j2sNative true || */
+ false;
+
+ private static Boolean isNoJSMac = null, isNoJSWin = null, isMac = null,
+ isWin = null;
+
+ // private static Boolean isHeadless = null;
+
+ /**
+ * added to group mouse events into Windows and nonWindows (mac, unix, linux)
+ *
+ * @return
+ */
+ public static boolean isMac()
+ {
+ return (isMac == null
+ ? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0))
+ : isMac);
+ }
+
+ /**
+ * added to group mouse events into Windows and nonWindows (mac, unix, linux)
+ *
+ * @return
+ */
+ public static boolean isWin()
+ {
+ return (isWin == null
+ ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0))
+ : isWin);
+ }
+
+ /**
+ *
+ * @return true if HTML5 JavaScript
+ */
+ public static boolean isJS()
+ {
+ return isJS;
+ }
+
+ /**
+ * sorry folks - Macs really are different
+ *
+ * BH: disabled for SwingJS -- will need to check key-press issues
+ *
+ * @return true if we do things in a special way.
+ */
+ public static boolean isAMacAndNotJS()
+ {
+ return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac);
+ }
+
+ /**
+ * Check if we are on a Microsoft plaform...
+ *
+ * @return true if we have to cope with another platform variation
+ */
+ public static boolean isWindowsAndNotJS()
+ {
+ return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
+ }
+
+ // /**
+ // *
+ // * @return true if we are running in non-interactive no UI mode
+ // */
+ // public static boolean isHeadless()
+ // {
+ // if (isHeadless == null)
+ // {
+ // isHeadless = "true".equals(System.getProperty("java.awt.headless"));
+ // }
+ // return isHeadless;
+ // }
+
+ /**
+ *
+ * @return nominal maximum command line length for this platform
+ */
+ public static int getMaxCommandLineLength()
+ {
+ // TODO: determine nominal limits for most platforms.
+ return 2046; // this is the max length for a windows NT system.
+ }
+
+ /**
+ * escape a string according to the local platform's escape character
+ *
+ * @param file
+ * @return escaped file
+ */
+ public static String escapeString(String file)
+ {
+ StringBuffer f = new StringBuffer();
+ int p = 0, lastp = 0;
+ while ((p = file.indexOf('\\', lastp)) > -1)
+ {
+ f.append(file.subSequence(lastp, p));
+ f.append("\\\\");
+ lastp = p + 1;
+ }
+ f.append(file.substring(lastp));
+ return f.toString();
+ }
+
+ /**
+ * Answers true if the mouse event has Meta-down (Command key on Mac) or
+ * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
+ * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
+ * Mac, you can use e.isPopupTrigger().
+ *
+ * @param e
+ * @return
+ */
+ public static boolean isControlDown(MouseEvent e)
+ {
+ return isControlDown(e, isMac());
+ }
+
+ /**
+ * Overloaded version of method (to allow unit testing)
+ *
+ * @param e
+ * @param aMac
+ * @return
+ */
+ protected static boolean isControlDown(MouseEvent e, boolean aMac)
+ {
+ if (!aMac)
+ {
+ return e.isControlDown();
+ }
+ // 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?
+ }
+
+ // BH: I don't know about that previous method. Here is what SwingJS uses.
+ // Notice the distinction in mouse events. (BUTTON3_MASK == META)
+ //
+ // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
+ // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
+ // if (isWin) {
+ // if (id != MouseEvent.MOUSE_RELEASED)
+ // return false;
+ ////
+ //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
+ //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
+ ////
+ //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
+ // because
+ //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
+ ////
+ // return rt;
+ // } else {
+ // // mac, linux, unix
+ // if (id != MouseEvent.MOUSE_PRESSED)
+ // return false;
+ // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
+ // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
+ // return rt || (ctrl && lt);
+ // }
+ // }
+ //
+
+ /**
+ * Windows (not Mac, Linux, or Unix) and right button to test for the
+ * right-mouse pressed event in Windows that would have opened a menu or a
+ * Mac.
