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biojs-vis-pdbviewer

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A BioJS 2.0 component to view protein structures

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Clazz.declarePackage ("JU"); Clazz.load (["java.util.Hashtable", "JU.DefaultLogger"], "JU.Logger", ["java.lang.Long"], function () { c$ = Clazz.declareType (JU, "Logger"); c$.getProperty = Clazz.defineMethod (c$, "getProperty", function (level, defaultValue) { try { var property = System.getProperty ("jmol.logger." + level, null); if (property != null) { return (property.equalsIgnoreCase ("true")); }} catch (e) { if (Clazz.exceptionOf (e, Exception)) { } else { throw e; } } return defaultValue; }, "~S,~B"); c$.setLogger = Clazz.defineMethod (c$, "setLogger", function (logger) { JU.Logger._logger = logger; JU.Logger.debugging = JU.Logger.isActiveLevel (5) || JU.Logger.isActiveLevel (6); JU.Logger.debuggingHigh = (JU.Logger.debugging && JU.Logger._activeLevels[6]); }, "JU.LoggerInterface"); c$.isActiveLevel = Clazz.defineMethod (c$, "isActiveLevel", function (level) { return JU.Logger._logger != null && level >= 0 && level < 7 && JU.Logger._activeLevels[level]; }, "~N"); c$.setActiveLevel = Clazz.defineMethod (c$, "setActiveLevel", function (level, active) { if (level < 0) level = 0; if (level >= 7) level = 6; JU.Logger._activeLevels[level] = active; JU.Logger.debugging = JU.Logger.isActiveLevel (5) || JU.Logger.isActiveLevel (6); JU.Logger.debuggingHigh = (JU.Logger.debugging && JU.Logger._activeLevels[6]); }, "~N,~B"); c$.setLogLevel = Clazz.defineMethod (c$, "setLogLevel", function (level) { for (var i = 7; --i >= 0; ) JU.Logger.setActiveLevel (i, i <= level); }, "~N"); c$.getLevel = Clazz.defineMethod (c$, "getLevel", function (level) { switch (level) { case 6: return "DEBUGHIGH"; case 5: return "DEBUG"; case 4: return "INFO"; case 3: return "WARN"; case 2: return "ERROR"; case 1: return "FATAL"; } return "????"; }, "~N"); c$.logLevel = Clazz.defineMethod (c$, "logLevel", function () { return JU.Logger._logLevel; }); c$.doLogLevel = Clazz.defineMethod (c$, "doLogLevel", function (log) { JU.Logger._logLevel = log; }, "~B"); c$.debug = Clazz.defineMethod (c$, "debug", function (txt) { if (!JU.Logger.debugging) return; try { JU.Logger._logger.debug (txt); } catch (t) { } }, "~S"); c$.info = Clazz.defineMethod (c$, "info", function (txt) { try { if (JU.Logger.isActiveLevel (4)) { JU.Logger._logger.info (txt); }} catch (t) { } }, "~S"); c$.warn = Clazz.defineMethod (c$, "warn", function (txt) { try { if (JU.Logger.isActiveLevel (3)) { JU.Logger._logger.warn (txt); }} catch (t) { } }, "~S"); c$.warnEx = Clazz.defineMethod (c$, "warnEx", function (txt, e) { try { if (JU.Logger.isActiveLevel (3)) { JU.Logger._logger.warnEx (txt, e); }} catch (t) { } }, "~S,Throwable"); c$.error = Clazz.defineMethod (c$, "error", function (txt) { try { if (JU.Logger.isActiveLevel (2)) { JU.Logger._logger.error (txt); }} catch (t) { } }, "~S"); c$.errorEx = Clazz.defineMethod (c$, "errorEx", function (txt, e) { try { if (JU.Logger.isActiveLevel (2)) { JU.Logger._logger.errorEx (txt, e); }} catch (t) { } }, "~S,Throwable"); c$.getLogLevel = Clazz.defineMethod (c$, "getLogLevel", function () { for (var i = 7; --i >= 0; ) if (JU.Logger.isActiveLevel (i)) return i; return 0; }); c$.fatal = Clazz.defineMethod (c$, "fatal", function (txt) { try { if (JU.Logger.isActiveLevel (1)) { JU.Logger._logger.fatal (txt); }} catch (t) { } }, "~S"); c$.fatalEx = Clazz.defineMethod (c$, "fatalEx", function (txt, e) { try { if (JU.Logger.isActiveLevel (1)) { JU.Logger._logger.fatalEx (txt, e); }} catch (t) { } }, "~S,Throwable"); c$.startTimer = Clazz.defineMethod (c$, "startTimer", function (msg) { if (msg != null) JU.Logger.htTiming.put (msg, Long.$valueOf (System.currentTimeMillis ())); }, "~S"); c$.getTimerMsg = Clazz.defineMethod (c$, "getTimerMsg", function (msg, time) { if (time == 0) time = JU.Logger.getTimeFrom (msg); return "Time for " + msg + ": " + (time) + " ms"; }, "~S,~N"); c$.getTimeFrom = Clazz.defineMethod (c$, "getTimeFrom", function (msg) { var t; return (msg == null || (t = JU.Logger.htTiming.get (msg)) == null ? -1 : System.currentTimeMillis () - t.longValue ()); }, "~S"); c$.checkTimer = Clazz.defineMethod (c$, "checkTimer", function (msg, andReset) { var time = JU.Logger.getTimeFrom (msg); if (time >= 0 && !msg.startsWith ("(")) JU.Logger.info (JU.Logger.getTimerMsg (msg, time)); if (andReset) JU.Logger.startTimer (msg); return time; }, "~S,~B"); c$.checkMemory = Clazz.defineMethod (c$, "checkMemory", function () { var bTotal = 0; var bFree = 0; var bMax = 0; { }JU.Logger.info ("Memory: Total-Free=" + (bTotal - bFree) + "; Total=" + bTotal + "; Free=" + bFree + "; Max=" + bMax); }); c$._logger = c$.prototype._logger = new JU.DefaultLogger (); Clazz.defineStatics (c$, "LEVEL_FATAL", 1, "LEVEL_ERROR", 2, "LEVEL_WARN", 3, "LEVEL_INFO", 4, "LEVEL_DEBUG", 5, "LEVEL_DEBUGHIGH", 6, "LEVEL_MAX", 7, "_activeLevels", Clazz.newBooleanArray (7, false), "_logLevel", false, "debugging", false, "debuggingHigh", false); { JU.Logger._activeLevels[6] = JU.Logger.getProperty ("debugHigh", false); JU.Logger._activeLevels[5] = JU.Logger.getProperty ("debug", false); JU.Logger._activeLevels[4] = JU.Logger.getProperty ("info", true); JU.Logger._activeLevels[3] = JU.Logger.getProperty ("warn", true); JU.Logger._activeLevels[2] = JU.Logger.getProperty ("error", true); JU.Logger._activeLevels[1] = JU.Logger.getProperty ("fatal", true); JU.Logger._logLevel = JU.Logger.getProperty ("logLevel", false); JU.Logger.debugging = (JU.Logger._logger != null && (JU.Logger._activeLevels[5] || JU.Logger._activeLevels[6])); JU.Logger.debuggingHigh = (JU.Logger.debugging && JU.Logger._activeLevels[6]); }c$.htTiming = c$.prototype.htTiming = new java.util.Hashtable (); });