1: /* Jmol 12.0 script library Jmol.js 5/20/2013 7:34:08 AM Bob Hanson
2:
3:
4: NOTE: THIS LIBRARY IS DEPRECATED STARTING WITH Jmol 13.0.
5: IT STILL WORKS (AND ALWAYS WILL, PROBABLY).
6: PLEASE USE the set JmolCore.js/JmolApplet.js/JmolControls.js/JmolApi.js
7: WITH OPTIONAL JmolCD.js (ChemDoodle Canvas and Canvas2D options) and JmolJSV.js (JSpecView)
8:
9: SEE http://chemapps.stolaf.edu/jmol/files/JmolCore.js for details
10: SEE http://chemapps.stolaf.edu/jmol/examples-12/simple2.htm for an example
11:
12: checkbox heirarchy -- see http://chemapps.stolaf.edu/jmol/docs/examples-11/check.htm
13:
14: based on:
15: *
16: * Copyright (C) 2004-2005 Miguel, Jmol Development, www.jmol.org
17: *
18: * Contact: hansonr@stolaf.edu
19: *
20: * This library is free software; you can redistribute it and/or
21: * modify it under the terms of the GNU Lesser General Public
22: * License as published by the Free Software Foundation; either
23: * version 2.1 of the License, or (at your option) any later version.
24: *
25: * This library is distributed in the hope that it will be useful,
26: * but WITHOUT ANY WARRANTY; without even the implied warranty of
27: * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
28: * Lesser General Public License for more details.
29: *
30: * You should have received a copy of the GNU Lesser General Public
31: * License along with this library; if not, write to the Free Software
32: * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
33: * 02111-1307 USA.
34: */
35:
36: // for documentation see www.jmol.org/jslibrary
37:
38: try{if(typeof(_jmol)!="undefined")exit()
39:
40: // place "?NOAPPLET" on your command line to check applet control action with a textarea
41: // place "?JMOLJAR=xxxxx" to use a specific jar file
42:
43: // bob hanson -- jmolResize(w,h) -- resizes absolutely or by percent (w or h 0.5 means 50%)
44: // angel herraez -- update of jmolResize(w,h,targetSuffix) so it is not tied to first applet
45: // bob hanson -- jmolEvaluate -- evaluates molecular math 8:37 AM 2/23/2007
46: // bob hanson -- jmolScriptMessage -- returns all "scriptStatus" messages 8:37 AM 2/23/2007
47: // bob hanson -- jmolScriptEcho -- returns all "scriptEcho" messages 8:37 AM 2/23/2007
48: // bob hanson -- jmolScriptWait -- 11:31 AM 5/2/2006
49: // bob hanson -- remove trailing separatorHTML in radio groups -- 12:18 PM 5/6/2006
50: // bob hanson -- adds support for dynamic DOM script nodes 7:04 AM 5/19/2006
51: // bob hanson -- adds try/catch for wiki - multiple code passes 7:05 AM 5/19/2006
52: // bob hanson -- auto-initiates to defaultdir/defaultjar -- change as desired.
53: // bob hanson -- adding save/restore orientation w/ and w/o delay 11:49 AM 5/25/2006
54: // bob hanson -- adding AjaxJS service 11:16 AM 6/3/2006
55: // bob hanson -- fix for iframes not available for finding applet
56: // bob hanson -- added applet fake ?NOAPPLET URL flag
57: // bob hanson -- added jmolSetCallback(calbackName, funcName) 3:32 PM 6/13/2006
58: // used PRIOR to jmolApplet() or jmolAppletInline()
59: // added 4th array element in jmolRadioGroup -- title
60: // added <span> and id around link, checkbox, radio, menu
61: // fixing AJAX loads for MSIE/Opera-Mozilla incompatibility
62: // -- renamed Jmol-11.js from Jmol-new.js; JmolApplet.jar from JmolAppletProto.jar
63: // renamed Jmol.js for Jmol 11 distribution
64: // -- modified jmolRestoreOrientation() to be immediate, no 1-second delay
65: // bob hanson -- jmolScriptWait always returns a string -- 11:23 AM 9/16/2006
66: // bh -- jmolCommandInput()
67: // bh -- jmolSetTranslation(TF) -- forces translation even if there might be message callback issues
68: // bh -- minor fixes suggested by Angel
69: // bh -- adds jmolSetSyncId() and jmolGetSyncId()
70: // bh 3/2008 -- adds jmolAppendInlineScript() and jmolAppendInlineArray()
71: // bh 3/2008 -- fixes IE7 bug in relation to jmolLoadInlineArray()
72: // bh 6/2008 -- adds jmolSetAppletWindow()
73: // Angel H. 6/2008 -- added html <label> tags to checkboxes and radio buttons [in jmolCheckbox() and _jmolRadio() functions]
74: // bh 7/2008 -- code fix "for(i..." not "for(var i..."
75: // bh 12/2008 -- jmolLoadInline, jmolLoadInlineArray, jmolLoadInlineScript, jmolAppendInlineScript, jmolAppendInlineArray all return error message or null (Jmol 11.7.16)
76: // bh 12/2008 -- jmolScriptWaitOutput() -- waits for script to complete and delivers output normally sent to console
77:
78: // bh 5/2009 -- Support for XHTML using jmolSetXHTML(id)
79: // ah & bh 6/2009 -- New jmolResizeApplet() more flexible, similar to jmolApplet() size syntax
80: // bh 11/2009 -- care in accessing top.document
81: // bh 12/2009 -- added jmolSetParameter(name, value)
82: // bh 12/2009 -- added PARAMS=name:value;name:value;name:value... for command line
83: // bh 12/2009 -- overhaul of target checking
84: // bh 1/2010 -- all _xxxx() methods ALWAYS have complete argument list
85: // bh 1/2010 -- adds option to run a JavaScript function from any Jmol control.
86: // This is accomplished by passing an array rather than a script:
87: // jmolHref([myfunc,"my param 1", "my param 2"], "testing")
88: // function myfunc(jmolControlObject, [myfunc,"my param 1", "my param 2"], target){...}
89: // and allows much more flexibility with responding to controls
90: // bh 4/2010 -- added jmolSetMemoryMb(nMb)
91: // ah 1/2011 -- wider detection of browsers; more browsers now use the object tag instead of the applet tag;
92: // fix of object tag (removed classid) accounts for change of behavior in Chrome
93: // bh 5/2013 -- fix for master checkbox click not actuating checkboxes
94:
95: var defaultdir = "."
96: var defaultjar = "JmolApplet.jar"
97:
98:
99: // Note added 12:41 PM 9/21/2008 by Bob Hanson, hansonr@stolaf.edu:
100:
101: // JMOLJAR=xxxxx.jar on the URL for this page will override
102: // the JAR file specified in the jmolInitialize() call.
103:
104: // The idea is that it can be very useful to test a web page with different JAR files
105: // Or for an expert user to substitute a signed applet for an unsigned one
106: // so as to use a broader range of models or to create JPEG files, for example.
107:
108: // If the JAR file is not in the current directory (has any sort of "/" in its name)
109: // then the user is presented with a warning and asked whether it is OK to change Jar files.
110: // The default action, if the user just presses "OK" is to NOT allow the change.
111: // The user must type the word "yes" in the prompt box for the change to be approved.
112:
113: // If you don't want people to be able to switch in their own JAR file on your page,
114: // simply set this next line to read "var allowJMOLJAR = false".
115:
116:
117: var undefined; // for IE 5 ... wherein undefined is undefined
118:
119: ////////////////////////////////////////////////////////////////
120: // Basic Scripting infrastruture
121: ////////////////////////////////////////////////////////////////
122:
123: function jmolInitialize(codebaseDirectory, fileNameOrUseSignedApplet) {
124: if (_jmol.initialized)
125: return;
126: _jmol.initialized = true;
127: if(_jmol.jmoljar) {
128: var f = _jmol.jmoljar;
129: if (f.indexOf("/") >= 0) {
130: alert ("This web page URL is requesting that the applet used be " + f + ". This is a possible security risk, particularly if the applet is signed, because signed applets can read and write files on your local machine or network.")
