-// JSmol.js -- Jmol pure JavaScript version\r
-// author: Bob Hanson, hansonr@stolaf.edu 4/16/2012\r
-// author: Takanori Nakane biochem_fan 6/12/2012\r
-\r
-// BH 3/28/2015 6:18:33 AM refactoring to generalize for non-Jmol-related SwingJS applications\r
-// BH 9/6/2014 5:42:32 PM two-point gestures broken\r
-// BH 5/8/2014 11:16:40 AM j2sPath starting with "/" fails to add idiom\r
-// BH 1/16/2014 8:44:03 PM __execDelayMS = 100; // FF bug when loading into a tab that is not \r
-// immediately focused and not using jQuery for adding the applet and having \r
-// multiple applets.\r
-// BH 12/6/2013 10:12:30 AM adding corejmoljsv.z.js\r
-// BH 9/17/2013 10:18:40 AM file transfer functions moved to JSmolCore \r
-// BH 3/5/2013 9:54:16 PM added support for a cover image: Info.coverImage, coverScript, coverTitle, deferApplet, deferUncover\r
-// BH 1/3/2013 4:54:01 AM mouse binding should return false -- see d.bind(...), and d.bind("contextmenu") is not necessary\r
-\r
-// This library requires prior inclusion of \r
-\r
-// jQuery 9 or higher\r
-// JSmoljQueryExt.js\r
-// JSmolCore.js\r
-// j2sjmol.js (Clazz and associated classes)\r
-\r
-// these:\r
-//\r
-// JSmolApplet.js\r
-// JSmolApi.js\r
-// JSmolThree.js\r
-// JSmolGLmol.js\r
-// \r
-// are optional \r
-\r
-;(function (Jmol) {\r
-\r
- Jmol._isAsync = false; // testing only\r
- Jmol._asyncCallbacks = {};\r
- \r
- Jmol._coreFiles = []; // required for package.js\r
-\r
-\r
-///////////////////\r
-// This section provides an asynchronous loading sequence\r
-//\r
-\r
-// methods and fields starting with double underscore are private to this .js file\r
-\r
- var __clazzLoaded = false;\r
- var __execLog = [];\r
- var __execStack = [];\r
- var __execTimer = 0;\r
- var __coreSet = [];\r
- var __coreMore = [];\r
- var __execDelayMS = 100; // must be > 55 ms for FF\r
-\r
- var __nextExecution = function(trigger) {\r
- arguments.length || (trigger = true);\r
- delete __execTimer;\r
- var es = __execStack;\r
- var e;\r
- while (es.length > 0 && (e = es[0])[4] == "done")\r
- es.shift();\r
- if (es.length == 0)\r
- return;\r
- if (!Jmol._isAsync && !trigger) {\r
- setTimeout(__nextExecution,10)\r
- return;\r
- }\r
- e.push("done");\r
- var s = "JSmol exec " + e[0]._id + " " + e[3] + " " + e[2];\r
- if (self.System)\r
- System.out.println(s);\r
- //alert(s)\r
- if (self.console)console.log(s + " -- OK")\r
- __execLog.push(s);\r
- e[1](e[0],e[2]); \r
- };\r
-\r
- var __loadClazz = function(applet) {\r
- if (!__clazzLoaded) {\r
- __clazzLoaded = true;\r
- // create the Clazz object\r
- LoadClazz();\r
- if (applet._noMonitor)\r
- Clazz._LoaderProgressMonitor.showStatus = function() {}\r
- LoadClazz = null;\r
- if (applet.__Info.uncompressed)\r
- Clazz.loadClass(); // for now; allows for no compression \r
- Clazz._Loader.onGlobalLoaded = function (file) {\r
- // not really.... just nothing more yet to do yet\r
- Clazz._LoaderProgressMonitor.showStatus("Application loaded.", true);\r
- if (!Jmol._debugCode || !Jmol.haveCore) {\r
- Jmol.haveCore = true;\r
- __nextExecution();\r
- }\r
- };\r
- // load package.js and j2s/core/core.z.js\r
- Clazz._Loader.loadPackageClasspath("java", null, true, __nextExecution);\r
- return;\r
- }\r
- __nextExecution();\r
- };\r
-\r
- var __loadClass = function(applet, javaClass) {\r
- Clazz._Loader.loadClass(javaClass, function() {__nextExecution()});\r
- };\r
-\r
- Jmol.showExecLog = function() { return __execLog.join("\n") }; \r
-\r
- Jmol._addExec = function(e) {\r
- e[1] || (e[1] = __loadClass);\r
- var s = "JSmol load " + e[0]._id + " " + e[3];\r
- if (self.console)console.log(s + "...")\r
- __execLog.push(s); \r
- __execStack.push(e);\r
- }\r
-\r
- Jmol._addCoreFile = function(type, path, more) {\r
- \r
- // BH 3/15: idea here is that when both Jmol and JSV are present, \r
- // we want to load a common core file -- jmoljsv.z.js --\r
- // instead of just one. Otherwise we do a lot of duplication.\r
- // It is not clear how this would play with other concurrent\r
- // apps. So this will take some thinking. But the basic idea is that\r
- // core file to load is \r
- \r
- type = type.toLowerCase().split(".")[0]; // package name only \r
-\r
- // return if type is already part of the set. \r
- if (__coreSet.join("").indexOf(type) >= 0) return;\r
- \r
- // create a concatenated lower-case name for a core file that includes\r
- // all Java applets on the page\r
- \r
- __coreSet.push(type);\r
- __coreSet.sort();\r
- Jmol._coreFiles = [path + "/core/core" + __coreSet.join("") + ".z.js" ];\r
- if (more && (more = more.split(" ")))\r
- for (var i = 0; i < more.length; i++)\r
- if (__coreMore.join("").indexOf(more[i]) < 0)\r
- __coreMore.push(path + "/core/core" + more[i] + ".z.js")\r
- for (var i = 0; i < __coreMore.length; i++)\r
- Jmol._coreFiles.push(__coreMore[i]);\r
- } \r
-\r