+ *
+ * @param e
+ * @return
+ */
+ public static boolean isWinRightButton(MouseEvent e)
+ {
+ // was !isAMac(), but that is true also for Linux and Unix and JS,
+
+ return isWin() && SwingUtilities.isRightMouseButton(e);
+ }
+
+ /**
+ * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
+ * without pressing the button.
+ *
+ * @param e
+ * @return
+ */
+ public static boolean isWinMiddleButton(MouseEvent e)
+ {
+ // was !isAMac(), but that is true also for Linux and Unix and JS
+ return isWin() && SwingUtilities.isMiddleMouseButton(e);
+ }
+
+ public static boolean allowMnemonics()
+ {
+ return !isMac();
+ }
+
+ public final static int TIME_RESET = 0;
+
+ public final static int TIME_MARK = 1;
+
+ public static final int TIME_SET = 2;
+
+ public static final int TIME_GET = 3;
+
+ public static long time, mark, set, duration;
+
+ /**
+ * typical usage:
+ *
+ * Platform.timeCheck(null, Platform.TIME_MARK);
+ *
+ * ...
+ *
+ * Platform.timeCheck("some message", Platform.TIME_MARK);
+ *
+ * @param msg
+ * @param mode
+ */
+ public static void timeCheck(String msg, int mode)
+ {
+ long t = System.currentTimeMillis();
+ switch (mode)
+ {
+ case TIME_RESET:
+ time = mark = t;
+ if (msg != null)
+ {
+ System.err.println("Platform: timer reset\t\t\t" + msg);
+ }
+ break;
+ case TIME_MARK:
+ if (set > 0)
+ {
+ duration += (t - set);
+ }
+ else
+ {
+ if (time == 0)
+ {
+ time = mark = t;
+ }
+ if (msg != null)
+ {
+ System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
+ + "\t" + ((t - mark) / 1000f) + "\t" + msg);
+ }
+ mark = t;
+ }
+ break;
+ case TIME_SET:
+ set = t;
+ break;
+ case TIME_GET:
+ if (msg != null)
+ {
+ System.err.println("Platform: timer dur\t" + ((t - time) / 1000f)
+ + "\t" + ((duration) / 1000f) + "\t" + msg);
+ }
+ set = 0;
+ break;
+ }
+ }
+
+ public static void cacheFileData(String path, Object data)
+ {
+ if (!isJS() || data == null)
+ {
+ return;
+ }
+ /**
+ * @j2sNative
+ *
+ * swingjs.JSUtil.cacheFileData$S$O(path, data);
+ *
+ */
+ }
+
+ public static void cacheFileData(File file)
+ {
+ byte[] data;
+ if (!isJS() || (data = Platform.getFileBytes(file)) == null)
+ {
+ return;
+ }
+ cacheFileData(file.toString(), data);
+ }
+
+ public static byte[] getFileBytes(File f)
+ {
+ // TODO temporary doubling of 秘bytes and _bytes;
+ // just remove _bytes when new transpiler has been installed
+ return /** @j2sNative f && (f.秘bytes || f._bytes) || */
+ null;
+ }
+
+ public static byte[] getFileAsBytes(String fileStr)
+ {
+ byte[] bytes = null;
+ // BH 2018 hack for no support for access-origin
+ /**
+ * @j2sNative bytes = swingjs.JSUtil.getFileAsBytes$O(fileStr)
+ */
+ cacheFileData(fileStr, bytes);
+ return bytes;
+ }
+
+ @SuppressWarnings("unused")
+ public static String getFileAsString(String url)
+ {
+ String ret = null;
+ /**
+ * @j2sNative
+ *
+ * ret = swingjs.JSUtil.getFileAsString$S(url);
+ *
+ *
+ */
+ cacheFileData(url, ret);
+ return ret;
+ }
+
+ public static boolean setFileBytes(File f, String urlstring)
+ {
+ if (!isJS())
+ {
+ return false;
+ }
+ @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.秘bytes = f._bytes = bytes;
+ */
+ return true;
+ }
+
+ public static void addJ2SBinaryType(String ext)
+ {
+ /**
+ * @j2sNative
+ *
+ * J2S._binaryTypes.push("." + ext + "?");
+ *
+ */
+ }
+
+ /**
+ * Encode the URI using JavaScript encodeURIComponent
