/*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
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.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
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
*
* @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 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)
*
* @return
*/
public static boolean isMac()
{
return (isMac == null
? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0))
: 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)
*
* @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 platform...
*
* @return true if we have to cope with another platform variation
*/
public static boolean isWindowsAndNotJS()
{
return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
}
/**
*
* @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.
}
/**
* Answers the input with every backslash replaced with a double backslash (an
* 'escaped' single backslash)
*
* @param s
* @return
*/
public static String escapeBackslashes(String s)
{
return s == null ? null : s.replace("\\", "\\\\");
}
/**
* 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)
{
//
// 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.
// 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);
*
* reset...[set/mark]n...get
*
* @param msg
* @param mode
*/
public static void timeCheck(String msg, int mode)
{
long t = System.currentTimeMillis();
switch (mode)
{
case TIME_RESET:
time = mark = t;
duration = 0;
if (msg != null)
{
System.err.println("Platform: timer reset\t\t\t" + msg);
}
break;
case TIME_MARK:
if (set > 0)
{
// total time between set/mark points
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)
{
jsutil.cachePathData(path, data);
}
}
public static void cacheFileData(File file)
{
if (isJS)
{
byte[] data = Platform.getFileBytes(file);
{
if (data != null)
{
cacheFileData(file.toString(), data);
}
}
}
}
public static byte[] getFileBytes(File f)
{
return (isJS && f != null ? jsutil.getBytes(f) : null);
}
public static byte[] getFileAsBytes(String fileStr)
{
if (isJS && fileStr != null)
{
byte[] bytes = (byte[]) jsutil.getFile(fileStr, false);
cacheFileData(fileStr, bytes);
return bytes;
}
return null;
}
public static String getFileAsString(String url)
{
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 && f != null && urlstring != null)
{
@SuppressWarnings("unused")
byte[] bytes = getFileAsBytes(urlstring);
jsutil.setFileBytes(f, bytes);
return true;
}
return false;
}
public static void addJ2SBinaryType(String ext)
{
if (isJS)
{
jsutil.addBinaryFileType(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())
{
return false;
}
/**
* @j2sNative
*
*
* window.open(url);
*/
return true;
}
public static String getUniqueAppletID()
{
return (isJS ? (String) jsutil.getAppletAttribute("_uniqueId") : 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)
{
String id = getUniqueAppletID();
String key = "";
String value = "";
@SuppressWarnings("unused")
Object info = jsutil.getAppletAttribute("__Info");
/**
* @j2sNative for (key in info) { value = info[key];
*/
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)
{
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
{
if (isJS)
{
jsutil.setFileBytes(outFile, is);
return;
}
FileOutputStream fio = new FileOutputStream(outFile);
try
{
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)
{
jsutil.addDirectDatabaseCall(domain);
System.out.println(
"Platform adding known access-control-allow-origin * for domain "
+ domain);
}
}
/**
* Allow for URL-line command arguments. Untested.
*
*/
public static void getURLCommandArguments()
{
try
{
/**
* 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(" "));
*
* System.out.println("URL arguments: " + a);
*/
} catch (Throwable t)
{
}
}
/**
* A (case sensitive) file path comparator that ignores the difference between
* / and \
*
* @param path1
* @param path2
* @return
*/
public static boolean pathEquals(String path1, String path2)
{
if (path1 == null)
{
return path2 == null;
}
if (path2 == null)
{
return false;
}
String p1 = path1.replace('\\', '/');
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 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());
}
}
}
}