- Jmol._Canvas2D = function(id, Info, type, checkOnly){\r
- // type: Jmol or JSV\r
- this._uniqueId = ("" + Math.random()).substring(3);\r
- this._id = id;\r
- this._is2D = true;\r
- this._isJava = false;\r
- this._jmolType = "Jmol._Canvas2D (" + type + ")";\r
- this._isLayered = Info._isLayered || false;\r
- this._isSwing = Info._isSwing || false;\r
- this._isJSV = Info._isJSV || false;\r
- this._isAstex = Info._isAstex || false; \r
- this._platform = Info._platform || "";\r
- if (checkOnly)\r
- return this;\r
- window[id] = this;\r
- this._createCanvas(id, Info);\r
- if (!Jmol._document || this._deferApplet)\r
- return this;\r
- this._init();\r
- return this;\r
- };\r
-\r
- Jmol._setAppletParams = function(availableParams, params, Info, isHashtable) {\r
- for (var i in Info)\r
- if(!availableParams || availableParams.indexOf(";" + i.toLowerCase() + ";") >= 0){\r
- if (Info[i] == null || i == "language" && !Jmol.featureDetection.supportsLocalization())\r
- continue;\r
- if (isHashtable)\r
- params.put(i, (Info[i] === true ? Boolean.TRUE: Info[i] === false ? Boolean.FALSE : Info[i]))\r
- else\r
- params[i] = Info[i];\r
- }\r
- } \r
- \r
- Jmol._jsSetPrototype = function(proto) {\r
- proto._init = function() {\r
- this._setupJS();\r
- this._showInfo(true); \r
- if (this._disableInitialConsole)\r
- this._showInfo(false);\r
- };\r
-\r
- proto._createCanvas = function(id, Info, glmol) {\r
- Jmol._setObject(this, id, Info);\r
- if (glmol) {\r
- this._GLmol = glmol;\r
- this._GLmol.applet = this;\r
- this._GLmol.id = this._id;\r
- } \r
- var t = Jmol._getWrapper(this, true);\r
- if (this._deferApplet) {\r
- } else if (Jmol._document) {\r
- Jmol._documentWrite(t);\r
- this._newCanvas(false); \r
- t = "";\r
- } else {\r
- this._deferApplet = true;\r
- t += '<script type="text/javascript">' + id + '._cover(false)</script>';\r
- }\r
- t += Jmol._getWrapper(this, false);\r
- if (Info.addSelectionOptions)\r
- t += Jmol._getGrabberOptions(this);\r
- if (Jmol._debugAlert && !Jmol._document)\r
- alert(t);\r
- this._code = Jmol._documentWrite(t);\r
- };\r
-\r
- proto._newCanvas = function(doReplace) {\r
- if (this._is2D)\r
- this._createCanvas2d(doReplace);\r
- else\r
- this._GLmol.create();\r
- };\r
-\r
-//////// swingjs.api.HTML5Applet interface \r
- proto._getHtml5Canvas = function() { return this._canvas }; \r
- proto._getWidth = function() { return this._canvas.width }; \r
- proto._getHeight = function() { return this._canvas.height };\r
- proto._getContentLayer = function() { return Jmol.$(this, "contentLayer")[0] };\r
- proto._repaintNow = function() { Jmol._repaint(this, false) }; \r
-////////\r
-\r
-\r
- proto._createCanvas2d = function(doReplace) {\r
- var container = Jmol.$(this, "appletdiv");\r
- //if (doReplace) {\r
- \r
- try {\r
- container[0].removeChild(this._canvas);\r
- if (this._canvas.frontLayer)\r
- container[0].removeChild(this._canvas.frontLayer);\r
- if (this._canvas.rearLayer)\r
- container[0].removeChild(this._canvas.rearLayer);\r
- if (this._canvas.contentLayer)\r
- container[0].removeChild(this._canvas.contentLayer);\r
- Jmol._jsUnsetMouse(this._mouseInterface);\r
- } catch (e) {}\r
- //}\r
- var w = Math.round(container.width());\r
- var h = Math.round(container.height());\r
- var canvas = document.createElement( 'canvas' );\r
- canvas.applet = this;\r
- this._canvas = canvas;\r
- canvas.style.width = "100%";\r
- canvas.style.height = "100%";\r
- canvas.width = w;\r
- canvas.height = h; // w and h used in setScreenDimension\r
- canvas.id = this._id + "_canvas2d";\r
- container.append(canvas);\r
- Jmol._$(canvas.id).css({"z-index":Jmol._getZ(this, "main")});\r
- if (this._isLayered){\r
- var img = document.createElement("div");\r
- canvas.contentLayer = img;\r
- img.id = this._id + "_contentLayer";\r
- container.append(img);\r
- Jmol._$(img.id).css({zIndex:Jmol._getZ(this, "image"),position:"absolute",left:"0px",top:"0px",\r
- width:(this._isSwing ? w : 0) + "px", height:(this._isSwing ? h : 0) +"px", overflow:"hidden"});\r
- if (this._isSwing) {\r
- var d = document.createElement("div");\r
- d.id = this._id + "_swingdiv";\r
- Jmol._$(this._id + "_appletinfotablediv").append(d);\r
- Jmol._$(d.id).css({zIndex:Jmol._getZ(this, "rear"),position:"absolute",left:"0px",top:"0px", width:w +"px", height:h+"px", overflow:"hidden"});\r
- this._mouseInterface = canvas.contentLayer;\r
- canvas.contentLayer.applet = this;\r
- } else {\r
- this._mouseInterface = this._getLayer("front", container, w, h, false);\r
- }\r
- //this._getLayer("rear", container, w, h, true);\r
- //Jmol._$(canvas.id).css({background:"rgb(0,0,0,0.001)", "z-index":Jmol._z.main}); \r
- } else {\r
- this._mouseInterface = canvas;\r
- }\r
- Jmol._jsSetMouse(this._mouseInterface);\r
- }\r
- \r
- proto._getLayer = function(name, container, w, h, isOpaque) {\r
- var c = document.createElement("canvas");\r
- this._canvas[name + "Layer"] = c;\r
- c.style.width = "100%";\r
- c.style.height = "100%";\r
- c.id = this._id + "_" + name + "Layer";\r
- c.width = w;\r
- c.height = h; // w and h used in setScreenDimension\r
- container.append(c);\r
- c.applet = this;\r
- Jmol._$(c.id).css({background:(isOpaque ? "rgb(0,0,0,1)" : "rgb(0,0,0,0.001)"), "z-index": Jmol._getZ(this,name),position:"absolute",left:"0px",top:"0px",overflow:"hidden"});\r
- return c; \r
- }\r
- \r
- \r
- proto._setupJS = function() {\r
- window["j2s.lib"] = {\r
- base : this._j2sPath + "/",\r
- alias : ".",\r
- console : this._console,\r
- monitorZIndex : Jmol._getZ(this, "monitorZIndex")\r
- };\r
- var isFirst = (__execStack.length == 0);\r
- if (isFirst)\r
- Jmol._addExec([this, __loadClazz, null, "loadClazz"]);\r
- this._addCoreFiles();\r
- Jmol._addExec([this, this.__startAppletJS, null, "start applet"])\r
- this._isSigned = true; // access all files via URL hook\r
- this._ready = false; \r
- this._applet = null;\r
- this._canScript = function(script) {return true;};\r
- this._savedOrientations = [];\r
- __execTimer && clearTimeout(__execTimer);\r
- __execTimer = setTimeout(__nextExecution, __execDelayMS);\r
- };\r
-\r
- proto.__startAppletJS = function(applet) {\r
- if (Jmol._version.indexOf("$Date: ") == 0)\r
- Jmol._version = (Jmol._version.substring(7) + " -").split(" -")[0] + " (JSmol/j2s)"\r
- var viewerOptions = Clazz._4Name("java.util.Hashtable").newInstance();\r
- Jmol._setAppletParams(applet._availableParams, viewerOptions, applet.__Info, true);\r
- viewerOptions.put("appletReadyCallback","Jmol._readyCallback");\r
- viewerOptions.put("applet", true);\r
- viewerOptions.put("name", applet._id);// + "_object");\r
- viewerOptions.put("syncId", Jmol._syncId);\r
- if (Jmol._isAsync)\r
- viewerOptions.put("async", true);\r
- if (applet._color) \r
- viewerOptions.put("bgcolor", applet._color);\r
- if (applet._startupScript)\r
- viewerOptions.put("script", applet._startupScript)\r
- if (Jmol._syncedApplets.length)\r
- viewerOptions.put("synccallback", "Jmol._mySyncCallback");\r
- viewerOptions.put("signedApplet", "true");\r
- viewerOptions.put("platform", applet._platform);\r
- if (applet._is2D)\r
- viewerOptions.put("display",applet._id + "_canvas2d");\r
-\r
- // viewerOptions.put("repaintManager", "J.render");\r
- viewerOptions.put("documentBase", document.location.href);\r
- var codePath = applet._j2sPath + "/";\r
- \r
- if (codePath.indexOf("://") < 0) {\r
- var base = document.location.href.split("#")[0].split("?")[0].split("/");\r
- if (codePath.indexOf("/") == 0)\r
- base = [base[0], codePath.substring(1)];\r
- else\r
- base[base.length - 1] = codePath;\r
- codePath = base.join("/");\r
- }\r
- viewerOptions.put("codePath", codePath);\r
- Jmol._registerApplet(applet._id, applet);\r
- try {\r
- applet._newApplet(viewerOptions);\r
- } catch (e) {\r
- System.out.println((Jmol._isAsync ? "normal async abort from " : "") + e);\r
- return;\r
- }\r
- \r
- applet._jsSetScreenDimensions();\r
- __nextExecution();\r
- };\r
-\r
- if (!proto._restoreState)\r
- proto._restoreState = function(clazzName, state) {\r
- // applet-dependent\r
- }\r
- \r
- proto._jsSetScreenDimensions = function() {\r
- if (!this._appletPanel)return\r
- // strangely, if CTRL+/CTRL- are used repeatedly, then the\r
- // applet div can be not the same size as the canvas if there\r
- // is a border in place.\r
- var d = Jmol._getElement(this, (this._is2D ? "canvas2d" : "canvas"));\r
- this._appletPanel.setScreenDimension(d.width, d.height);\r
- };\r
-\r
- proto._show = function(tf) {\r
- Jmol.$setVisible(Jmol.$(this,"appletdiv"), tf);\r
- if (tf)\r
- Jmol._repaint(this, true);\r
- };\r
-\r
- proto._canScript = function(script) {return true};\r
-\r
-// proto._delay = function(eval, sc, millis) {\r
-// alert("_delay???")\r
-// // does not take into account that scripts may be added after this and\r
-// // need to be cached.\r
-// this._delayID = setTimeout(function(){eval.resumeEval(sc,false)}, millis); \r
-// }\r
-/*\r
- proto._createDomNode = function(id, data) { // moved to org.jmol.adapter.readers.xml.XmlReader.java\r
- id = this._id + "_" + id;\r
- var d = document.getElementById(id);\r
- if (d)\r
- document.body.removeChild(d);\r
- if (!data)\r
- return;\r
- if (data.indexOf("<?") == 0)\r
- data = data.substring(data.indexOf("<", 1));\r
- if (data.indexOf("/>") >= 0) {\r
- // no doubt there is a more efficient way to do this.\r
- // Firefox, at least, does not recognize "/>" in HTML blocks\r
- // that are added this way.\r
- var D = data.split("/>");\r
- for (var i = D.length - 1; --i >= 0;) {\r
- var s = D[i];\r
- var pt = s.lastIndexOf("<") + 1;\r
- var pt2 = pt;\r
- var len = s.length;\r
- var name = "";\r
- while (++pt2 < len) {\r
- if (" \t\n\r".indexOf(s.charAt(pt2))>= 0) {\r
- var name = s.substring(pt, pt2);\r
- D[i] = s + "></"+name+">";\r
- break;\r
- } \r
- }\r
- }\r
- data = D.join('');\r
- }\r
- d = document.createElement("_xml")\r
- d.id = id;\r
- d.innerHTML = data;\r
- d.style.display = "none";\r
- document.body.appendChild(d);\r
- return d;\r
- } \r
-*/\r
- proto.equals = function(a) { return this == a };\r
- proto.clone = function() { return this };\r
- proto.hashCode = function() { return parseInt(this._uniqueId) }; \r
-\r
-\r
- proto._processGesture = function(touches) {\r
- return this._appletPanel.processTwoPointGesture(touches);\r
- }\r
-\r
- proto._processEvent = function(type, xym) {\r
- this._appletPanel.processMouseEvent(type,xym[0],xym[1],xym[2],System.currentTimeMillis());\r
- }\r
-\r
- proto._resize = function() {\r
- var s = "__resizeTimeout_" + this._id;\r
- // only at end\r
- if (Jmol[s])\r
- clearTimeout(Jmol[s]);\r
- var me = this;\r
- Jmol[s] = setTimeout(function() {Jmol._repaint(me, true);Jmol[s]=null}, 100);\r
- }\r
-\r
- return proto;\r
- };\r
-\r
- Jmol._repaint = function(applet, asNewThread) {\r
- // asNewThread: true is from RepaintManager.repaintNow()\r
- // false is from Repaintmanager.requestRepaintAndWait()\r
- // called from apiPlatform Display.repaint()\r
-\r
- //alert("_repaint " + Clazz.getStackTrace())\r
- if (!applet || !applet._appletPanel)return;\r
-\r
- // asNewThread = false;\r
- var container = Jmol.$(applet, "appletdiv");\r
- var w = Math.round(container.width());\r
- var h = Math.round(container.height());\r
- if (applet._is2D && (applet._canvas.width != w || applet._canvas.height != h)) {\r
- applet._newCanvas(true);\r
- applet._appletPanel.setDisplay(applet._canvas);\r
- }\r
- applet._appletPanel.setScreenDimension(w, h);\r
- var f = function(){\r
- if (applet._appletPanel.paint)\r
- applet._appletPanel.paint(null);\r
- else\r
- applet._appletPanel.update(null)\r
- };\r
- if (asNewThread) {\r
- setTimeout(f);\r
- } else {\r
- f();\r
- }\r
- // System.out.println(applet._appletPanel.getFullName())\r
- }\r
-\r
- Jmol._getHiddenCanvas = function(applet, id, width, height, forceNew) {\r
- id = applet._id + "_" + id;\r
- var d = document.getElementById(id);\r
- if (d && forceNew) {\r
- d = null;\r
- }\r
- if (!d)\r
- d = document.createElement( 'canvas' );\r
- // for some reason both these need to be set, or maybe just d.width?\r
- d.width = d.style.width = width;\r
- d.height = d.style.height = height;\r
- // d.style.display = "none";\r
- if (d.id != id) {\r
- d.id = id;\r
- }\r
- return d;\r
- }\r
-\r
- Jmol._loadImage = function(platform, echoNameAndPath, bytes, fOnload, image) {\r
- // bytes would be from a ZIP file -- will have to reflect those back from\r
- // server as an image after conversion to base64\r
- // ah, but that's a problem, because that image would be needed to be\r
- // posted, but you can't post an image call.\r
- // so we would have to go with <image data:> which does not work in all\r
- // browsers. Hmm.\r
-\r
- var path = echoNameAndPath[1];\r
-\r
- if (image == null) {\r
- var image = new Image();\r
- image.onload = function() {Jmol._loadImage(platform, echoNameAndPath, null, fOnload, image)};\r
-\r
- if (bytes != null) { \r
- bytes = J.io.Base64.getBase64(bytes).toString(); \r
- var filename = path.substring(url.lastIndexOf("/") + 1); \r
- var mimetype = (filename.indexOf(".png") >= 0 ? "image/png" : filename.indexOf(".jpg") >= 0 ? "image/jpg" : "");\r
- // now what?\r
- }\r
- image.src = path;\r
- return true; // as far as we can tell!\r
- }\r
- var width = image.width;\r
- var height = image.height; \r
- var id = "echo_" + echoNameAndPath[0]; \r
- var canvas = Jmol._getHiddenCanvas(platform.vwr.html5Applet, id, width, height, true);\r
- canvas.imageWidth = width;\r
- canvas.imageHeight = height;\r
- canvas.id = id;\r
- canvas.image=image;\r
- Jmol._setCanvasImage(canvas, width, height);\r
- // return a null canvas and the error in path if there is a problem\r
- fOnload(canvas,path);\r
- };\r
-\r
- Jmol._setCanvasImage = function(canvas, width, height) {\r
- // called from org.jmol.awtjs2d.Platform\r
- canvas.buf32 = null;\r
- canvas.width = width;\r
- canvas.height = height;\r
- canvas.getContext("2d").drawImage(canvas.image, 0, 0, width, height);\r
- };\r
-\r
-})(Jmol);\r
+// JSmol.js -- Jmol pure JavaScript version
+// author: Bob Hanson, hansonr@stolaf.edu 4/16/2012
+// author: Takanori Nakane biochem_fan 6/12/2012
+
+// BH 3/28/2015 6:18:33 AM refactoring to generalize for non-Jmol-related SwingJS applications
+// BH 9/6/2014 5:42:32 PM two-point gestures broken
+// BH 5/8/2014 11:16:40 AM j2sPath starting with "/" fails to add idiom
+// BH 1/16/2014 8:44:03 PM __execDelayMS = 100; // FF bug when loading into a tab that is not
+// immediately focused and not using jQuery for adding the applet and having
+// multiple applets.
+// BH 12/6/2013 10:12:30 AM adding corejmoljsv.z.js
+// BH 9/17/2013 10:18:40 AM file transfer functions moved to JSmolCore
+// BH 3/5/2013 9:54:16 PM added support for a cover image: Info.coverImage, coverScript, coverTitle, deferApplet, deferUncover
+// BH 1/3/2013 4:54:01 AM mouse binding should return false -- see d.bind(...), and d.bind("contextmenu") is not necessary
+
+// This library requires prior inclusion of
+
+// jQuery 9 or higher
+// JSmoljQueryExt.js
+// JSmolCore.js
+// j2sjmol.js (Clazz and associated classes)
+
+// these:
+//
+// JSmolApplet.js
+// JSmolApi.js
+// JSmolThree.js
+// JSmolGLmol.js
+//
+// are optional
+
+;(function (Jmol) {
+
+ Jmol._isAsync = false; // testing only
+ Jmol._asyncCallbacks = {};
+
+ Jmol._coreFiles = []; // required for package.js
+
+
+///////////////////
+// This section provides an asynchronous loading sequence
+//
+
+// methods and fields starting with double underscore are private to this .js file
+
+ var __clazzLoaded = false;
+ var __execLog = [];
+ var __execStack = [];
+ var __execTimer = 0;
+ var __coreSet = [];
+ var __coreMore = [];
+ var __execDelayMS = 100; // must be > 55 ms for FF
+
+ var __nextExecution = function(trigger) {
+ arguments.length || (trigger = true);
+ delete __execTimer;
+ var es = __execStack;
+ var e;
+ while (es.length > 0 && (e = es[0])[4] == "done")
+ es.shift();
+ if (es.length == 0)
+ return;
+ if (!Jmol._isAsync && !trigger) {
+ setTimeout(__nextExecution,10)
+ return;
+ }
+ e.push("done");
+ var s = "JSmol exec " + e[0]._id + " " + e[3] + " " + e[2];
+ if (self.System)
+ System.out.println(s);
+ //alert(s)
+ if (self.console)console.log(s + " -- OK")
+ __execLog.push(s);
+ e[1](e[0],e[2]);
+ };
+
+ var __loadClazz = function(applet) {
+ if (!__clazzLoaded) {
+ __clazzLoaded = true;
+ // create the Clazz object
+ LoadClazz();
+ if (applet._noMonitor)
+ Clazz._LoaderProgressMonitor.showStatus = function() {}
+ LoadClazz = null;
+ if (applet.__Info.uncompressed)
+ Clazz.loadClass(); // for now; allows for no compression
+ Clazz._Loader.onGlobalLoaded = function (file) {
+ // not really.... just nothing more yet to do yet
+ Clazz._LoaderProgressMonitor.showStatus("Application loaded.", true);
+ if (!Jmol._debugCode || !Jmol.haveCore) {
+ Jmol.haveCore = true;
+ __nextExecution();
+ }
+ };
+ // load package.js and j2s/core/core.z.js
+ Clazz._Loader.loadPackageClasspath("java", null, true, __nextExecution);
+ return;
+ }
+ __nextExecution();
+ };
+
+ var __loadClass = function(applet, javaClass) {
+ Clazz._Loader.loadClass(javaClass, function() {__nextExecution()});
+ };
+
+ Jmol.showExecLog = function() { return __execLog.join("\n") };
+
+ Jmol._addExec = function(e) {
+ e[1] || (e[1] = __loadClass);
+ var s = "JSmol load " + e[0]._id + " " + e[3];
+ if (self.console)console.log(s + "...")
+ __execLog.push(s);
+ __execStack.push(e);
+ }
+
+ Jmol._addCoreFile = function(type, path, more) {
+
+ // BH 3/15: idea here is that when both Jmol and JSV are present,
+ // we want to load a common core file -- jmoljsv.z.js --
+ // instead of just one. Otherwise we do a lot of duplication.
+ // It is not clear how this would play with other concurrent
+ // apps. So this will take some thinking. But the basic idea is that
+ // core file to load is
+
+ type = type.toLowerCase().split(".")[0]; // package name only
+
+ // return if type is already part of the set.
+ if (__coreSet.join("").indexOf(type) >= 0) return;
+
+ // create a concatenated lower-case name for a core file that includes
+ // all Java applets on the page
+
+ __coreSet.push(type);
+ __coreSet.sort();
+ Jmol._coreFiles = [path + "/core/core" + __coreSet.join("") + ".z.js" ];
+ if (more && (more = more.split(" ")))
+ for (var i = 0; i < more.length; i++)
+ if (__coreMore.join("").indexOf(more[i]) < 0)
+ __coreMore.push(path + "/core/core" + more[i] + ".z.js")
+ for (var i = 0; i < __coreMore.length; i++)
+ Jmol._coreFiles.push(__coreMore[i]);
+ }
+
+ Jmol._Canvas2D = function(id, Info, type, checkOnly){
+ // type: Jmol or JSV
+ this._uniqueId = ("" + Math.random()).substring(3);
+ this._id = id;
+ this._is2D = true;
+ this._isJava = false;
+ this._jmolType = "Jmol._Canvas2D (" + type + ")";
+ this._isLayered = Info._isLayered || false;
+ this._isSwing = Info._isSwing || false;
+ this._isJSV = Info._isJSV || false;
+ this._isAstex = Info._isAstex || false;
+ this._platform = Info._platform || "";
+ if (checkOnly)
+ return this;
+ window[id] = this;
+ this._createCanvas(id, Info);
+ if (!Jmol._document || this._deferApplet)
+ return this;
+ this._init();
+ return this;
+ };
+
+ Jmol._setAppletParams = function(availableParams, params, Info, isHashtable) {
+ for (var i in Info)
+ if(!availableParams || availableParams.indexOf(";" + i.toLowerCase() + ";") >= 0){
+ if (Info[i] == null || i == "language" && !Jmol.featureDetection.supportsLocalization())
+ continue;
+ if (isHashtable)
+ params.put(i, (Info[i] === true ? Boolean.TRUE: Info[i] === false ? Boolean.FALSE : Info[i]))
+ else
+ params[i] = Info[i];
+ }
+ }
+
+ Jmol._jsSetPrototype = function(proto) {
+ proto._init = function() {
+ this._setupJS();
+ this._showInfo(true);
+ if (this._disableInitialConsole)
+ this._showInfo(false);
+ };
+
+ proto._createCanvas = function(id, Info, glmol) {
+ Jmol._setObject(this, id, Info);
+ if (glmol) {
+ this._GLmol = glmol;
+ this._GLmol.applet = this;
+ this._GLmol.id = this._id;
+ }
+ var t = Jmol._getWrapper(this, true);
+ if (this._deferApplet) {
+ } else if (Jmol._document) {
+ Jmol._documentWrite(t);
+ this._newCanvas(false);
+ t = "";
+ } else {
+ this._deferApplet = true;
+ t += '<script type="text/javascript">' + id + '._cover(false)</script>';
+ }
+ t += Jmol._getWrapper(this, false);
+ if (Info.addSelectionOptions)
+ t += Jmol._getGrabberOptions(this);
+ if (Jmol._debugAlert && !Jmol._document)
+ alert(t);
+ this._code = Jmol._documentWrite(t);
+ };
+
+ proto._newCanvas = function(doReplace) {
+ if (this._is2D)
+ this._createCanvas2d(doReplace);
+ else
+ this._GLmol.create();
+ };
+
+//////// swingjs.api.HTML5Applet interface
+ proto._getHtml5Canvas = function() { return this._canvas };
+ proto._getWidth = function() { return this._canvas.width };
+ proto._getHeight = function() { return this._canvas.height };
+ proto._getContentLayer = function() { return Jmol.$(this, "contentLayer")[0] };
+ proto._repaintNow = function() { Jmol._repaint(this, false) };
+////////
+
+
+ proto._createCanvas2d = function(doReplace) {
+ var container = Jmol.$(this, "appletdiv");
+ //if (doReplace) {
+
+ try {
+ container[0].removeChild(this._canvas);
+ if (this._canvas.frontLayer)
+ container[0].removeChild(this._canvas.frontLayer);
+ if (this._canvas.rearLayer)
+ container[0].removeChild(this._canvas.rearLayer);
+ if (this._canvas.contentLayer)
+ container[0].removeChild(this._canvas.contentLayer);
+ Jmol._jsUnsetMouse(this._mouseInterface);
+ } catch (e) {}
+ //}
+ var w = Math.round(container.width());
+ var h = Math.round(container.height());
+ var canvas = document.createElement( 'canvas' );
+ canvas.applet = this;
+ this._canvas = canvas;
+ canvas.style.width = "100%";
+ canvas.style.height = "100%";
+ canvas.width = w;
+ canvas.height = h; // w and h used in setScreenDimension
+ canvas.id = this._id + "_canvas2d";
+ container.append(canvas);
+ Jmol._$(canvas.id).css({"z-index":Jmol._getZ(this, "main")});
+ if (this._isLayered){
+ var img = document.createElement("div");
+ canvas.contentLayer = img;
+ img.id = this._id + "_contentLayer";
+ container.append(img);
+ Jmol._$(img.id).css({zIndex:Jmol._getZ(this, "image"),position:"absolute",left:"0px",top:"0px",
+ width:(this._isSwing ? w : 0) + "px", height:(this._isSwing ? h : 0) +"px", overflow:"hidden"});
+ if (this._isSwing) {
+ var d = document.createElement("div");
+ d.id = this._id + "_swingdiv";
+ Jmol._$(this._id + "_appletinfotablediv").append(d);
+ Jmol._$(d.id).css({zIndex:Jmol._getZ(this, "rear"),position:"absolute",left:"0px",top:"0px", width:w +"px", height:h+"px", overflow:"hidden"});
+ this._mouseInterface = canvas.contentLayer;
+ canvas.contentLayer.applet = this;
+ } else {
+ this._mouseInterface = this._getLayer("front", container, w, h, false);
+ }
+ //this._getLayer("rear", container, w, h, true);
+ //Jmol._$(canvas.id).css({background:"rgb(0,0,0,0.001)", "z-index":Jmol._z.main});
+ } else {
+ this._mouseInterface = canvas;
+ }
+ Jmol._jsSetMouse(this._mouseInterface);
+ }
+
+ proto._getLayer = function(name, container, w, h, isOpaque) {
+ var c = document.createElement("canvas");
+ this._canvas[name + "Layer"] = c;
+ c.style.width = "100%";
+ c.style.height = "100%";
+ c.id = this._id + "_" + name + "Layer";
+ c.width = w;
+ c.height = h; // w and h used in setScreenDimension
+ container.append(c);
+ c.applet = this;
+ Jmol._$(c.id).css({background:(isOpaque ? "rgb(0,0,0,1)" : "rgb(0,0,0,0.001)"), "z-index": Jmol._getZ(this,name),position:"absolute",left:"0px",top:"0px",overflow:"hidden"});
+ return c;
+ }
+
+
+ proto._setupJS = function() {
+ window["j2s.lib"] = {
+ base : this._j2sPath + "/",
+ alias : ".",
+ console : this._console,
+ monitorZIndex : Jmol._getZ(this, "monitorZIndex")
+ };
+ var isFirst = (__execStack.length == 0);
+ if (isFirst)
+ Jmol._addExec([this, __loadClazz, null, "loadClazz"]);
+ this._addCoreFiles();
+ Jmol._addExec([this, this.__startAppletJS, null, "start applet"])
+ this._isSigned = true; // access all files via URL hook
+ this._ready = false;
+ this._applet = null;
+ this._canScript = function(script) {return true;};
+ this._savedOrientations = [];
+ __execTimer && clearTimeout(__execTimer);
+ __execTimer = setTimeout(__nextExecution, __execDelayMS);
+ };
+
+ proto.__startAppletJS = function(applet) {
+ if (Jmol._version.indexOf("$Date: ") == 0)
+ Jmol._version = (Jmol._version.substring(7) + " -").split(" -")[0] + " (JSmol/j2s)"
+ var viewerOptions = Clazz._4Name("java.util.Hashtable").newInstance();
+ Jmol._setAppletParams(applet._availableParams, viewerOptions, applet.__Info, true);
+ viewerOptions.put("appletReadyCallback","Jmol._readyCallback");
+ viewerOptions.put("applet", true);
+ viewerOptions.put("name", applet._id);// + "_object");
+ viewerOptions.put("syncId", Jmol._syncId);
+ if (Jmol._isAsync)
+ viewerOptions.put("async", true);
+ if (applet._color)
+ viewerOptions.put("bgcolor", applet._color);
+ if (applet._startupScript)
+ viewerOptions.put("script", applet._startupScript)
+ if (Jmol._syncedApplets.length)
+ viewerOptions.put("synccallback", "Jmol._mySyncCallback");
+ viewerOptions.put("signedApplet", "true");
+ viewerOptions.put("platform", applet._platform);
+ if (applet._is2D)
+ viewerOptions.put("display",applet._id + "_canvas2d");
+
+ // viewerOptions.put("repaintManager", "J.render");
+ viewerOptions.put("documentBase", document.location.href);
+ var codePath = applet._j2sPath + "/";
+
+ if (codePath.indexOf("://") < 0) {
+ var base = document.location.href.split("#")[0].split("?")[0].split("/");
+ if (codePath.indexOf("/") == 0)
+ base = [base[0], codePath.substring(1)];
+ else
+ base[base.length - 1] = codePath;
+ codePath = base.join("/");
+ }
+ viewerOptions.put("codePath", codePath);
+ Jmol._registerApplet(applet._id, applet);
+ try {
+ applet._newApplet(viewerOptions);
+ } catch (e) {
+ System.out.println((Jmol._isAsync ? "normal async abort from " : "") + e);
+ return;
+ }
+
+ applet._jsSetScreenDimensions();
+ __nextExecution();
+ };
+
+ if (!proto._restoreState)
+ proto._restoreState = function(clazzName, state) {
+ // applet-dependent
+ }
+
+ proto._jsSetScreenDimensions = function() {
+ if (!this._appletPanel)return
+ // strangely, if CTRL+/CTRL- are used repeatedly, then the
+ // applet div can be not the same size as the canvas if there
+ // is a border in place.
+ var d = Jmol._getElement(this, (this._is2D ? "canvas2d" : "canvas"));
+ this._appletPanel.setScreenDimension(d.width, d.height);
+ };
+
+ proto._show = function(tf) {
+ Jmol.$setVisible(Jmol.$(this,"appletdiv"), tf);
+ if (tf)
+ Jmol._repaint(this, true);
+ };
+
+ proto._canScript = function(script) {return true};
+
+// proto._delay = function(eval, sc, millis) {
+// alert("_delay???")
+// // does not take into account that scripts may be added after this and
+// // need to be cached.
+// this._delayID = setTimeout(function(){eval.resumeEval(sc,false)}, millis);
+// }
+/*
+ proto._createDomNode = function(id, data) { // moved to org.jmol.adapter.readers.xml.XmlReader.java
+ id = this._id + "_" + id;
+ var d = document.getElementById(id);
+ if (d)
+ document.body.removeChild(d);
+ if (!data)
+ return;
+ if (data.indexOf("<?") == 0)
+ data = data.substring(data.indexOf("<", 1));
+ if (data.indexOf("/>") >= 0) {
+ // no doubt there is a more efficient way to do this.
+ // Firefox, at least, does not recognize "/>" in HTML blocks
+ // that are added this way.
+ var D = data.split("/>");
+ for (var i = D.length - 1; --i >= 0;) {
+ var s = D[i];
+ var pt = s.lastIndexOf("<") + 1;
+ var pt2 = pt;
+ var len = s.length;
+ var name = "";
+ while (++pt2 < len) {
+ if (" \t\n\r".indexOf(s.charAt(pt2))>= 0) {
+ var name = s.substring(pt, pt2);
+ D[i] = s + "></"+name+">";
+ break;
+ }
+ }
+ }
+ data = D.join('');
+ }
+ d = document.createElement("_xml")
+ d.id = id;
+ d.innerHTML = data;
+ d.style.display = "none";
+ document.body.appendChild(d);
+ return d;
+ }
+*/
+ proto.equals = function(a) { return this == a };
+ proto.clone = function() { return this };
+ proto.hashCode = function() { return parseInt(this._uniqueId) };
+
+
+ proto._processGesture = function(touches) {
+ return this._appletPanel.processTwoPointGesture(touches);
+ }
+
+ proto._processEvent = function(type, xym) {
+ this._appletPanel.processMouseEvent(type,xym[0],xym[1],xym[2],System.currentTimeMillis());
+ }
+
+ proto._resize = function() {
+ var s = "__resizeTimeout_" + this._id;
+ // only at end
+ if (Jmol[s])
+ clearTimeout(Jmol[s]);
+ var me = this;
+ Jmol[s] = setTimeout(function() {Jmol._repaint(me, true);Jmol[s]=null}, 100);
+ }
+
+ return proto;
+ };
+
+ Jmol._repaint = function(applet, asNewThread) {
+ // asNewThread: true is from RepaintManager.repaintNow()
+ // false is from Repaintmanager.requestRepaintAndWait()
+ // called from apiPlatform Display.repaint()
+
+ //alert("_repaint " + Clazz.getStackTrace())
+ if (!applet || !applet._appletPanel)return;
+
+ // asNewThread = false;
+ var container = Jmol.$(applet, "appletdiv");
+ var w = Math.round(container.width());
+ var h = Math.round(container.height());
+ if (applet._is2D && (applet._canvas.width != w || applet._canvas.height != h)) {
+ applet._newCanvas(true);
+ applet._appletPanel.setDisplay(applet._canvas);
+ }
+ applet._appletPanel.setScreenDimension(w, h);
+ var f = function(){
+ if (applet._appletPanel.paint)
+ applet._appletPanel.paint(null);
+ else
+ applet._appletPanel.update(null)
+ };
+ if (asNewThread) {
+ setTimeout(f);
+ } else {
+ f();
+ }
+ // System.out.println(applet._appletPanel.getFullName())
+ }
+
+ Jmol._getHiddenCanvas = function(applet, id, width, height, forceNew) {
+ id = applet._id + "_" + id;
+ var d = document.getElementById(id);
+ if (d && forceNew) {
+ d = null;
+ }
+ if (!d)
+ d = document.createElement( 'canvas' );
+ // for some reason both these need to be set, or maybe just d.width?
+ d.width = d.style.width = width;
+ d.height = d.style.height = height;
+ // d.style.display = "none";
+ if (d.id != id) {
+ d.id = id;
+ }
+ return d;
+ }
+
+ Jmol._loadImage = function(platform, echoNameAndPath, bytes, fOnload, image) {
+ // bytes would be from a ZIP file -- will have to reflect those back from
+ // server as an image after conversion to base64
+ // ah, but that's a problem, because that image would be needed to be
+ // posted, but you can't post an image call.
+ // so we would have to go with <image data:> which does not work in all
+ // browsers. Hmm.
+
+ var path = echoNameAndPath[1];
+
+ if (image == null) {
+ var image = new Image();
+ image.onload = function() {Jmol._loadImage(platform, echoNameAndPath, null, fOnload, image)};
+
+ if (bytes != null) {
+ bytes = J.io.Base64.getBase64(bytes).toString();
+ var filename = path.substring(url.lastIndexOf("/") + 1);
+ var mimetype = (filename.indexOf(".png") >= 0 ? "image/png" : filename.indexOf(".jpg") >= 0 ? "image/jpg" : "");
+ // now what?
+ }
+ image.src = path;
+ return true; // as far as we can tell!
+ }
+ var width = image.width;
+ var height = image.height;
+ var id = "echo_" + echoNameAndPath[0];
+ var canvas = Jmol._getHiddenCanvas(platform.vwr.html5Applet, id, width, height, true);
+ canvas.imageWidth = width;
+ canvas.imageHeight = height;
+ canvas.id = id;
+ canvas.image=image;
+ Jmol._setCanvasImage(canvas, width, height);
+ // return a null canvas and the error in path if there is a problem
+ fOnload(canvas,path);
+ };
+
+ Jmol._setCanvasImage = function(canvas, width, height) {
+ // called from org.jmol.awtjs2d.Platform
+ canvas.buf32 = null;
+ canvas.width = width;
+ canvas.height = height;
+ canvas.getContext("2d").drawImage(canvas.image, 0, 0, width, height);
+ };
+
+})(Jmol);
git://source.jalview.org / jalviewjs.git / blobdiff