+ *
+ * @param value
+ * @return encoded value
+ */
+ public static String encodeURI(String value)
+ {
+ /**
+ * @j2sNative value = encodeURIComponent(value);
+ */
+ return value;
+ }
+
+ /**
+ * Open the URL using a simple window call if this is JavaScript
+ *
+ * @param url
+ * @return true if window has been opened
+ */
+ public static boolean openURL(String url) throws IOException
+ {
+ if (!isJS())
+ {
+ BrowserLauncher.openURL(url);
+ return false;
+ }
+ /**
+ * @j2sNative
+ *
+ *
+ * window.open(url);
+ */
+ return true;
+ }
+
+ public static String getUniqueAppletID()
+ {
+ @SuppressWarnings("unused")
+ ThreadGroup g = Thread.currentThread().getThreadGroup();
+ /**
+ * @j2sNative return g.秘html5Applet._uniqueId;
+ *
+ */
+ return null;
+
+ }
+
+ /**
+ * Read the Info block for this applet.
+ *
+ * @param prefix
+ * "jalview_"
+ * @param p
+ * @return unique id for this applet
+ */
+ public static void readInfoProperties(String prefix, Properties p)
+ {
+ if (!isJS())
+ {
+ return;
+ }
+ @SuppressWarnings("unused")
+ ThreadGroup g = Thread.currentThread().getThreadGroup();
+ String id = getUniqueAppletID();
+ String key = "", value = "";
+ /**
+ * @j2sNative var info = g.秘html5Applet.__Info || {}; for (var key in info)
+ * { if (key.indexOf(prefix) == 0) { value = "" + info[key];
+ */
+
+ System.out.println(
+ "Platform id=" + id + " reading Info." + key + " = " + value);
+ p.put(key, value);
+
+ /**
+ * @j2sNative
+ *
+ *
+ * } }
+ */
+ }
+
+ public static void setAjaxJSON(URL url)
+ {
+ if (isJS())
+ {
+ JSON.setAjax(url);
+ }
+ }
+
+ public static Object parseJSON(InputStream response)
+ throws IOException, ParseException
+ {
+ if (isJS())
+ {
+ return JSON.parse(response);
+ }
+
+ BufferedReader br = null;
+ try
+ {
+ br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
+ return new JSONParser().parse(br);
+ } finally
+ {
+ if (br != null)
+ {
+ try
+ {
+ br.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+ }
+
+ public static Object parseJSON(String json) throws ParseException
+ {
+ return (isJS() ? JSON.parse(json)
+ : new JSONParser().parse(json));
+ }
+
+ public static Object parseJSON(Reader r)
+ throws IOException, ParseException
+ {
+ if (r == null)
+ {
+ return null;
+ }
+
+ if (!isJS())
+ {
+ return new JSONParser().parse(r);
+ }
+ // Using a file reader is not currently supported in SwingJS JavaScript
+
+ if (r instanceof FileReader)
+ {
+ throw new IOException(
+ "StringJS does not support FileReader parsing for JSON -- but it could...");
+ }
+ return JSON.parse(r);
+
+ }
+
+ /**
+ * Dump the input stream to an output file.
+ *
+ * @param is
+ * @param outFile
+ * @throws IOException
+ * if the file cannot be created or there is a problem reading the
+ * input stream.
+ */
+ public static void streamToFile(InputStream is, File outFile)
+ throws IOException
+ {
+ FileOutputStream fio = new FileOutputStream(outFile);
+ try
+ {
+ if (isJS()
+ && /**
+ * @j2sNative outFile.setBytes$O && outFile.setBytes$O(is) &&
+ */
+ true)
+ {
+ return;
+ }
+ byte[] bb = new byte[32 * 1024];
+ int l;
+ while ((l = is.read(bb)) > 0)
+ {
+ fio.write(bb, 0, l);
+ }
+ } finally
+ {
+ fio.close();
+ }
+ }
+
+ /**
+ * Add a known domain that implements access-control-allow-origin:*
+ *
+ * These should be reviewed periodically.