131: var ok = prompt("Do you want to use applet " + f + "? ","yes or no")
132: if (ok == "yes") {
133: codebaseDirectory = f.substring(0, f.lastIndexOf("/"));
134: fileNameOrUseSignedApplet = f.substring(f.lastIndexOf("/") + 1);
135: } else {
136: _jmolGetJarFilename(fileNameOrUseSignedApplet);
137: alert("The web page URL was ignored. Continuing using " + _jmol.archivePath + ' in directory "' + codebaseDirectory + '"');
138: }
139: } else {
140: fileNameOrUseSignedApplet = f;
141: }
142: }
143: _jmolSetCodebase(codebaseDirectory);
144: _jmolGetJarFilename(fileNameOrUseSignedApplet);
145: _jmolOnloadResetForms();
146: }
147:
148: function jmolSetTranslation(TF) {
149: _jmol.params.doTranslate = ''+TF;
150: }
151:
152: function _jmolGetJarFilename(fileNameOrFlag) {
153: _jmol.archivePath =
154: (typeof(fileNameOrFlag) == "string" ? fileNameOrFlag : (fileNameOrFlag ? "JmolAppletSigned" : "JmolApplet") + "0.jar");
155: }
156:
157: function jmolSetDocument(doc) {
158: _jmol.currentDocument = doc;
159: }
160:
161: function jmolSetAppletColor(boxbgcolor, boxfgcolor, progresscolor) {
162: _jmolInitCheck();
163: _jmol.params.boxbgcolor = boxbgcolor;
164: if (boxfgcolor)
165: _jmol.params.boxfgcolor = boxfgcolor
166: else if (boxbgcolor == "white" || boxbgcolor == "#FFFFFF")
167: _jmol.params.boxfgcolor = "black";
168: else
169: _jmol.params.boxfgcolor = "white";
170: if (progresscolor)
171: _jmol.params.progresscolor = progresscolor;
172: if (_jmol.debugAlert)
173: alert(" boxbgcolor=" + _jmol.params.boxbgcolor +
174: " boxfgcolor=" + _jmol.params.boxfgcolor +
175: " progresscolor=" + _jmol.params.progresscolor);
176: }
177:
178: function jmolSetAppletWindow(w) {
179: _jmol.appletWindow = w;
180: }
181:
182: function jmolApplet(size, script, nameSuffix) {
183: _jmolInitCheck();
184: return _jmolApplet(size, null, script, nameSuffix);
185: }
186:
187: ////////////////////////////////////////////////////////////////
188: // Basic controls
189: ////////////////////////////////////////////////////////////////
190:
191: // undefined means it wasn't there; null means it was explicitly listed as null (so as to skip it)
192:
193: function jmolButton(script, label, id, title) {
194: _jmolInitCheck();
195: id != undefined && id != null || (id = "jmolButton" + _jmol.buttonCount);
196: label != undefined && label != null || (label = script.substring(0, 32));
197: ++_jmol.buttonCount;
198: var scriptIndex = _jmolAddScript(script);
199: var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input type='button' name='" + id + "' id='" + id +
200: "' value='" + label +
201: "' onclick='_jmolClick(this," + scriptIndex + _jmol.targetText +
202: ")' onmouseover='_jmolMouseOver(" + scriptIndex +
203: ");return true' onmouseout='_jmolMouseOut()' " +
204: _jmol.buttonCssText + " /></span>";
205: if (_jmol.debugAlert)
206: alert(t);
207: return _jmolDocumentWrite(t);
208: }
209:
210: function jmolCheckbox(scriptWhenChecked, scriptWhenUnchecked,
211: labelHtml, isChecked, id, title) {
212: _jmolInitCheck();
213: id != undefined && id != null || (id = "jmolCheckbox" + _jmol.checkboxCount);
214: ++_jmol.checkboxCount;
215: if (scriptWhenChecked == undefined || scriptWhenChecked == null ||
216: scriptWhenUnchecked == undefined || scriptWhenUnchecked == null) {
217: alert("jmolCheckbox requires two scripts");
218: return;
219: }
220: if (labelHtml == undefined || labelHtml == null) {
221: alert("jmolCheckbox requires a label");
222: return;
223: }
224: var indexChecked = _jmolAddScript(scriptWhenChecked);
225: var indexUnchecked = _jmolAddScript(scriptWhenUnchecked);
226: var eospan = "</span>"
227: var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input type='checkbox' name='" + id + "' id='" + id +
228: "' onclick='_jmolCbClick(this," +
229: indexChecked + "," + indexUnchecked + _jmol.targetText +
230: ")' onmouseover='_jmolCbOver(this," + indexChecked + "," +
231: indexUnchecked +
232: ");return true' onmouseout='_jmolMouseOut()' " +
233: (isChecked ? "checked='true' " : "")+ _jmol.checkboxCssText + " />"
234: if (labelHtml.toLowerCase().indexOf("<td>")>=0) {
235: t += eospan
236: eospan = "";
237: }
238: t += "<label for=\"" + id + "\">" + labelHtml + "</label>" +eospan;
239: if (_jmol.debugAlert)
240: alert(t);
241: return _jmolDocumentWrite(t);
242: }
243:
244: function jmolStartNewRadioGroup() {
245: ++_jmol.radioGroupCount;
246: }
247:
248: function jmolRadioGroup(arrayOfRadioButtons, separatorHtml, groupName, id, title) {
249: /*
250:
251: array: [radio1,radio2,radio3...]
252: where radioN = ["script","label",isSelected,"id","title"]
253:
254: */
255:
256: _jmolInitCheck();
257: var type = typeof arrayOfRadioButtons;
258: if (type != "object" || type == null || ! arrayOfRadioButtons.length) {
259: alert("invalid arrayOfRadioButtons");
260: return;
261: }
262: separatorHtml != undefined && separatorHtml != null || (separatorHtml = " ");
263: var len = arrayOfRadioButtons.length;
264: jmolStartNewRadioGroup();
265: groupName || (groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1));
266: var t = "<span id='"+(id ? id : groupName)+"'>";
267: for (var i = 0; i < len; ++i) {
268: if (i == len - 1)
269: separatorHtml = "";
270: var radio = arrayOfRadioButtons[i];
271: type = typeof radio;
272: if (type == "object") {
273: t += _jmolRadio(radio[0], radio[1], radio[2], separatorHtml, groupName, (radio.length > 3 ? radio[3]: (id ? id : groupName)+"_"+i), (radio.length > 4 ? radio[4] : 0), title);
274: } else {
275: t += _jmolRadio(radio, null, null, separatorHtml, groupName, (id ? id : groupName)+"_"+i, title);
276: }
277: }
278: t+="</span>"
279: if (_jmol.debugAlert)
280: alert(t);
281: return _jmolDocumentWrite(t);
282: }
283:
284:
285: function jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {
286: _jmolInitCheck();
287: if (_jmol.radioGroupCount == 0)
288: ++_jmol.radioGroupCount;
289: var t = _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, (id ? id : groupName + "_" + _jmol.radioCount), title ? title : 0);
290: if (_jmol.debugAlert)
291: alert(t);
292: return _jmolDocumentWrite(t);
293: }
294:
295: function jmolLink(script, label, id, title) {
296: _jmolInitCheck();
297: id != undefined && id != null || (id = "jmolLink" + _jmol.linkCount);
298: label != undefined && label != null || (label = script.substring(0, 32));
299: ++_jmol.linkCount;
300: var scriptIndex = _jmolAddScript(script);
301: var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><a name='" + id + "' id='" + id +
302: "' href='javascript:_jmolClick(this," + scriptIndex + _jmol.targetText + ");' onmouseover='_jmolMouseOver(" + scriptIndex +
303: ");return true;' onmouseout='_jmolMouseOut()' " +
304: _jmol.linkCssText + ">" + label + "</a></span>";
305: if (_jmol.debugAlert)
306: alert(t);
307: return _jmolDocumentWrite(t);
308: }
309:
310: function jmolCommandInput(label, size, id, title) {
311: _jmolInitCheck();
312: id != undefined && id != null || (id = "jmolCmd" + _jmol.cmdCount);
313: label != undefined && label != null || (label = "Execute");
314: size != undefined && !isNaN(size) || (size = 60);
315: ++_jmol.cmdCount;
316: var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input name='" + id + "' id='" + id +
317: "' size='"+size+"' onkeypress='_jmolCommandKeyPress(event,\""+id+"\"" + _jmol.targetText + ")'><input type=button value = '"+label+"' onclick='jmolScript(document.getElementById(\""+id+"\").value" + _jmol.targetText + ")' /></span>";
318: if (_jmol.debugAlert)
319: alert(t);
320: return _jmolDocumentWrite(t);
321: }
322:
323: function _jmolCommandKeyPress(e, id, target) {
324: var keycode = (window.event ? window.event.keyCode : e ? e.which : 0);
325: if (keycode == 13) {
326: var inputBox = document.getElementById(id)
327: _jmolScriptExecute(inputBox, inputBox.value, target)
328: }
329: }
330:
331: function _jmolScriptExecute(element,script,target) {
332: if (typeof(script) == "object")
333: script[0](element, script, target)
334: else if (typeof(script) == "function")
335: script(target);
336: else
337: jmolScript(script, target)
338: }
339:
340: function jmolMenu(arrayOfMenuItems, size, id, title) {
341: _jmolInitCheck();
342: id != undefined && id != null || (id = "jmolMenu" + _jmol.menuCount);
343: ++_jmol.menuCount;
344: var type = typeof arrayOfMenuItems;
345: if (type != null && type == "object" && arrayOfMenuItems.length) {
346: var len = arrayOfMenuItems.length;
347: if (typeof size != "number" || size == 1)
348: size = null;
349: else if (size < 0)
350: size = len;
351: var sizeText = size ? " size='" + size + "' " : "";
352: var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><select name='" + id + "' id='" + id +
353: "' onChange='_jmolMenuSelected(this" + _jmol.targetText + ")'" +
354: sizeText + _jmol.menuCssText + ">";
355: for (var i = 0; i < len; ++i) {
356: var menuItem = arrayOfMenuItems[i];
357: type = typeof menuItem;
358: var script, text;
359: var isSelected = undefined;
360: if (type == "object" && menuItem != null) {
361: script = menuItem[0];
362: text = menuItem[1];
363: isSelected = menuItem[2];
364: } else {
365: script = text = menuItem;
366: }
367: text != undefined && text != null || (text = script);
368: if (script=="#optgroup") {
369: t += "<optgroup label='" + text + "'>";
370: } else if (script=="#optgroupEnd") {
371: t += "</optgroup>";
372: } else {
373: var scriptIndex = _jmolAddScript(script);
374: var selectedText = isSelected ? "' selected='true'>" : "'>";
375: t += "<option value='" + scriptIndex + selectedText + text + "</option>";
376: }
377: }
378: t += "</select></span>";
379: if (_jmol.debugAlert)
380: alert(t);
381: return _jmolDocumentWrite(t);
382: }
383: }
384:
385: function jmolHtml(html) {
386: return _jmolDocumentWrite(html);
387: }
388:
389: function jmolBr() {
390: return _jmolDocumentWrite("<br />");
391: }
392:
393: ////////////////////////////////////////////////////////////////
394: // advanced scripting functions
395: ////////////////////////////////////////////////////////////////
396:
397: function jmolDebugAlert(enableAlerts) {
398: _jmol.debugAlert = (enableAlerts == undefined || enableAlerts)
399: }
400:
401: function jmolAppletInline(size, inlineModel, script, nameSuffix) {
402: _jmolInitCheck();
403: return _jmolApplet(size, _jmolSterilizeInline(inlineModel),
404: script, nameSuffix);
405: }
406:
407: function jmolSetTarget(targetSuffix) {
408: _jmol.targetSuffix = targetSuffix;
409: _jmol.targetText = targetSuffix ? ",\"" + targetSuffix + "\"" : ",0";
410: }
411:
412: function jmolScript(script, targetSuffix) {
413: if (script) {
414: _jmolCheckBrowser();
415: if (targetSuffix == "all") {
416: with (_jmol) {
417: for (var i = 0; i < appletSuffixes.length; ++i) {
418: var applet = _jmolGetApplet(appletSuffixes[i]);
419: if (applet) applet.script(script);
420: }
421: }
422: } else {
423: var applet=_jmolGetApplet(targetSuffix);
424: if (applet) applet.script(script);
425: }
426: }
427: }
428:
429: function jmolLoadInline(model, targetSuffix) {
430: if (!model)return "ERROR: NO MODEL"
431: var applet=_jmolGetApplet(targetSuffix);
432: if (!applet)return "ERROR: NO APPLET"
433: if (typeof(model) == "string")
434: return applet.loadInlineString(model, "", false);
435: else
436: return applet.loadInlineArray(model, "", false);
437: }
438:
439:
440: function jmolLoadInlineScript(model, script, targetSuffix) {
441: if (!model)return "ERROR: NO MODEL"
442: var applet=_jmolGetApplet(targetSuffix);
443: if (!applet)return "ERROR: NO APPLET"
444: return applet.loadInlineString(model, script, false);
445: }
446:
447:
448: function jmolLoadInlineArray(ModelArray, script, targetSuffix) {
449: if (!model)return "ERROR: NO MODEL"
450: script || (script="")
451: var applet=_jmolGetApplet(targetSuffix);
452: if (!applet)return "ERROR: NO APPLET"
453: try {
454: return applet.loadInlineArray(ModelArray, script, false);
455: } catch (err) {
456: //IE 7 bug
457: return applet.loadInlineString(ModelArray.join("\n"), script, false);
458: }
459: }
460:
461: function jmolAppendInlineArray(ModelArray, script, targetSuffix) {
462: if (!model)return "ERROR: NO MODEL"
463: script || (script="")
464: var applet=_jmolGetApplet(targetSuffix);
465: if (!applet)return "ERROR: NO APPLET"
466: try {
467: return applet.loadInlineArray(ModelArray, script, true);
468: } catch (err) {
469: //IE 7 bug
470: return applet.loadInlineString(ModelArray.join("\n"), script, true);
471: }
472: }
473:
474: function jmolAppendInlineScript(model, script, targetSuffix) {
475: if (!model)return "ERROR: NO MODEL"
476: var applet=_jmolGetApplet(targetSuffix);
477: if (!applet)return "ERROR: NO APPLET"
478: return applet.loadInlineString(model, script, true);
479: }
480:
481: function jmolCheckBrowser(action, urlOrMessage, nowOrLater) {
482: if (typeof action == "string") {
483: action = action.toLowerCase();
484: action == "alert" || action == "redirect" || action == "popup" || (action = null);
485: }
486: if (typeof action != "string")
487: alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" +
488: "action must be 'alert', 'redirect', or 'popup'");
489: else {
490: if (typeof urlOrMessage != "string")
491: alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" +
492: "urlOrMessage must be a string");
493: else {
494: _jmol.checkBrowserAction = action;
495: _jmol.checkBrowserUrlOrMessage = urlOrMessage;
496: }
497: }
498: if (typeof nowOrLater == "string" && nowOrLater.toLowerCase() == "now")
499: _jmolCheckBrowser();
500: }
501:
502: ////////////////////////////////////////////////////////////////
503: // Cascading Style Sheet Class support
504: ////////////////////////////////////////////////////////////////
505:
506: function jmolSetAppletCssClass(appletCssClass) {
507: if (_jmol.hasGetElementById) {
508: _jmol.appletCssClass = appletCssClass;
509: _jmol.appletCssText = appletCssClass ? "class='" + appletCssClass + "' " : "";
510: }
511: }
512:
513: function jmolSetButtonCssClass(buttonCssClass) {
514: if (_jmol.hasGetElementById) {
515: _jmol.buttonCssClass = buttonCssClass;
516: _jmol.buttonCssText = buttonCssClass ? "class='" + buttonCssClass + "' " : "";
517: }
518: }
519:
520: function jmolSetCheckboxCssClass(checkboxCssClass) {
521: if (_jmol.hasGetElementById) {
522: _jmol.checkboxCssClass = checkboxCssClass;
523: _jmol.checkboxCssText = checkboxCssClass ? "class='" + checkboxCssClass + "' " : "";
524: }
525: }
526:
527: function jmolSetRadioCssClass(radioCssClass) {
528: if (_jmol.hasGetElementById) {
529: _jmol.radioCssClass = radioCssClass;
530: _jmol.radioCssText = radioCssClass ? "class='" + radioCssClass + "' " : "";
531: }
532: }
533:
534: function jmolSetLinkCssClass(linkCssClass) {
535: if (_jmol.hasGetElementById) {
536: _jmol.linkCssClass = linkCssClass;
537: _jmol.linkCssText = linkCssClass ? "class='" + linkCssClass + "' " : "";
538: }
539: }
540:
541: function jmolSetMenuCssClass(menuCssClass) {
542: if (_jmol.hasGetElementById) {
543: _jmol.menuCssClass = menuCssClass;
544: _jmol.menuCssText = menuCssClass ? "class='" + menuCssClass + "' " : "";
545: }
546: }
547:
548: ////////////////////////////////////////////////////////////////
549: // functions for INTERNAL USE ONLY which are subject to change
550: // use at your own risk ... you have been WARNED!
551: ////////////////////////////////////////////////////////////////
552: var _jmol = {
553: currentDocument: document,
554:
555: debugAlert: false,
556:
557: codebase: "",
558: modelbase: ".",
559:
560: appletCount: 0,
561: appletSuffixes: [],
562: appletWindow: null,
563: allowedJmolSize: [25, 2048, 300], // min, max, default (pixels)
564: /* By setting the _jmol.allowedJmolSize[] variable in the webpage
565: before calling jmolApplet(), limits for applet size can be overriden.
566: 2048 standard for GeoWall (http://geowall.geo.lsa.umich.edu/home.html)
567: */
568: buttonCount: 0,
569: checkboxCount: 0,
570: linkCount: 0,
571: cmdCount: 0,
572: menuCount: 0,
573: radioCount: 0,
574: radioGroupCount: 0,
575:
576: appletCssClass: null,
577: appletCssText: "",
578: buttonCssClass: null,
579: buttonCssText: "",
580: checkboxCssClass: null,
581: checkboxCssText: "",
582: java_arguments: "-Xmx512m",
583: radioCssClass: null,
584: radioCssText: "",
585: linkCssClass: null,
586: linkCssText: "",
587: menuCssClass: null,
588: menuCssText: "",
589:
590: targetSuffix: 0,
591: targetText: ",0",
592: scripts: [""],
593: params: {
594: syncId: ("" + Math.random()).substring(3),
595: progressbar: "true",
596: progresscolor: "blue",
597: boxbgcolor: "black",
598: boxfgcolor: "white",
599: boxmessage: "Downloading JmolApplet ..."
600: },
601: ua: navigator.userAgent.toLowerCase(),
602: // uaVersion: parseFloat(navigator.appVersion), // not used
603:
604: os: "unknown",
605: browser: "unknown",
606: browserVersion: 0,
607: hasGetElementById: !!document.getElementById,
608: isJavaEnabled: navigator.javaEnabled(),
609: // isNetscape47Win: false, // not used, N4.7 is no longer supported even for detection
610: useIEObject: false,
611: useHtml4Object: false,
612:
613: windowsClassId: "clsid:8AD9C840-044E-11D1-B3E9-00805F499D93",
614: windowsCabUrl:
615: "http://java.sun.com/update/1.6.0/jinstall-6u22-windows-i586.cab",
616:
617: isBrowserCompliant: false,
618: isJavaCompliant: false,
619: isFullyCompliant: false,
620:
621: initialized: false,
622: initChecked: false,
623:
624: browserChecked: false,
625: checkBrowserAction: "alert",
626: checkBrowserUrlOrMessage: null,
627:
628: archivePath: null, // JmolApplet0.jar OR JmolAppletSigned0.jar
629:
630: previousOnloadHandler: null,
631:
632: jmoljar: null,
633: useNoApplet: false,
634:
635: ready: {}
636: }
637:
638: with (_jmol) {
639: function _jmolTestUA(candidate) {
640: var ua = _jmol.ua;
641: var index = ua.indexOf(candidate);
642: if (index < 0)
643: return false;
644: _jmol.browser = candidate;
645: _jmol.browserVersion = parseFloat(ua.substring(index+candidate.length+1));
646: return true;
647: }
648:
649: function _jmolTestOS(candidate) {
650: if (_jmol.ua.indexOf(candidate) < 0)
651: return false;
652: _jmol.os = candidate;
653: return true;
654: }
655:
656: _jmolTestUA("konqueror") ||
657: _jmolTestUA("webkit") ||
658: _jmolTestUA("omniweb") ||
659: _jmolTestUA("opera") ||
660: _jmolTestUA("webtv") ||
661: _jmolTestUA("icab") ||
662: _jmolTestUA("msie") ||
663: (_jmol.ua.indexOf("compatible") < 0 && _jmolTestUA("mozilla")); //Netscape, Mozilla, Seamonkey, Firefox and anything assimilated
664:
665: _jmolTestOS("linux") ||
666: _jmolTestOS("unix") ||
667: _jmolTestOS("mac") ||
668: _jmolTestOS("win");
669:
670: isBrowserCompliant = hasGetElementById;
671: // known exceptions (old browsers):
672: if (browser == "opera" && browserVersion <= 7.54 && os == "mac"
673: || browser == "webkit" && browserVersion < 125.12
674: || browser == "msie" && os == "mac"
675: || browser == "konqueror" && browserVersion <= 3.3
676: ) {
677: isBrowserCompliant = false;
678: }
679:
680: // possibly more checks in the future for this
681: isJavaCompliant = isJavaEnabled;
682:
683: isFullyCompliant = isBrowserCompliant && isJavaCompliant;
684:
685: useIEObject = (os == "win" && browser == "msie" && browserVersion >= 5.5);
686: useHtml4Object =
687: (browser == "mozilla" && browserVersion >= 5) ||
688: (browser == "opera" && browserVersion >= 8) ||
689: (browser == "webkit" && browserVersion >= 412.2);
690: try {
691: if (top.location.search.indexOf("JMOLJAR=")>=0)
692: jmoljar = top.location.search.split("JMOLJAR=")[1].split("&")[0];
693: } catch(e) {
694: // can't access top.location
695: }
696: try {
697: useNoApplet = (top.location.search.indexOf("NOAPPLET")>=0);
698: } catch(e) {
699: // can't access top.document
700: }
701: }
702:
703: function jmolSetMemoryMb(nMb) {
704: _jmol.java_arguments = "-Xmx" + Math.round(nMb) + "m"
705: }
706:
707: function jmolSetParameter(name,value) {
708: _jmol.params[name] = value
709: }
710:
711: function jmolSetCallback(callbackName,funcName) {
712: _jmol.params[callbackName] = funcName
713: }
714:
715: try {
716: // note this is done FIRST, so it cannot override a setting done by the developer
717: if (top.location.search.indexOf("PARAMS=")>=0) {
718: var pars = unescape(top.location.search.split("PARAMS=")[1].split("&")[0]).split(";");
719: for (var i = 0; i < pars.length; i++) {
720: var p = pars[i].split(":");
721: jmolSetParameter(p[0],p[1]);
722: }
723: }
724: } catch(e) {
725: // can't access top.location
726: }
727:
728: function jmolSetSyncId(n) {
729: return _jmol.params["syncId"] = n
730: }
731:
732: function jmolGetSyncId() {
733: return _jmol.params["syncId"]
734: }
735:
736: function jmolSetLogLevel(n) {
737: _jmol.params.logLevel = ''+n;
738: }
739:
740: /* AngelH, mar2007:
741: By (re)setting these variables in the webpage before calling jmolApplet(),
742: a custom message can be provided (e.g. localized for user's language) when no Java is installed.
743: */
744: if (noJavaMsg==undefined) var noJavaMsg =
745: "You do not have Java applets enabled in your web browser, or your browser is blocking this applet.<br />\n" +
746: "Check the warning message from your browser and/or enable Java applets in<br />\n" +
747: "your web browser preferences, or install the Java Runtime Environment from <a href='http://www.java.com'>www.java.com</a><br />";
748: if (noJavaMsg2==undefined) var noJavaMsg2 =
749: "You do not have the<br />\n" +
750: "Java Runtime Environment<br />\n" +
751: "installed for applet support.<br />\n" +
752: "Visit <a href='http://www.java.com'>www.java.com</a>";
753: function _jmolApplet(size, inlineModel, script, nameSuffix) {
754: /* AngelH, mar2007
755: Fixed percent / pixel business, to avoid browser errors:
756: put "px" where needed, avoid where not.
757:
758: Bob Hanson, 1/2010
759: Fixed inline escape changing returns to |
760: */
761: with (_jmol) {
762: nameSuffix == undefined && (nameSuffix = appletCount);
763: appletSuffixes.push(nameSuffix);
764: ++appletCount;
765: script || (script = "select *");
766: var sz = _jmolGetAppletSize(size);
767: var widthAndHeight = " width='" + sz[0] + "' height='" + sz[1] + "' ";
768: var tHeader, tFooter;
769: codebase || jmolInitialize(".");
770: params.name = "jmolApplet" + nameSuffix
771: params.permissions = (archivePath.indexOf("Signed") >= 0 ? "all-permissions" : "sandbox");
772:
773: if (useIEObject || useHtml4Object) {
774: params.archive = archivePath;
775: params.mayscript = 'true';
776: params.codebase = codebase;
777: params.code = 'JmolApplet.class';
778: tHeader =
779: "<object name='jmolApplet" + nameSuffix +
780: "' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +
781: widthAndHeight + "\n";
782: tFooter = "</object>";
783: }
784: if (java_arguments)
785: params.java_arguments = java_arguments;
786: if (useIEObject) { // use MSFT IE6 object tag with .cab file reference
787: tHeader += " classid='" + windowsClassId + "'\n" +
788: (windowsCabUrl ? " codebase='" + windowsCabUrl + "'\n" : "") + ">\n";
789: } else if (useHtml4Object) { // use HTML4 object tag
790: tHeader += " type='application/x-java-applet'\n>\n";
791: /* " classid='java:JmolApplet'\n" + AH removed this
792: Chromium Issue 62076: Java Applets using an <object> with a classid paramater don't load.
793: http://code.google.com/p/chromium/issues/detail?id=62076
794: They say this is the correct behavior according to the spec, and there's no indication at this point
795: that WebKit will be changing the handling, so eventually Safari will acquire this behavior too.
796: Removing the classid parameter seems to be well tolerated by all browsers (even IE!).
797: */
798: } else { // use applet tag
799: tHeader =
800: "<applet name='jmolApplet" + nameSuffix +
801: "' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +
802: widthAndHeight + "\n" +
803: " code='JmolApplet'" +
804: " archive='" + archivePath + "' codebase='" + codebase + "'\n" +
805: " mayscript='true'>\n";
806: tFooter = "</applet>";
807: }
808: var visitJava;
809: if (useIEObject || useHtml4Object) {
810: var szX = "width:" + sz[0]
811: if ( szX.indexOf("%")==-1 ) szX+="px"
812: var szY = "height:" + sz[1]
813: if ( szY.indexOf("%")==-1 ) szY+="px"
814: visitJava =
815: "<p style='background-color:yellow; color:black; " +
816: szX + ";" + szY + ";" +
817: // why doesn't this vertical-align work?
818: "text-align:center;vertical-align:middle;'>\n" +
819: noJavaMsg +
820: "</p>";
821: } else {
822: visitJava =
823: "<table bgcolor='yellow'><tr>" +
824: "<td align='center' valign='middle' " + widthAndHeight + "><font color='black'>\n" +
825: noJavaMsg2 +
826: "</font></td></tr></table>";
827: }
828: params.loadInline = (inlineModel ? inlineModel : "");
829: params.script = (script ? _jmolSterilizeScript(script) : "");
830: var t = tHeader + _jmolParams() + visitJava + tFooter;
831: jmolSetTarget(nameSuffix);
832: ready["jmolApplet" + nameSuffix] = false;
833: if (_jmol.debugAlert)
834: alert(t);
835: return _jmolDocumentWrite(t);
836: }
837: }
838:
839: function _jmolParams() {
840: var t = "";
841: for (var i in _jmol.params)
842: if(_jmol.params[i]!="")
843: t+=" <param name='"+i+"' value='"+_jmol.params[i]+"' />\n";
844: return t
845: }
846:
847: function _jmolInitCheck() {
848: if (_jmol.initChecked)
849: return;
850: _jmol.initChecked = true;
851: jmolInitialize(defaultdir, defaultjar)
852: }
853:
854: function _jmolCheckBrowser() {
855: with (_jmol) {
856: if (browserChecked)
857: return;
858: browserChecked = true;
859:
860: if (isFullyCompliant)
861: return true;
862:
863: if (checkBrowserAction == "redirect")
864: location.href = checkBrowserUrlOrMessage;
865: else if (checkBrowserAction == "popup")
866: _jmolPopup(checkBrowserUrlOrMessage);
867: else {
868: var msg = checkBrowserUrlOrMessage;
869: if (msg == null)
870: msg = "Your web browser is not fully compatible with Jmol\n\n" +
871: "browser: " + browser +
872: " version: " + browserVersion +
873: " os: " + os +
874: " isBrowserCompliant: " + isBrowserCompliant +
875: " isJavaCompliant: " + isJavaCompliant +
876: "\n\n" + ua;
877: alert(msg);
878: }
879: }
880: return false;
881: }
882:
883: function jmolSetXHTML(id) {
884: _jmol.isXHTML = true
885: _jmol.XhtmlElement = null
886: _jmol.XhtmlAppendChild = false
887: if (id){
888: _jmol.XhtmlElement = document.getElementById(id)
889: _jmol.XhtmlAppendChild = true
890: }
891: }
892:
893: function _jmolDocumentWrite(text) {
894: if (_jmol.currentDocument) {
895: if (_jmol.isXHTML && !_jmol.XhtmlElement) {
896: var s = document.getElementsByTagName("script")
897: _jmol.XhtmlElement = s.item(s.length - 1)
898: _jmol.XhtmlAppendChild = false
899: }
900: if (_jmol.XhtmlElement) {
901: _jmolDomDocumentWrite(text)
902: } else {
903: _jmol.currentDocument.write(text);
904: }
905: }
906: return text;
907: }
908:
909: function _jmolDomDocumentWrite(data) {
910: var pt = 0
911: var Ptr = []
912: Ptr[0] = 0
913: while (Ptr[0] < data.length) {
914: var child = _jmolGetDomElement(data, Ptr)
915: if (!child)break
916: if (_jmol.XhtmlAppendChild)
917: _jmol.XhtmlElement.appendChild(child)
918: else
919: _jmol.XhtmlElement.parentNode.insertBefore(child, _jmol.XhtmlElement);
920: }
921: }
922: function _jmolGetDomElement(data, Ptr, closetag, lvel) {
923: var e = document.createElement("span")
924: e.innerHTML = data
925: Ptr[0] = data.length
926: return e
927:
928: //unnecessary?
929:
930: closetag || (closetag = "")
931: lvel || (lvel = 0)
932: var pt0 = Ptr[0]
933: var pt = pt0
934: while (pt < data.length && data.charAt(pt) != "<") pt++
935: if (pt != pt0) {
936: var text = data.substring(pt0, pt)
937: Ptr[0] = pt
938: return document.createTextNode(text)
939: }
940: pt0 = ++pt
941: var ch
942: while (pt < data.length && "\n\r\t >".indexOf(ch = data.charAt(pt)) < 0) pt++
943: var tagname = data.substring(pt0, pt)
944: var e = (tagname == closetag || tagname == "/" ? ""
945: : document.createElementNS ? document.createElementNS('http://www.w3.org/1999/xhtml', tagname)
946: : document.createElement(tagname));
947: if (ch == ">") {
948: Ptr[0] = ++pt
949: return e
950: }
951: while (pt < data.length && (ch = data.charAt(pt)) != ">") {
952: while (pt < data.length && "\n\r\t ".indexOf(ch = data.charAt(pt)) >= 0) pt++
953: pt0 = pt
954: while (pt < data.length && "\n\r\t =/>".indexOf(ch = data.charAt(pt)) < 0) pt++
955: var attrname = data.substring(pt0, pt).toLowerCase()
956: if (attrname && ch != "=")
957: e.setAttribute(attrname, "true")
958: while (pt < data.length && "\n\r\t ".indexOf(ch = data.charAt(pt)) >= 0) pt++
959: if (ch == "/") {
960: Ptr[0] = pt + 2
961: return e
962: } else if (ch == "=") {
963: var quote = data.charAt(++pt)
964: pt0 = ++pt
965: while (pt < data.length && (ch = data.charAt(pt)) != quote) pt++
966: var attrvalue = data.substring(pt0, pt)
967: e.setAttribute(attrname, attrvalue)
968: pt++
969: }
970: }
971: Ptr[0] = ++pt
972: while (Ptr[0] < data.length) {
973: var child = _jmolGetDomElement(data, Ptr, "/" + tagname, lvel+1)
974: if (!child)break
975: e.appendChild(child)
976: }
977: return e
978: }
979:
980: function _jmolPopup(url) {
981: var popup = window.open(url, "JmolPopup",
982: "left=150,top=150,height=400,width=600," +
983: "directories=yes,location=yes,menubar=yes," +
984: "toolbar=yes," +
985: "resizable=yes,scrollbars=yes,status=yes");
986: if (popup.focus)
987: poup.focus();
988: }
989:
990: function _jmolReadyCallback(name) {
991: if (_jmol.debugAlert)
992: alert(name + " is ready");
993: _jmol.ready["" + name] = true;
994: }
995:
996: function _jmolSterilizeScript(script) {
997: script = script.replace(/'/g, "'");
998: if (_jmol.debugAlert)
999: alert("script:\n" + script);
1000: return script;
1001: }
1002:
1003: function _jmolSterilizeInline(model) {
1004: model = model.replace(/\r|\n|\r\n/g, (model.indexOf("|") >= 0 ? "\\/n" : "|")).replace(/'/g, "'");
1005: if (_jmol.debugAlert)
1006: alert("inline model:\n" + model);
1007: return model;
1008: }
1009:
1010: function _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {
1011: ++_jmol.radioCount;
1012: groupName != undefined && groupName != null || (groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1));
1013: if (!script)
1014: return "";
1015: labelHtml != undefined && labelHtml != null || (labelHtml = script.substring(0, 32));
1016: separatorHtml || (separatorHtml = "")
1017: var scriptIndex = _jmolAddScript(script);
1018: var eospan = "</span>"
1019: var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input name='"
1020: + groupName + "' id='"+id+"' type='radio' onclick='_jmolClick(this," +
1021: scriptIndex + _jmol.targetText + ");return true;' onmouseover='_jmolMouseOver(" +
1022: scriptIndex + ");return true;' onmouseout='_jmolMouseOut()' " +
1023: (isChecked ? "checked='true' " : "") + _jmol.radioCssText + " />"
1024: if (labelHtml.toLowerCase().indexOf("<td>")>=0) {
1025: t += eospan
1026: eospan = "";
1027: }
1028: t += "<label for=\"" + id + "\">" + labelHtml + "</label>" +eospan + separatorHtml;
1029:
1030: return t;
1031: }
1032:
1033: function _jmolFindApplet(target) {
1034: // first look for the target in the current window
1035: var applet = _jmolFindAppletInWindow(_jmol.appletWindow != null ? _jmol.appletWindow : window, target);
1036: // THEN look for the target in child frames
1037: if (applet == undefined)
1038: applet = _jmolSearchFrames(window, target);
1039: // FINALLY look for the target in sibling frames
1040: if (applet == undefined)
1041: applet = _jmolSearchFrames(top, target); // look starting in top frame
1042: return applet;
1043: }
1044:
1045: function _jmolGetApplet(targetSuffix){
1046: var target = "jmolApplet" + (targetSuffix ? targetSuffix : "0");
1047: var applet = _jmolFindApplet(target);
1048: if (applet) return applet
1049: _jmol.alerted || alert("could not find applet " + target);
1050: _jmol.alerted = true;
1051: return null
1052: }
1053:
1054: function _jmolSearchFrames(win, target) {
1055: var applet;
1056: var frames = win.frames;
1057: if (frames && frames.length) { // look in all the frames below this window
1058: try{
1059: for (var i = 0; i < frames.length; ++i) {
1060: applet = _jmolSearchFrames(frames[i], target);
1061: if (applet)
1062: return applet;
1063: }
1064: }catch(e) {
1065: if (_jmol.debugAlert)
1066: alert("Jmol.js _jmolSearchFrames cannot access " + win.name + ".frame[" + i + "] consider using jmolSetAppletWindow()")
1067: }
1068: }
1069: return applet = _jmolFindAppletInWindow(win, target)
1070: }
1071:
1072: function _jmolFindAppletInWindow(win, target) {
1073: var doc = win.document;
1074: if (doc.getElementById(target))
1075: return doc.getElementById(target);
1076: if (doc.applets)
1077: return doc.applets[target];
1078: return doc[target];
1079: }
1080:
1081: function _jmolAddScript(script) {
1082: if (!script)
1083: return 0;
1084: var index = _jmol.scripts.length;
1085: _jmol.scripts[index] = script;
1086: return index;
1087: }
1088:
1089: function _jmolClick(elementClicked, scriptIndex, targetSuffix) {
1090: _jmol.element = elementClicked;
1091: _jmolScriptExecute(elementClicked, _jmol.scripts[scriptIndex], targetSuffix);
1092: }
1093:
1094: function _jmolMenuSelected(menuObject, targetSuffix) {
1095: var scriptIndex = menuObject.value;
1096: if (scriptIndex != undefined) {
1097: _jmolScriptExecute(menuObject, _jmol.scripts[scriptIndex], targetSuffix);
1098: return;
1099: }
1100: var len = menuObject.length;
1101: if (typeof len == "number") {
1102: for (var i = 0; i < len; ++i) {
1103: if (menuObject[i].selected) {
1104: _jmolClick(menuObject[i], menuObject[i].value, targetSuffix);
1105: return;
1106: }
1107: }
1108: }
1109: alert("?Que? menu selected bug #8734");
1110: }
1111:
1112:
1113: _jmol.checkboxMasters = {};
1114: _jmol.checkboxItems = {};
1115:
1116: function jmolSetCheckboxGroup(chkMaster,chkBox) {
1117: var id = chkMaster;
1118: if(typeof(id)=="number")id = "jmolCheckbox" + id;
1119: chkMaster = document.getElementById(id);
1120: if (!chkMaster)alert("jmolSetCheckboxGroup: master checkbox not found: " + id);
1121: var m = _jmol.checkboxMasters[id] = {};
1122: m.chkMaster = chkMaster;
1123: m.chkGroup = {};
1124: for (var i = 1; i < arguments.length; i++){
1125: var id = arguments[i];
1126: if(typeof(id)=="number")id = "jmolCheckbox" + id;
1127: checkboxItem = document.getElementById(id);
1128: if (!checkboxItem)alert("jmolSetCheckboxGroup: group checkbox not found: " + id);
1129: m.chkGroup[id] = checkboxItem;
1130: _jmol.checkboxItems[id] = m;
1131: }
1132: }
1133:
1134: function _jmolNotifyMaster(m){
1135: //called when a group item is checked
1136: var allOn = true;
1137: var allOff = true;
1138: for (var chkBox in m.chkGroup){
1139: if(m.chkGroup[chkBox].checked)
1140: allOff = false;
1141: else
1142: allOn = false;
1143: }
1144: if (allOn)m.chkMaster.checked = true;
1145: if (allOff)m.chkMaster.checked = false;
1146: if ((allOn || allOff) && _jmol.checkboxItems[m.chkMaster.id])
1147: _jmolNotifyMaster(_jmol.checkboxItems[m.chkMaster.id])
1148: }
1149:
1150: function _jmolNotifyGroup(m, isOn){
1151: //called when a master item is checked
1152: for (var chkBox in m.chkGroup){
1153: var item = m.chkGroup[chkBox]
1154: if (item.checked != isOn)
1155: item.click();
1156: if (_jmol.checkboxMasters[item.id])
1157: _jmolNotifyGroup(_jmol.checkboxMasters[item.id], isOn)
1158: }
1159: }
1160:
1161: function _jmolCbClick(ckbox, whenChecked, whenUnchecked, targetSuffix) {
1162: _jmol.control = ckbox
1163: _jmolClick(ckbox, ckbox.checked ? whenChecked : whenUnchecked, targetSuffix);
1164: if(_jmol.checkboxMasters[ckbox.id])
1165: _jmolNotifyGroup(_jmol.checkboxMasters[ckbox.id], ckbox.checked)
1166: if(_jmol.checkboxItems[ckbox.id])
1167: _jmolNotifyMaster(_jmol.checkboxItems[ckbox.id])
1168: }
1169:
1170: function _jmolCbOver(ckbox, whenChecked, whenUnchecked) {
1171: window.status = _jmol.scripts[ckbox.checked ? whenUnchecked : whenChecked];
1172: }
1173:
1174: function _jmolMouseOver(scriptIndex) {
1175: window.status = _jmol.scripts[scriptIndex];
1176: }
1177:
1178: function _jmolMouseOut() {
1179: window.status = " ";
1180: return true;
1181: }
1182:
1183: function _jmolSetCodebase(codebase) {
1184: _jmol.codebase = codebase ? codebase : ".";
1185: if (_jmol.debugAlert)
1186: alert("jmolCodebase=" + _jmol.codebase);
1187: }
1188:
1189: function _jmolOnloadResetForms() {
1190: // must be evaluated ONLY once
1191: _jmol.previousOnloadHandler = window.onload;
1192: window.onload =
1193: function() {
1194: with (_jmol) {
1195: if (buttonCount+checkboxCount+menuCount+radioCount+radioGroupCount > 0) {
1196: var forms = document.forms;
1197: for (var i = forms.length; --i >= 0; )
1198: forms[i].reset();
1199: }
1200: if (previousOnloadHandler)
1201: previousOnloadHandler();
1202: }
1203: }
1204: }
1205:
1206: ////////////////////////////////////
1207: /////extensions for getProperty/////
1208: ////////////////////////////////////
1209:
1210:
1211: function _jmolEvalJSON(s,key){
1212: s=s+""
1213:
1214: if(!s)return []
1215: if(s.charAt(0)!="{"){
1216: if(s.indexOf(" | ")>=0)s=s.replace(/\ \|\ /g, "\n")
1217: return s
1218: }
1219: var A = eval("("+s+")")
1220: if(!A)return
1221: if(key && A[key])A=A[key]
1222: return A
1223: }
1224:
1225: function _jmolEnumerateObject(A,key){
1226: var sout=""
1227: if(typeof(A) == "string" && A!="null"){
1228: sout+="\n"+key+"=\""+A+"\""
1229: }else if(!isNaN(A)||A==null){
1230: sout+="\n"+key+"="+(A+""==""?"null":A)
1231: }else if(A.length){
1232: sout+=key+"=[]"
1233: for(var i=0;i<A.length;i++){
1234: sout+="\n"
1235: if(typeof(A[i]) == "object"||typeof(A[i]) == "array"){
1236: sout+=_jmolEnumerateObject(A[i],key+"["+i+"]")
1237: }else{
1238: sout+=key+"["+i+"]="+(typeof(A[i]) == "string" && A[i]!="null"?"\""+A[i].replace(/\"/g,"\\\"")+"\"":A[i])
1239: }
1240: }
1241: }else{
1242: if(key != ""){
1243: sout+=key+"={}"
1244: key+="."
1245: }
1246:
1247: for(var i in A){
1248: sout+="\n"
1249: if(typeof(A[i]) == "object"||typeof(A[i]) == "array"){
1250: sout+=_jmolEnumerateObject(A[i],key+i)
1251: }else{
1252: sout+=key+i+"="+(typeof(A[i]) == "string" && A[i]!="null"?"\""+A[i].replace(/\"/g,"\\\"")+"\"":A[i])
1253: }
1254: }
1255: }
1256: return sout
1257: }
1258:
1259:
1260: function _jmolSortKey0(a,b){
1261: return (a[0]<b[0]?1:a[0]>b[0]?-1:0)
1262: }
1263:
1264: function _jmolSortMessages(A){
1265: if(!A || typeof(A)!="object")return []
1266: var B = []
1267: for(var i=A.length-1;i>=0;i--)for(var j=0;j<A[i].length;j++)B[B.length]=A[i][j]
1268: if(B.length == 0) return
1269: B=B.sort(_jmolSortKey0)
1270: return B
1271: }
1272:
1273: /////////additional extensions //////////
1274:
1275:
1276: function _jmolDomScriptLoad(URL){
1277: //open(URL) //to debug
1278: _jmol.servercall=URL
1279: var node = document.getElementById("_jmolScriptNode")
1280: if (node && _jmol.browser!="msie"){
1281: document.getElementsByTagName("HEAD")[0].removeChild(node)
1282: node=null
1283: }
1284: if (node) {
1285: node.setAttribute("src",URL)
1286: } else {
1287: node=document.createElement("script")
1288: node.setAttribute("id","_jmolScriptNode")
1289: node.setAttribute("type","text/javascript")
1290: node.setAttribute("src",URL)
1291: document.getElementsByTagName("HEAD")[0].appendChild(node)
1292: }
1293: }
1294:
1295:
1296: function _jmolExtractPostData(url){
1297: S=url.split("&POST:")
1298: var s=""
1299: for(var i=1;i<S.length;i++){
1300: KV=S[i].split("=")
1301: s+="&POSTKEY"+i+"="+KV[0]
1302: s+="&POSTVALUE"+i+"="+KV[1]
1303: }
1304: return "&url="+escape(S[0])+s
1305: }
1306:
1307: function _jmolLoadModel(targetSuffix,remoteURL,array,isError,errorMessage){
1308: //called by server, but in client
1309: //overload this function to customize return
1310: _jmol.remoteURL=remoteURL
1311: isError && alert(errorMessage)
1312: jmolLoadInlineScript(array.join("\n"),_jmol.optionalscript,targetSuffix)
1313: }
1314:
1315: //////////user property/status functions/////////
1316:
1317: function jmolGetStatus(strStatus,targetSuffix){
1318: return _jmolSortMessages(jmolGetPropertyAsArray("jmolStatus",strStatus,targetSuffix))
1319: }
1320:
1321: function jmolGetPropertyAsArray(sKey,sValue,targetSuffix) {
1322: return _jmolEvalJSON(jmolGetPropertyAsJSON(sKey,sValue,targetSuffix),sKey)
1323: }
1324:
1325: function jmolGetPropertyAsString(sKey,sValue,targetSuffix) {
1326: var applet = _jmolGetApplet(targetSuffix);
1327: sValue == undefined && (sValue="");
1328: return (applet ? applet.getPropertyAsString(sKey,sValue) + "" : "")
1329: }
1330:
1331: function jmolGetPropertyAsJSON(sKey,sValue,targetSuffix) {
1332: sValue == undefined && (sValue = "")
1333: var applet = _jmolGetApplet(targetSuffix);
1334: try {
1335: return (applet ? applet.getPropertyAsJSON(sKey,sValue) + "" : "")
1336: } catch(e) {
1337: return ""
1338: }
1339: }
1340:
1341: function jmolGetPropertyAsJavaObject(sKey,sValue,targetSuffix) {
1342: sValue == undefined && (sValue = "")
1343: var applet = _jmolGetApplet(targetSuffix);
1344: return (applet ? applet.getProperty(sKey,sValue) : null)
1345: }
1346:
1347:
1348: function jmolDecodeJSON(s) {
1349: return _jmolEnumerateObject(_jmolEvalJSON(s),"")
1350: }
1351:
1352:
1353: ///////// synchronous scripting ////////
1354:
1355: function jmolScriptWait(script, targetSuffix) {
1356: targetSuffix == undefined && (targetSuffix="0")
1357: var Ret=jmolScriptWaitAsArray(script, targetSuffix)
1358: var s = ""
1359: for(var i=Ret.length;--i>=0;)
1360: for(var j=0;j< Ret[i].length;j++)
1361: s+=Ret[i][j]+"\n"
1362: return s
1363: }
1364:
1365: function jmolScriptWaitOutput(script, targetSuffix) {
1366: targetSuffix == undefined && (targetSuffix="0")
1367: var ret = ""
1368: try{
1369: if (script) {
1370: _jmolCheckBrowser();
1371: var applet=_jmolGetApplet(targetSuffix);
1372: if (applet) ret += applet.scriptWaitOutput(script);
1373: }
1374: }catch(e){
1375: }
1376: return ret;
1377: }
1378:
1379: function jmolEvaluate(molecularMath, targetSuffix) {
1380:
1381: //carries out molecular math on a model
1382:
1383: targetSuffix == undefined && (targetSuffix="0")
1384: var result = "" + jmolGetPropertyAsJavaObject("evaluate", molecularMath, targetSuffix);
1385: var s = result.replace(/\-*\d+/,"")
1386: if (s == "" && !isNaN(parseInt(result)))return parseInt(result);
1387: var s = result.replace(/\-*\d*\.\d*/,"")
1388: if (s == "" && !isNaN(parseFloat(result)))return parseFloat(result);
1389: return result;
1390: }
1391:
1392: function jmolScriptEcho(script, targetSuffix) {
1393: // returns a newline-separated list of all echos from a script
1394: targetSuffix == undefined && (targetSuffix="0")
1395: var Ret=jmolScriptWaitAsArray(script, targetSuffix)
1396: var s = ""
1397: for(var i=Ret.length;--i>=0;)
1398: for(var j=Ret[i].length;--j>=0;)
1399: if (Ret[i][j][1] == "scriptEcho")s+=Ret[i][j][3]+"\n"
1400: return s.replace(/ \| /g, "\n")
1401: }
1402:
1403:
1404: function jmolScriptMessage(script, targetSuffix) {
1405: // returns a newline-separated list of all messages from a script, ending with "script completed\n"
1406: targetSuffix == undefined && (targetSuffix="0")
1407: var Ret=jmolScriptWaitAsArray(script, targetSuffix)
1408: var s = ""
1409: for(var i=Ret.length;--i>=0;)
1410: for(var j=Ret[i].length;--j>=0;)
1411: if (Ret[i][j][1] == "scriptStatus")s+=Ret[i][j][3]+"\n"
1412: return s.replace(/ \| /g, "\n")
1413: }
1414:
1415:
1416: function jmolScriptWaitAsArray(script, targetSuffix) {
1417: var ret = ""
1418: try{
1419: jmolGetStatus("scriptEcho,scriptMessage,scriptStatus,scriptError",targetSuffix)
1420: if (script) {
1421: _jmolCheckBrowser();
1422: var applet=_jmolGetApplet(targetSuffix);
1423: if (applet) ret += applet.scriptWait(script);
1424: ret = _jmolEvalJSON(ret,"jmolStatus")
1425: if(typeof ret == "object")
1426: return ret
1427: }
1428: }catch(e){
1429: }
1430: return [[ret]]
1431: }
1432:
1433:
1434:
1435: //////////// save/restore orientation /////////////
1436:
1437: function jmolSaveOrientation(id, targetSuffix) {
1438: targetSuffix == undefined && (targetSuffix="0")
1439: return _jmol["savedOrientation"+id] = jmolGetPropertyAsArray("orientationInfo","info",targetSuffix).moveTo
1440: }
1441:
1442: function jmolRestoreOrientation(id, targetSuffix) {
1443: targetSuffix == undefined && (targetSuffix="0")
1444: var s=_jmol["savedOrientation"+id]
1445: if (!s || s == "")return
1446: s=s.replace(/1\.0/,"0")
1447: return jmolScriptWait(s,targetSuffix)
1448: }
1449:
1450: function jmolRestoreOrientationDelayed(id, delay, targetSuffix) {
1451: arguments.length < 2 && (delay=1)
1452: targetSuffix == undefined && (targetSuffix="0")
1453: var s=_jmol["savedOrientation"+id]
1454: if (!s || s == "")return
1455: s=s.replace(/1\.0/,delay)
1456: return jmolScriptWait(s,targetSuffix)
1457: }
1458:
1459: //////////// add parameter /////////////
1460: /*
1461: * for adding callbacks or other parameters. Use:
1462:
1463: jmolSetDocument(0)
1464: var s= jmolApplet(....)
1465: s = jmolAppletAddParam(s,"messageCallback", "myFunctionName")
1466: document.write(s)
1467: jmolSetDocument(document) // if you want to then write buttons and such normally
1468:
1469: */
1470:
1471: function jmolAppletAddParam(appletCode,name,value){
1472: return (value == "" ? appletCode : appletCode.replace(/\<param/,"\n<param name='"+name+"' value='"+value+"' />\n<param"))
1473: }
1474:
1475: ///////////////auto load Research Consortium for Structural Biology (RCSB) data ///////////
1476:
1477: function jmolLoadAjax_STOLAF_RCSB(fileformat,pdbid,optionalscript,targetSuffix){
1478:
1479: _jmol.thismodel || (_jmol.thismodel = "1crn")
1480: _jmol.serverURL || (_jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm")
1481: _jmol.RCSBserver || (_jmol.RCSBserver="http://www.rcsb.org")
1482: _jmol.defaultURL_RCSB || (_jmol.defaultURL_RCSB=_jmol.RCSBserver+"/pdb/files/1CRN.CIF")
1483: fileformat || (fileformat="PDB")
1484: pdbid || (pdbid=prompt("Enter a 4-digit PDB ID:",_jmol.thismodel))
1485: if(!pdbid || pdbid.length != 4)return ""
1486: targetSuffix || (targetSuffix="0")
1487: optionalscript || (optionalscript="")
1488: var url=_jmol.defaultURL_RCSB.replace(/1CRN/g,pdbid.toUpperCase())
1489: fileformat=="CIF" || (url=url.replace(/CIF/,fileformat))
1490: _jmol.optionalscript=optionalscript
1491: _jmol.thismodel=pdbid
1492: _jmol.thistargetsuffix=targetSuffix
1493: _jmol.thisurl=url
1494: _jmol.modelArray = []
1495: url=_jmol.serverURL+"?returnfunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix+_jmolExtractPostData(url)
1496: _jmolDomScriptLoad(url)
1497: return url
1498: }
1499:
1500: /////////////// St. Olaf College AJAX server -- ANY URL ///////////
1501:
1502: function jmolLoadAjax_STOLAF_ANY(url, userid, optionalscript,targetSuffix){
1503: _jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm"
1504: _jmol.thisurlANY || (_jmol.thisurlANY = "http://www.stolaf.edu/depts/chemistry/mo/struc/data/ycp3-1.mol")
1505: url || (url=prompt("Enter any (uncompressed file) URL:", _jmol.thisurlANY))
1506: userid || (userid="0")
1507: targetSuffix || (targetSuffix="0")
1508: optionalscript || (optionalscript="")
1509: _jmol.optionalscript=optionalscript
1510: _jmol.thistargetsuffix=targetSuffix
1511: _jmol.modelArray = []
1512: _jmol.thisurl = url
1513: url=_jmol.serverURL+"?returnfunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix+_jmolExtractPostData(url)
1514: _jmolDomScriptLoad(url)
1515: }
1516:
1517:
1518: /////////////// Mineralogical Society of America (MSA) data /////////
1519:
1520: function jmolLoadAjax_MSA(key,value,optionalscript,targetSuffix){
1521:
1522: _jmol.thiskeyMSA || (_jmol.thiskeyMSA = "mineral")
1523: _jmol.thismodelMSA || (_jmol.thismodelMSA = "quartz")
1524: _jmol.ajaxURL_MSA || (_jmol.ajaxURL_MSA="http://rruff.geo.arizona.edu/AMS/result.php?mineral=quartz&viewing=ajaxjs")
1525: key || (key=prompt("Enter a field:", _jmol.thiskeyMSA))
1526: if(!key)return ""
1527: value || (value=prompt("Enter a "+key+":", _jmol.thismodelMSA))
1528: if(!value)return ""
1529: targetSuffix || (targetSuffix="0")
1530: optionalscript || (optionalscript="")
1531: optionalscript == 1 && (optionalscript='load "" {1 1 1}')
1532: var url=_jmol.ajaxURL_MSA.replace(/mineral/g,key).replace(/quartz/g,value)
1533: _jmol.optionalscript=optionalscript
1534: _jmol.thiskeyMSA=key
1535: _jmol.thismodelMSA=value
1536: _jmol.thistargetsuffix=targetSuffix
1537: _jmol.thisurl=url
1538: _jmol.modelArray = []
1539: loadModel=_jmolLoadModel
1540: _jmolDomScriptLoad(url)
1541: return url
1542: }
1543:
1544:
1545:
1546: function jmolLoadAjaxJS(url, userid, optionalscript,targetSuffix){
1547: userid || (userid="0")
1548: targetSuffix || (targetSuffix="0")
1549: optionalscript || (optionalscript="")
1550: _jmol.optionalscript=optionalscript
1551: _jmol.thismodel=userid
1552: _jmol.thistargetsuffix=targetSuffix
1553: _jmol.modelArray = []
1554: _jmol.thisurl = url
1555: url+="&returnFunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix
1556: _jmolDomScriptLoad(url)
1557: }
1558:
1559:
1560: //// in case Jmol library has already been loaded:
1561:
1562: }catch(e){}
1563:
1564: ///////////////moving atoms //////////////
1565:
1566: // HIGHLY experimental!!
1567:
1568: function jmolSetAtomCoord(i,x,y,z,targetSuffix){
1569: _jmolCheckBrowser();
1570: var applet=_jmolGetApplet(targetSuffix);
1571: if (applet) applet.getProperty('jmolViewer').setAtomCoord(i,x,y,z)
1572: }
1573:
1574: function jmolSetAtomCoordRelative(i,x,y,z,targetSuffix){
1575: _jmolCheckBrowser();
1576: var applet=_jmolGetApplet(targetSuffix);
1577: if (applet) applet.getProperty('jmolViewer').setAtomCoordRelative(i,x,y,z)
1578: }
1579:
1580:
1581: ///////////////applet fake for testing buttons/////////////
1582:
1583:
1584: if(_jmol.useNoApplet){
1585: jmolApplet = function(w){
1586: var s="<table style='background-color:black' width="+w+"><tr height="+w+">"
1587: +"<td align=center valign=center style='background-color:white'>"
1588: +"Applet would be here"
1589: +"<p><textarea id=fakeApplet rows=5 cols=50></textarea>"
1590: +"</td></tr></table>"
1591: return _jmolDocumentWrite(s)
1592: }
1593:
1594: _jmolFindApplet = function(){return jmolApplet0}
1595:
1596: jmolApplet0 = {
1597: script: function(script){document.getElementById("fakeApplet").value="\njmolScript:\n"+script}
1598: ,scriptWait: function(script){document.getElementById("fakeApplet").value="\njmolScriptWait:\n"+script}
1599: ,loadInline: function(data,script){document.getElementById("fakeApplet").value="\njmolLoadInline data:\n"+data+"\n\nscript:\n"+script}
1600: }
1601: }
1602:
1603:
1604: ///////////////////////////////////////////
1605:
1606: // This should no longer be needed, jmolResizeApplet() is better; kept for backwards compatibility
1607: /*
1608: Resizes absolutely (pixels) or by percent of window (w or h 0.5 means 50%).
1609: targetSuffix is optional and defaults to zero (first applet in page).
1610: Both w and h are optional, but needed if you want to use targetSuffix.
1611: h defaults to w
1612: w defaults to 100% of window
1613: If either w or h is between 0 and 1, then it is taken as percent/100.
1614: If either w or h is greater than 1, then it is taken as a size (pixels).
1615: */
1616: function jmolResize(w,h,targetSuffix) {
1617: _jmol.alerted = true;
1618: var percentW = (!w ? 100 : w <= 1 && w > 0 ? w * 100 : 0);
1619: var percentH = (!h ? percentW : h <= 1 && h > 0 ? h * 100 : 0);
1620: if (_jmol.browser=="msie") {
1621: var width=document.body.clientWidth;
1622: var height=document.body.clientHeight;
1623: } else {
1624: var netscapeScrollWidth=15;
1625: var width=window.innerWidth - netscapeScrollWidth;
1626: var height=window.innerHeight-netscapeScrollWidth;
1627: }
1628: var applet = _jmolGetApplet(targetSuffix);
1629: if(!applet)return;
1630: applet.style.width = (percentW ? width * percentW/100 : w)+"px";
1631: applet.style.height = (percentH ? height * percentH/100 : (h ? h : w))+"px";
1632: //title=width + " " + height + " " + (new Date());
1633: }
1634:
1635: // 13 Jun 09 -- makes jmolResize() obsolete (kept for backwards compatibility)
1636: function jmolResizeApplet(size,targetSuffix) {
1637: // See _jmolGetAppletSize() for the formats accepted as size [same used by jmolApplet()]
1638: // Special case: an empty value for width or height is accepted, meaning no change in that dimension.
1639: _jmol.alerted = true;
1640: var applet = _jmolGetApplet(targetSuffix);
1641: if(!applet)return;
1642: var sz = _jmolGetAppletSize(size, "px");
1643: sz[0] && (applet.style.width = sz[0]);
1644: sz[1] && (applet.style.height = sz[1]);
1645: }
1646:
1647: function _jmolGetAppletSize(size, units) {
1648: /* Accepts single number or 2-value array, each one can be one of:
1649: percent (text string ending %), decimal 0 to 1 (percent/100), number, or text string (interpreted as nr.)
1650: [width, height] array of strings is returned, with units added if specified.
1651: Percent is relative to container div or element (which should have explicitly set size).
1652: */
1653: var width, height;
1654: if ( (typeof size) == "object" && size != null ) {
1655: width = size[0]; height = size[1];
1656: } else {
1657: width = height = size;
1658: }
1659: return [_jmolFixDim(width, units), _jmolFixDim(height, units)];
1660: }
1661:
1662: function _jmolFixDim(x, units) {
1663: var sx = "" + x;
1664: return (sx.length == 0 ? (units ? "" : _jmol.allowedJmolSize[2])
1665: : sx.indexOf("%") == sx.length-1 ? sx
1666: : (x = parseFloat(x)) <= 1 && x > 0 ? x * 100 + "%"
1667: : (isNaN(x = Math.floor(x)) ? _jmol.allowedJmolSize[2]
1668: : x < _jmol.allowedJmolSize[0] ? _jmol.allowedJmolSize[0]
1669: : x > _jmol.allowedJmolSize[1] ? _jmol.allowedJmolSize[1]
1670: : x) + (units ? units : ""));
1671: }
1672:
1673:
1674:
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