+ *
+ * @param domain
+ * for a service that is not allowing ajax
+ *
+ * @author hansonr@stolaf.edu
+ *
+ */
+ public static void addJ2SDirectDatabaseCall(String domain)
+ {
+
+ if (isJS())
+ {
+ System.out.println(
+ "Platform adding known access-control-allow-origin * for domain "
+ + domain);
+ /**
+ * @j2sNative
+ *
+ * J2S.addDirectDatabaseCall(domain);
+ */
+ }
+
+ }
+
+ public static void getURLCommandArguments()
+ {
+
+ /**
+ * Retrieve the first query field as command arguments to Jalview. Include
+ * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
+ * element to this value.
+ *
+ * @j2sNative var a =
+ * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
+ * + "?").split("?")[1].split("#")[0]); a &&
+ * (J2S.thisApplet.__Info.args = a.split(" "));
+ */
+
+ }
+
+ public static URL getDocumentBase()
+ {
+ try
+ {
+ if (isJS())
+ {
+ @SuppressWarnings("unused")
+ Object g = Thread.currentThread().getThreadGroup();
+ return new URL(/**
+ * @j2sNative g.秘html5Applet._appletPanel.appletDocumentBase
+ * ||
+ */
+ "");
+ }
+ } catch (MalformedURLException e)
+ {
+ }
+ return null;
+ }
+
+ public static URL getCodeBase()
+ {
+ try
+ {
+ if (isJS())
+ {
+ @SuppressWarnings("unused")
+ Object g = Thread.currentThread().getThreadGroup();
+ return new URL(/**
+ * @j2sNative g.秘html5Applet._appletPanel.appletCodeBase
+ * ||
+ */
+ "");
+ }
+ } catch (MalformedURLException e)
+ {
+ }
+ return null;
+ }
+
+ /**
+ * 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(Object resourcePath,
+ String className)
+ {
+ /**
+ *
+ * @j2sNative if (!swingjs.JSUtil.isClassLoaded$S(className))
+ * swingjs.JSUtil.loadStaticResource$S(resourcePath);
+ */
+ }
+
+ public static void ensureRegex()
+ {
+ loadStaticResource("core/core_stevesoft.z.js",
+ "com.stevesoft.pat.Regex");
+ }
+
+ 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);
+ }
+
+ /**
+ * @param c
+ */
+ public static Color getColorFromName(String name)
+ {
+ if (name == null)
+ {
+ return null;
+ }
+ /**
+ * @j2sNative
+ *
+ * return swingjs.JSUtil.getColorFromName$S(name);
+ */
+ {
+ // or make a static map; or use reflection on the field name
+ switch (name.toLowerCase())
+ {
+ case "black":
+ return Color.black;
+ case "blue":
+ return Color.blue;
+ case "cyan":
+ return Color.cyan;
+ case "darkgray":
+ return Color.darkGray;
+ case "gray":
+ return Color.gray;
+ case "green":
+ return Color.green;
+ case "lightgray":
+ return Color.lightGray;
+ case "magenta":
+ return Color.magenta;
+ case "orange":
+ return Color.orange;
+ case "pink":
+ return Color.pink;
+ case "red":
+ return Color.red;
+ case "white":
+ return Color.white;
+ case "yellow":
+ return Color.yellow;
+ default:
+ return null;
+ }
+
+ }
+ }
+
+ /**
+ * 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);
+ }
+ }
+ }
+
+ /**
+ * 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())
+ {
+ return;
+ }
+ @SuppressWarnings("unused")
+ Thread t = Thread.currentThread();
+ /**
+ * Set up "testApplet.app" to be this instance
+ *
+ * @j2sNative
+ *
+ * try {self[t.name].app = j}catch(e){}
+ */
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff