Clazz.declarePackage("JV");
Clazz.load(["javajs.api.BytePoster", "java.util.Hashtable"], "JV.FileManager", ["java.net.URL", "$.URLEncoder", "JU.AU", "$.Base64", "$.LimitedLineReader", "$.Lst", "$.OC", "$.PT", "$.Rdr", "$.SB", "J.adapter.smarter.Resolver", "J.api.Interface", "J.i18n.GT", "J.io.FileReader", "JU.Escape", "$.Logger", "JV.JC", "$.JmolAsyncException", "$.Viewer"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.vwr = null;
this.spartanDoc = null;
this.jzu = null;
this.pathForAllFiles = "";
this.nameAsGiven = "zapped";
this.fullPathName = null;
this.lastFullPathName = null;
this.lastNameAsGiven = "zapped";
this.fileName = null;
this.lastFileType = null;
this.appletDocumentBaseURL = null;
this.appletProxy = null;
this.cache = null;
this.pngjCache = null;
this.spardirCache = null;
this.staticJmolDataReader = null;
Clazz.instantialize(this, arguments);}, JV, "FileManager", null, javajs.api.BytePoster);
Clazz.prepareFields (c$, function(){
this.cache =  new java.util.Hashtable();
});
Clazz.makeConstructor(c$, 
function(vwr){
this.vwr = vwr;
this.clear();
}, "JV.Viewer");
Clazz.defineMethod(c$, "spartanUtil", 
function(){
return (this.spartanDoc == null ? this.spartanDoc = (J.api.Interface.getInterface("J.adapter.readers.spartan.SpartanUtil", this.vwr, "fm getSpartanUtil()")).set(this) : this.spartanDoc);
});
Clazz.defineMethod(c$, "getJzu", 
function(){
return (this.jzu == null ? this.jzu = J.api.Interface.getOption("io.JmolUtil", this.vwr, "file") : this.jzu);
});
Clazz.defineMethod(c$, "clear", 
function(){
this.setFileInfo( Clazz.newArray(-1, [this.vwr.getZapName()]));
this.spardirCache = null;
});
Clazz.defineMethod(c$, "setLoadState", 
function(htParams){
if (this.vwr.getPreserveState()) {
htParams.put("loadState", this.vwr.g.getLoadState(htParams));
}}, "java.util.Map");
Clazz.defineMethod(c$, "getPathForAllFiles", 
function(){
return this.pathForAllFiles;
});
Clazz.defineMethod(c$, "setPathForAllFiles", 
function(value){
if (value.length > 0 && !value.endsWith("/") && !value.endsWith("|")) value += "/";
return this.pathForAllFiles = value;
}, "~S");
Clazz.defineMethod(c$, "setFileInfo", 
function(fileInfo){
if (fileInfo == null) {
this.fullPathName = this.lastFullPathName;
this.nameAsGiven = this.lastNameAsGiven;
return;
}this.fullPathName = fileInfo[0];
this.fileName = fileInfo[Math.min(1, fileInfo.length - 1)];
this.nameAsGiven = fileInfo[Math.min(2, fileInfo.length - 1)];
if (!this.nameAsGiven.equals("zapped")) {
this.lastNameAsGiven = this.nameAsGiven;
this.lastFullPathName = this.fullPathName;
}}, "~A");
Clazz.defineMethod(c$, "getFileInfo", 
function(){
return  Clazz.newArray(-1, [this.fullPathName, this.fileName, this.nameAsGiven]);
});
Clazz.defineMethod(c$, "getFullPathName", 
function(orPrevious){
var f = (this.fullPathName != null ? this.fullPathName : this.nameAsGiven);
return (!orPrevious || !f.equals("zapped") && !f.equals("string") ? f : this.lastFullPathName != null ? this.lastFullPathName : this.lastNameAsGiven);
}, "~B");
Clazz.defineMethod(c$, "getLastReadFileType", 
function(){
return this.lastFileType;
});
Clazz.defineMethod(c$, "setFileType", 
function(fileType){
if (!"JmolData".equals(fileType)) this.lastFileType = fileType;
}, "~S");
Clazz.defineMethod(c$, "getFileName", 
function(){
return this.fileName != null ? this.fileName : this.nameAsGiven;
});
Clazz.defineMethod(c$, "getAppletDocumentBase", 
function(){
return (this.appletDocumentBaseURL == null ? "" : this.appletDocumentBaseURL.toString());
});
Clazz.defineMethod(c$, "setAppletContext", 
function(documentBase){
try {
System.out.println("setting document base to \"" + documentBase + "\"");
this.appletDocumentBaseURL = (documentBase.length == 0 ? null :  new java.net.URL(Clazz.castNullAs("java.net.URL"), documentBase, null));
} catch (e) {
if (Clazz.exceptionOf(e,"java.net.MalformedURLException")){
System.out.println("error setting document base to " + documentBase);
} else {
throw e;
}
}
}, "~S");
Clazz.defineMethod(c$, "setAppletProxy", 
function(appletProxy){
this.appletProxy = (appletProxy == null || appletProxy.length == 0 ? null : appletProxy);
}, "~S");
Clazz.defineMethod(c$, "createAtomSetCollectionFromFile", 
function(name, htParams, isAppend){
if (htParams.get("atomDataOnly") == null) this.setLoadState(htParams);
var name0 = name;
var pt = name.indexOf("::");
if (pt < 0) name = this.vwr.resolveDatabaseFormat(name);
if (!name0.equals(name) && name0.indexOf("/") < 0 && JV.Viewer.hasDatabasePrefix(name0)) {
htParams.put("dbName", name0);
}if (name.endsWith("%2D%")) {
var filter = htParams.get("filter");
htParams.put("filter", (filter == null ? "" : filter) + "2D");
name = name.substring(0, name.length - 4);
}var nameAsGiven = (pt >= 0 ? name.substring(pt + 2) : name);
var fileType = (pt >= 0 ? name.substring(0, pt) : null);
JU.Logger.info("\nFileManager.getAtomSetCollectionFromFile(" + nameAsGiven + ")" + (name.equals(nameAsGiven) ? "" : " //" + name));
var names = this.getClassifiedName(nameAsGiven, true);
if (names.length == 1) return names[0];
var fullPathName = names[0];
var fileName = names[1];
this.setFileType(fileType);
htParams.put("fullPathName", (fileType == null ? "" : fileType + "::") + JV.FileManager.fixDOSName(fullPathName));
if (this.vwr.getBoolean(603979879) && this.vwr.getBoolean(603979825)) this.vwr.getChimeMessenger().update(fullPathName);
var fileReader =  new J.io.FileReader(this.vwr, fileName, fullPathName, nameAsGiven, fileType, null, htParams, isAppend);
fileReader.run();
return fileReader.getAtomSetCollection();
}, "~S,java.util.Map,~B");
Clazz.defineMethod(c$, "createAtomSetCollectionFromFiles", 
function(fileNames, htParams, isAppend){
this.setLoadState(htParams);
var fullPathNames =  new Array(fileNames.length);
var namesAsGiven =  new Array(fileNames.length);
var fileTypes =  new Array(fileNames.length);
for (var i = 0; i < fileNames.length; i++) {
var pt = fileNames[i].indexOf("::");
var nameAsGiven = (pt >= 0 ? fileNames[i].substring(pt + 2) : fileNames[i]);
var fileType = (pt >= 0 ? fileNames[i].substring(0, pt) : null);
var names = this.getClassifiedName(nameAsGiven, true);
if (names.length == 1) return names[0];
fullPathNames[i] = names[0];
fileNames[i] = JV.FileManager.fixDOSName(names[0]);
fileTypes[i] = fileType;
namesAsGiven[i] = nameAsGiven;
}
htParams.put("fullPathNames", fullPathNames);
htParams.put("fileTypes", fileTypes);
var filesReader = this.newFilesReader(fullPathNames, namesAsGiven, fileTypes, null, htParams, isAppend);
filesReader.run();
return filesReader.getAtomSetCollection();
}, "~A,java.util.Map,~B");
Clazz.defineMethod(c$, "createAtomSetCollectionFromString", 
function(strModel, htParams, isAppend){
this.setLoadState(htParams);
var isAddH = (strModel.indexOf("Viewer.AddHydrogens") >= 0);
var fnames = (isAddH ? this.getFileInfo() : null);
var fileReader =  new J.io.FileReader(this.vwr, "string", null, null, null, (strModel.startsWith(";base64,") ? JU.Base64.decodeBase64(strModel) : JU.Rdr.getBR(strModel)), htParams, isAppend);
fileReader.run();
if (fnames != null) this.setFileInfo(fnames);
if (!isAppend && !((typeof(fileReader.getAtomSetCollection())=='string'))) {
this.setFileInfo( Clazz.newArray(-1, [strModel === "5\n\nC 0 0 0\nH .63 .63 .63\nH -.63 -.63 .63\nH -.63 .63 -.63\nH .63 -.63 -.63" ? "Jmol Model Kit" : "string"]));
}return fileReader.getAtomSetCollection();
}, "~S,java.util.Map,~B");
Clazz.defineMethod(c$, "createAtomSeCollectionFromStrings", 
function(arrayModels, loadScript, htParams, isAppend){
if (!htParams.containsKey("isData")) {
var oldSep = "\"" + this.vwr.getDataSeparator() + "\"";
var tag = "\"" + (isAppend ? "append" : "model") + " inline\"";
var sb =  new JU.SB();
sb.append("set dataSeparator \"~~~next file~~~\";\ndata ").append(tag);
for (var i = 0; i < arrayModels.length; i++) {
if (i > 0) sb.append("~~~next file~~~");
sb.append(arrayModels[i]);
}
sb.append("end ").append(tag).append(";set dataSeparator ").append(oldSep);
loadScript.appendSB(sb);
}this.setLoadState(htParams);
JU.Logger.info("FileManager.getAtomSetCollectionFromStrings(string[])");
var fullPathNames =  new Array(arrayModels.length);
var readers =  new Array(arrayModels.length);
for (var i = 0; i < arrayModels.length; i++) {
fullPathNames[i] = "string[" + i + "]";
readers[i] = JV.FileManager.newDataReader(this.vwr, arrayModels[i]);
}
var filesReader = this.newFilesReader(fullPathNames, fullPathNames, null, readers, htParams, isAppend);
filesReader.run();
return filesReader.getAtomSetCollection();
}, "~A,JU.SB,java.util.Map,~B");
Clazz.defineMethod(c$, "createAtomSeCollectionFromArrayData", 
function(arrayData, htParams, isAppend){
JU.Logger.info("FileManager.getAtomSetCollectionFromArrayData(Vector)");
var nModels = arrayData.size();
var fullPathNames =  new Array(nModels);
var readers =  new Array(nModels);
for (var i = 0; i < nModels; i++) {
fullPathNames[i] = "String[" + i + "]";
readers[i] = JV.FileManager.newDataReader(this.vwr, arrayData.get(i));
}
var filesReader = this.newFilesReader(fullPathNames, fullPathNames, null, readers, htParams, isAppend);
filesReader.run();
return filesReader.getAtomSetCollection();
}, "JU.Lst,java.util.Map,~B");
c$.newDataReader = Clazz.defineMethod(c$, "newDataReader", 
function(vwr, data){
var reader = ((typeof(data)=='string') ? "String" : JU.AU.isAS(data) ? "Array" : Clazz.instanceOf(data,"JU.Lst") ? "List" : null);
if (reader == null) return null;
var dr = J.api.Interface.getInterface("JU." + reader + "DataReader", vwr, "file");
return dr.setData(data);
}, "JV.Viewer,~O");
Clazz.defineMethod(c$, "newFilesReader", 
function(fullPathNames, namesAsGiven, fileTypes, readers, htParams, isAppend){
var fr = J.api.Interface.getOption("io.FilesReader", this.vwr, "file");
fr.set(this, this.vwr, fullPathNames, namesAsGiven, fileTypes, readers, htParams, isAppend);
return fr;
}, "~A,~A,~A,~A,java.util.Map,~B");
Clazz.defineMethod(c$, "createAtomSetCollectionFromReader", 
function(fullPathName, name, reader, htParams){
var fileReader =  new J.io.FileReader(this.vwr, name, fullPathName, null, null, reader, htParams, false);
fileReader.run();
return fileReader.getAtomSetCollection();
}, "~S,~S,~O,java.util.Map");
Clazz.defineMethod(c$, "getBufferedInputStream", 
function(fullPathName){
var ret = this.getBufferedReaderOrErrorMessageFromName(fullPathName,  new Array(2), true, true);
return (Clazz.instanceOf(ret,"java.io.BufferedInputStream") ? ret : null);
}, "~S");
Clazz.defineMethod(c$, "getBufferedInputStreamOrErrorMessageFromName", 
function(name, fullName, showMsg, checkOnly, outputBytes, allowReader, allowCached){
var bis = null;
var ret = null;
var errorMessage = null;
allowCached = allowCached || name.startsWith("cache://");
var cacheBytes = (allowCached && outputBytes == null ? cacheBytes = this.getPngjOrDroppedBytes(fullName, name) : null);
try {
if (allowCached && name.indexOf(".png") >= 0 && this.pngjCache == null && !this.vwr.getBoolean(603979960)) this.pngjCache =  new java.util.Hashtable();
if (cacheBytes == null) {
var isPngjBinaryPost = (name.indexOf("?POST?_PNGJBIN_") >= 0);
var isPngjPost = (isPngjBinaryPost || name.indexOf("?POST?_PNGJ_") >= 0);
if (name.indexOf("?POST?_PNG_") > 0 || isPngjPost) {
var errMsg =  new Array(1);
var bytes = this.vwr.getImageAsBytes(isPngjPost ? "PNGJ" : "PNG", 0, 0, -1, errMsg);
if (errMsg[0] != null) return errMsg[0];
if (isPngjBinaryPost) {
outputBytes = bytes;
name = JU.PT.rep(name, "?_", "=_");
} else {
name =  new JU.SB().append(name).append("=").appendSB(JU.Base64.getBase64(bytes)).toString();
}}var iurl = JU.OC.urlTypeIndex(name);
var isURL = (iurl >= 0);
var post = null;
if (isURL && (iurl = name.indexOf("?POST?")) >= 0) {
post = name.substring(iurl + 6);
name = name.substring(0, iurl);
}var isApplet = (this.appletDocumentBaseURL != null);
if (isApplet || isURL) {
if (isApplet && isURL && this.appletProxy != null) name = this.appletProxy + "?url=" + this.urlEncode(name);
var url = (isApplet ?  new java.net.URL(this.appletDocumentBaseURL, name, null) :  new java.net.URL(Clazz.castNullAs("java.net.URL"), name, null));
if (checkOnly) return null;
name = url.toString();
if (showMsg && name.toLowerCase().indexOf("password") < 0) JU.Logger.info("FileManager opening url " + name);
ret = this.vwr.apiPlatform.getURLContents(url, outputBytes, post, false);
var bytes = null;
if (Clazz.instanceOf(ret,"JU.SB")) {
var sb = ret;
if (allowReader && !JU.Rdr.isBase64(sb)) return JU.Rdr.getBR(sb.toString());
bytes = JU.Rdr.getBytesFromSB(sb);
} else if (JU.AU.isAB(ret)) {
bytes = ret;
}if (bytes != null) ret = JU.Rdr.getBIS(bytes);
} else if (!allowCached || (cacheBytes = this.cacheGet(name, true)) == null) {
if (showMsg) JU.Logger.info("FileManager opening file " + name);
ret = this.vwr.apiPlatform.getBufferedFileInputStream(name);
}if ((typeof(ret)=='string')) return ret;
}bis = (cacheBytes == null ? ret : JU.Rdr.getBIS(cacheBytes));
if (checkOnly) {
bis.close();
bis = null;
}return bis;
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
try {
if (bis != null) bis.close();
} catch (e1) {
if (Clazz.exceptionOf(e1,"java.io.IOException")){
} else {
throw e1;
}
}
errorMessage = "" + e;
} else {
throw e;
}
}
return errorMessage;
}, "~S,~S,~B,~B,~A,~B,~B");
c$.getBufferedReaderForResource = Clazz.defineMethod(c$, "getBufferedReaderForResource", 
function(vwr, resourceClass, classPath, resourceName){
var url;
{
}resourceName = (url == null ? vwr.vwrOptions.get("codePath") + classPath + resourceName : url.getFile());
if (vwr.async) {
var bytes = vwr.fm.cacheGet(resourceName, false);
if (bytes == null) throw  new JV.JmolAsyncException(resourceName);
return JU.Rdr.getBufferedReader(JU.Rdr.getBIS(bytes), null);
}return vwr.fm.getBufferedReaderOrErrorMessageFromName(resourceName,  Clazz.newArray(-1, [null, null]), false, true);
}, "JV.Viewer,Class,~S,~S");
Clazz.defineMethod(c$, "urlEncode", 
function(name){
try {
return java.net.URLEncoder.encode(name, "utf-8");
} catch (e) {
if (Clazz.exceptionOf(e,"java.io.UnsupportedEncodingException")){
return name;
} else {
throw e;
}
}
}, "~S");
Clazz.defineMethod(c$, "getFullPathNameOrError", 
function(filename, getStream, ret){
var names = this.getClassifiedName(JV.JC.fixProtocol(filename), true);
if (names == null || names[0] == null || names.length < 2) return  Clazz.newArray(-1, [null, "cannot read file name: " + filename]);
var name = names[0];
var fullPath = JV.FileManager.fixDOSName(names[0]);
name = JU.Rdr.getZipRoot(name);
if (name.endsWith("#_DOCACHE_")) name = name.substring(0, name.length - "#_DOCACHE_".length);
var errMsg = this.getBufferedInputStreamOrErrorMessageFromName(name, fullPath, false, !getStream, null, false, !getStream);
ret[0] = fullPath;
if ((typeof(errMsg)=='string')) ret[1] = errMsg;
return errMsg;
}, "~S,~B,~A");
Clazz.defineMethod(c$, "getBufferedReaderOrErrorMessageFromName", 
function(name, fullPathNameReturn, isBinary, doSpecialLoad){
name = JV.JC.fixProtocol(name);
var data = this.cacheGet(name, false);
var isBytes = JU.AU.isAB(data);
var bytes = (isBytes ? data : null);
if (name.startsWith("cache://")) {
if (data == null) return "cannot read " + name;
if (isBytes) {
bytes = data;
} else {
return JU.Rdr.getBR(data);
}}var names = this.getClassifiedName(name, true);
if (names == null) return "cannot read file name: " + name;
if (fullPathNameReturn != null) fullPathNameReturn[0] = JV.FileManager.fixDOSName(names[0]);
return this.getUnzippedReaderOrStreamFromName(names[0], bytes, false, isBinary, false, doSpecialLoad, null);
}, "~S,~A,~B,~B");
Clazz.defineMethod(c$, "getUnzippedReaderOrStreamFromName", 
function(name, bytesOrStream, allowZipStream, forceInputStream, isTypeCheckOnly, doSpecialLoad, htParams){
if (doSpecialLoad && bytesOrStream == null) {
var o = (name.endsWith(".spt") ?  Clazz.newArray(-1, [null, null, null]) : name.indexOf(".spardir") < 0 ? null : this.spartanUtil().getFileList(name, isTypeCheckOnly));
if (o != null) return o;
}name = JV.JC.fixProtocol(name);
if (bytesOrStream == null && (bytesOrStream = this.getCachedPngjBytes(name)) != null && htParams != null) htParams.put("sourcePNGJ", Boolean.TRUE);
name = name.$replace("#_DOCACHE_", "");
var fullName = name;
var subFileList = null;
if (name.indexOf("|") >= 0) {
subFileList = JU.PT.split(name.$replace('\\', '/'), "|");
if (bytesOrStream == null) JU.Logger.info("FileManager opening zip " + name);
name = subFileList[0];
}var t = (bytesOrStream == null ? this.getBufferedInputStreamOrErrorMessageFromName(name, fullName, true, false, null, !forceInputStream, true) : JU.AU.isAB(bytesOrStream) ? JU.Rdr.getBIS(bytesOrStream) : bytesOrStream);
try {
if ((typeof(t)=='string') || Clazz.instanceOf(t,"java.io.BufferedReader")) return t;
var bis = t;
if (JU.Rdr.isGzipS(bis)) bis = JU.Rdr.getUnzippedInputStream(this.vwr.getJzt(), bis);
 else if (JU.Rdr.isBZip2S(bis)) bis = JU.Rdr.getUnzippedInputStreamBZip2(this.vwr.getJzt(), bis);
if (forceInputStream && subFileList == null) return bis;
if (JU.Rdr.isCompoundDocumentS(bis)) {
var doc = J.api.Interface.getInterface("JU.CompoundDocument", this.vwr, "file");
doc.setDocStream(this.vwr.getJzt(), bis);
var s = doc.getAllDataFiles("Molecule", "Input").toString();
return (forceInputStream ? JU.Rdr.getBIS(s.getBytes()) : JU.Rdr.getBR(s));
}if (JU.Rdr.isMessagePackS(bis) || JU.Rdr.isPickleS(bis)) return bis;
bis = JU.Rdr.getPngZipStream(bis, true);
var o = null;
if (JU.Rdr.isZipS(bis)) {
if (allowZipStream) return this.vwr.getJzt().newZipInputStream(bis);
o = this.vwr.getJzt().getZipFileDirectory(bis, subFileList, 1, forceInputStream);
} else if (JU.Rdr.isTar(bis)) {
o = this.vwr.getJzt().getZipFileDirectory(bis, subFileList, 1, forceInputStream);
} else if (JU.Rdr.isBinary(bis, 32)) {
return bis;
}if (o != null) {
if (!(Clazz.instanceOf(o,"java.io.BufferedInputStream"))) return ((typeof(o)=='string') ? JU.Rdr.getBR(o) : o);
bis = JU.Rdr.getUnzippedInputStream(this.vwr.getJzt(), o);
}return (forceInputStream ? bis : JU.Rdr.getBufferedReader(bis, null));
} catch (ioe) {
if (Clazz.exceptionOf(ioe, Exception)){
return ioe.toString();
} else {
throw ioe;
}
}
}, "~S,~O,~B,~B,~B,~B,java.util.Map");
Clazz.defineMethod(c$, "getZipDirectory", 
function(fileName, addManifest, allowCached){
var t = this.getBufferedInputStreamOrErrorMessageFromName(fileName, fileName, false, false, null, false, allowCached);
return this.vwr.getJzt().getZipDirectoryAndClose(t, addManifest ? "JmolManifest" : null);
}, "~S,~B,~B");
Clazz.defineMethod(c$, "getFileAsBytes", 
function(name, out){
if (name == null) return null;
var fullName = name;
var subFileList = null;
if (name.indexOf("|") >= 0) {
subFileList = JU.PT.split(name, "|");
name = subFileList[0];
}var bytes = (subFileList != null ? null : this.getPngjOrDroppedBytes(fullName, name));
if (bytes == null) {
var t = this.getBufferedInputStreamOrErrorMessageFromName(name, fullName, false, false, null, false, true);
if ((typeof(t)=='string')) return "Error:" + t;
try {
var bis = t;
bytes = (out != null || subFileList == null || subFileList.length <= 1 || !JU.Rdr.isZipS(bis) && !JU.Rdr.isPngZipStream(bis) && !JU.Rdr.isTar(bis) ? JU.Rdr.getStreamAsBytes(bis, out) : this.vwr.getJzt().getZipFileContentsAsBytes(bis, subFileList, 1));
bis.close();
} catch (ioe) {
if (Clazz.exceptionOf(ioe, Exception)){
return ioe.toString();
} else {
throw ioe;
}
}
}if (out == null || !JU.AU.isAB(bytes)) return bytes;
out.write(bytes, 0, -1);
return (bytes).length + " bytes";
}, "~S,JU.OC");
Clazz.defineMethod(c$, "getFileAsMap", 
function(name, type, asBytes){
var bdata = (asBytes ? null :  new java.util.Hashtable());
var t;
if (name == null) {
var errMsg =  new Array(1);
var bytes = this.vwr.getImageAsBytes(type, -1, -1, -1, errMsg);
if (errMsg[0] != null) {
if (asBytes) return  Clazz.newByteArray (0, 0);
bdata.put("_ERROR_", errMsg[0]);
return bdata;
}if (asBytes) return bytes;
t = JU.Rdr.getBIS(bytes);
} else {
var data =  new Array(2);
t = this.getFullPathNameOrError(name, true, data);
if ((typeof(t)=='string')) {
if (asBytes) return  Clazz.newByteArray (0, 0);
bdata.put("_ERROR_", t);
return bdata;
}if (!this.checkSecurity(data[0])) {
if (asBytes) return  Clazz.newByteArray (0, 0);
bdata.put("_ERROR_", "java.io. Security exception: cannot read file " + data[0]);
return bdata;
}}try {
if (asBytes) {
return JU.Rdr.streamToBytes(t);
}this.vwr.getJzt().readFileAsMap(t, bdata, name);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
if (asBytes) return  Clazz.newByteArray (0, 0);
bdata.clear();
bdata.put("_ERROR_", "" + e);
} else {
throw e;
}
}
return bdata;
}, "~S,~S,~B");
Clazz.defineMethod(c$, "getFileDataAsString", 
function(data, nBytesMax, doSpecialLoad, allowBinary, checkProtected){
data[1] = "";
var name = data[0];
if (name == null) return false;
var t = this.getBufferedReaderOrErrorMessageFromName(name, data, false, doSpecialLoad);
if ((typeof(t)=='string')) {
data[1] = t;
return false;
}if (checkProtected && !this.checkSecurity(data[0])) {
data[1] = "java.io. Security exception: cannot read file " + data[0];
return false;
}try {
if (Clazz.instanceOf(t,"java.io.BufferedInputStream")) {
if (name.toUpperCase().endsWith(".PNG") || JV.FileManager.isEmbeddable(name)) t = JU.Rdr.getBufferedReader(t, null);
}return JU.Rdr.readAllAsString(t, nBytesMax, allowBinary, data, 1);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
return false;
} else {
throw e;
}
}
}, "~A,~N,~B,~B,~B");
Clazz.defineMethod(c$, "checkSecurity", 
function(f){
if (!f.startsWith("file:")) return true;
var pt = f.lastIndexOf('/');
if (f.lastIndexOf(":/") == pt - 1 || f.indexOf("/.") >= 0 || f.lastIndexOf('.') < f.lastIndexOf('/')) return false;
return true;
}, "~S");
Clazz.defineMethod(c$, "loadImage", 
function(nameOrBytes, echoName, forceSync){
var image = null;
var nameOrError = null;
var bytes = null;
var isPopupImage = (echoName != null && echoName.startsWith("\1"));
if (isPopupImage) {
if (echoName.equals("\1closeall\1null")) return this.vwr.loadImageData(Boolean.TRUE, "\1closeall", "\1closeall", null);
if ("\1close".equals(nameOrBytes)) return this.vwr.loadImageData(Boolean.FALSE, "\1close", echoName, null);
}if (Clazz.instanceOf(nameOrBytes,"java.util.Map")) {
nameOrBytes = ((nameOrBytes).containsKey("_DATA_") ? (nameOrBytes).get("_DATA_") : (nameOrBytes).get("_IMAGE_"));
}if (Clazz.instanceOf(nameOrBytes,"JS.SV")) nameOrBytes = (nameOrBytes).value;
var name = ((typeof(nameOrBytes)=='string') ? nameOrBytes : null);
var isAsynchronous = false;
if (name != null && name.startsWith(";base64,")) {
bytes = JU.Base64.decodeBase64(name);
} else if (Clazz.instanceOf(nameOrBytes,"JU.BArray")) {
bytes = (nameOrBytes).data;
} else if (JU.AU.isAB(nameOrBytes)) {
bytes = nameOrBytes;
} else if (echoName == null || (typeof(nameOrBytes)=='string')) {
var names = this.getClassifiedName(nameOrBytes, true);
nameOrError = (names == null ? "cannot read file name: " + nameOrBytes : JV.FileManager.fixDOSName(names[0]));
if (names != null) image = this.getImage(nameOrError, echoName, forceSync);
isAsynchronous = (image == null);
} else {
image = nameOrBytes;
}if (bytes != null) {
image = this.getImage(bytes, echoName, true);
isAsynchronous = false;
}if ((typeof(image)=='string')) {
nameOrError = image;
image = null;
}if (!JV.Viewer.isJS && image != null && bytes != null) nameOrError = ";base64," + JU.Base64.getBase64(bytes).toString();
if (!JV.Viewer.isJS || isPopupImage && nameOrError == null || !isPopupImage && image != null) return this.vwr.loadImageData(image, nameOrError, echoName, null);
return isAsynchronous;
}, "~O,~S,~B");
Clazz.defineMethod(c$, "getImage", 
function(nameOrBytes, echoName, forceSync){
return this.getJzu().getImage(this.vwr, nameOrBytes, echoName, forceSync);
}, "~O,~S,~B");
Clazz.defineMethod(c$, "getClassifiedName", 
function(name, isFullLoad){
if (name == null) return  Clazz.newArray(-1, [null]);
var doSetPathForAllFiles = (this.pathForAllFiles.length > 0);
if (name.startsWith("?") || name.startsWith("http://?") || name.startsWith("https://?")) {
if (!JV.Viewer.isJS && (name = this.vwr.dialogAsk("Load", name, null)) == null) return  Clazz.newArray(-1, [isFullLoad ? "#CANCELED#" : null]);
doSetPathForAllFiles = false;
}var file = null;
var url = null;
var names = null;
if (name.startsWith("cache://")) {
names =  new Array(3);
names[0] = names[2] = name;
names[1] = JV.FileManager.stripPath(names[0]);
return names;
}name = this.vwr.resolveDatabaseFormat(name);
if (name == null) return  Clazz.newArray(-1, [null]);
if (name.startsWith("file:///") && name.indexOf('|') == 9) name = name.substring(0, 9) + ':' + name.substring(10);
if (name.indexOf(":") < 0 && name.indexOf('/') != 0 && name.indexOf('\\') != 0) name = JV.FileManager.addDirectory(this.vwr.getDefaultDirectory(), name);
if (this.appletDocumentBaseURL == null) {
if (JU.OC.urlTypeIndex(name) >= 0 || this.vwr.haveAccess(JV.Viewer.ACCESS.NONE) || this.vwr.haveAccess(JV.Viewer.ACCESS.READSPT) && !name.endsWith(".spt") && !name.endsWith("/") || !this.vwr.haveAccessInternal(name)) {
try {
url =  new java.net.URL(Clazz.castNullAs("java.net.URL"), name, null);
} catch (e) {
if (Clazz.exceptionOf(e,"java.net.MalformedURLException")){
return  Clazz.newArray(-1, [isFullLoad ? e.toString() : null]);
} else {
throw e;
}
}
} else {
file = this.vwr.apiPlatform.newFile(name);
var s = file.getFullPath();
var fname = file.getName();
names =  Clazz.newArray(-1, [(s == null ? fname : s), fname, (s == null ? fname : "file:/" + s.$replace('\\', '/'))]);
}} else {
try {
if (name.indexOf(":\\") == 1 || name.indexOf(":/") == 1) name = "file:/" + name;
url =  new java.net.URL(this.appletDocumentBaseURL, name, null);
} catch (e) {
if (Clazz.exceptionOf(e,"java.net.MalformedURLException")){
return  Clazz.newArray(-1, [isFullLoad ? e.toString() : null]);
} else {
throw e;
}
}
}if (url != null) {
names =  new Array(3);
names[0] = names[2] = url.toString();
names[1] = JV.FileManager.stripPath(names[0]);
}if (doSetPathForAllFiles) {
var name0 = names[0];
names[0] = this.pathForAllFiles + names[1];
JU.Logger.info("FileManager substituting " + name0 + " --> " + names[0]);
}var path = names[0];
if (isFullLoad && JU.OC.isLocal(path) && !path.startsWith("file:/")) {
if (file == null) path = JU.PT.trim(path.substring(path.indexOf(":") + 1), "/");
var pt = path.length - names[1].length - 1;
if (pt > 0) {
path = path.substring(0, pt).$replace('|', ':');
JV.FileManager.setLocalPath(this.vwr, path, true);
}}return names;
}, "~S,~B");
c$.addDirectory = Clazz.defineMethod(c$, "addDirectory", 
function(defaultDirectory, name){
if (defaultDirectory.length == 0 || defaultDirectory.equals(".")) return name;
var ch = (name.length > 0 ? name.charAt(0) : ' ');
var s = defaultDirectory.toLowerCase();
if ((s.endsWith(".zip") || s.endsWith(".tar")) && ch != '|' && ch != '/') defaultDirectory += "|";
return defaultDirectory + (ch == '/' || ch == '/' || (ch = defaultDirectory.charAt(defaultDirectory.length - 1)) == '|' || ch == '/' ? "" : "/") + name;
}, "~S,~S");
Clazz.defineMethod(c$, "getDefaultDirectory", 
function(name){
var names = this.getClassifiedName(name, true);
if (names == null) return "";
name = JV.FileManager.fixPath(names[0]);
return (name == null ? "" : name.substring(0, name.lastIndexOf("/")));
}, "~S");
c$.fixPath = Clazz.defineMethod(c$, "fixPath", 
function(path){
path = JV.FileManager.fixDOSName(path);
path = JU.PT.rep(path, "/./", "/");
var pt = path.lastIndexOf("//") + 1;
if (pt < 1) pt = path.indexOf(":/") + 1;
if (pt < 1) pt = path.indexOf("/");
if (pt < 0) return null;
var protocol = path.substring(0, pt);
path = path.substring(pt);
while ((pt = path.lastIndexOf("/../")) >= 0) {
var pt0 = path.substring(0, pt).lastIndexOf("/");
if (pt0 < 0) return JU.PT.rep(protocol + path, "/../", "/");
path = path.substring(0, pt0) + path.substring(pt + 3);
}
if (path.length == 0) path = "/";
return protocol + path;
}, "~S");
Clazz.defineMethod(c$, "getFilePath", 
function(name, addUrlPrefix, asShortName){
var names = this.getClassifiedName(name, false);
return (names == null || names.length == 1 ? "" : asShortName ? names[1] : addUrlPrefix ? names[2] : names[0] == null ? "" : JV.FileManager.fixDOSName(names[0]));
}, "~S,~B,~B");
c$.getLocalDirectory = Clazz.defineMethod(c$, "getLocalDirectory", 
function(vwr, forDialog){
var localDir = vwr.getP(forDialog ? "currentLocalPath" : "defaultDirectoryLocal");
if (forDialog && localDir.length == 0) localDir = vwr.getP("defaultDirectoryLocal");
if (localDir.length == 0) return (JV.Viewer.isJS ? null : vwr.apiPlatform.newFile(System.getProperty("user.dir", ".")));
if (vwr.isApplet && localDir.indexOf("file:/") == 0) localDir = localDir.substring(6);
var f = vwr.apiPlatform.newFile(localDir);
try {
return f.isDirectory() ? f : f.getParentAsFile();
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
return null;
} else {
throw e;
}
}
}, "JV.Viewer,~B");
c$.setLocalPath = Clazz.defineMethod(c$, "setLocalPath", 
function(vwr, path, forDialog){
while (path.endsWith("/") || path.endsWith("\\")) path = path.substring(0, path.length - 1);

vwr.setStringProperty("currentLocalPath", path);
if (!forDialog) vwr.setStringProperty("defaultDirectoryLocal", path);
}, "JV.Viewer,~S,~B");
c$.getLocalPathForWritingFile = Clazz.defineMethod(c$, "getLocalPathForWritingFile", 
function(vwr, file, forDialog){
if (file.startsWith("http://") || file.startsWith("https://")) return file;
file = JU.PT.rep(file, "?", "");
if (file.indexOf("file:/") == 0) {
var pt = file.indexOf('|');
if (pt > 5 && pt < 10) file = file.substring(0, pt) + ':' + file.substring(pt + 1);
pt = file.indexOf(':', 5);
return file.substring(pt > 0 ? pt - 1 : 5);
}if (file.indexOf('/') == 0 || file.indexOf('\\') == 0 || file.indexOf(":") >= 0) return file;
var dir = null;
try {
dir = JV.FileManager.getLocalDirectory(vwr, forDialog);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
return (dir == null ? file : JV.FileManager.fixPath(dir.toString() + "/" + file));
}, "JV.Viewer,~S,~B");
c$.fixDOSName = Clazz.defineMethod(c$, "fixDOSName", 
function(fileName){
return (fileName.indexOf(":\\") >= 0 ? fileName.$replace('\\', '/') : fileName);
}, "~S");
c$.stripPath = Clazz.defineMethod(c$, "stripPath", 
function(name){
var pt = Math.max(name.lastIndexOf("|"), name.lastIndexOf("/"));
return name.substring(pt + 1);
}, "~S");
c$.isScriptType = Clazz.defineMethod(c$, "isScriptType", 
function(fname){
return JU.PT.isOneOf(fname.toLowerCase().substring(fname.lastIndexOf(".") + 1), ";pse;spt;png;pngj;jmol;zip;");
}, "~S");
c$.determineSurfaceFileType = Clazz.defineMethod(c$, "determineSurfaceFileType", 
function(bufferedReader){
var line = null;
if (Clazz.instanceOf(bufferedReader,"JU.Rdr.StreamReader")) {
var is = (bufferedReader).getStream();
if (is.markSupported()) {
try {
is.mark(300);
var buf =  Clazz.newByteArray (300, 0);
is.read(buf, 0, 300);
is.reset();
if ((buf[0] & 0xFF) == 0x83) {
return (J.adapter.smarter.Resolver.checkBCIF(buf, false) ? "BCifDensity" : null);
}if (buf[0] == 80 && buf[1] == 77 && buf[2] == 1 && buf[3] == 0) return "Pmesh";
if (buf[208] == 77 && buf[209] == 65 && buf[210] == 80) return "Mrc";
if (buf[0] == 20 && buf[1] == 0 && buf[2] == 0 && buf[3] == 0) return "DelPhi";
if (buf[36] == 0 && buf[37] == 100) return "Dsn6";
} catch (e) {
if (Clazz.exceptionOf(e,"java.io.IOException")){
} else {
throw e;
}
}
}}var br = null;
try {
br =  new JU.LimitedLineReader(bufferedReader, 16000);
line = br.getHeader(0);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
if (br == null || line == null || line.length == 0) return null;
var pt0 = line.indexOf('\0');
if (pt0 >= 0) {
if ((line.charAt(0)).charCodeAt(0) == 0x83) {
return (line.charAt(10) == 'D' && line.charAt(11) == 'e' && line.charAt(12) == 'n' ? "BCifDensity" : null);
}if (line.indexOf("PM\u0001\u0000") == 0) return "Pmesh";
if (line.indexOf("MAP ") == 208) return "Mrc";
if (line.indexOf("\u0014\u0000\u0000\u0000") == 0) return "DelPhi";
if (line.length > 37 && ((line.charAt(36)).charCodeAt(0) == 0 && (line.charAt(37)).charCodeAt(0) == 100 || (line.charAt(36)).charCodeAt(0) == 0 && (line.charAt(37)).charCodeAt(0) == 100)) {
return "Dsn6";
}}switch ((line.charAt(0)).charCodeAt(0)) {
case 64:
if (line.indexOf("@text") == 0) return "Kinemage";
break;
case 35:
if (line.indexOf(".obj") >= 0) return "Obj";
if (line.indexOf("MSMS") >= 0) return "Msms";
if (line.indexOf("Menu") >= 0) return "MENU";
break;
case 60:
if (line.startsWith("<?xml") && line.indexOf("<jvxl ") > 0) return "JvxlXml";
if (line.indexOf("<efvet ") >= 0) return "Efvet";
break;
case 38:
if (line.indexOf("&plot") == 0) return "Jaguar";
break;
case 13:
case 10:
if (line.indexOf("ZYX") >= 0) return "Xplor";
break;
}
if (line.indexOf("Here is your gzipped map") >= 0) return "UPPSALA" + line;
if (line.startsWith("data_SERVER")) return "CifDensity";
if (line.startsWith("4MESHC")) return "Pmesh4";
if (line.indexOf("! nspins") >= 0) return "CastepDensity";
if (line.indexOf("#JVXL+") >= 0) return "Jvxl+";
if (line.indexOf("#JVXL") >= 0) return "Jvxl";
if (line.indexOf("#JmolPmesh") >= 0) return "Pmesh";
if (line.indexOf("#obj") >= 0) return "Obj";
if (line.indexOf("#pmesh") >= 0) return "Obj";
if (line.indexOf("usemtl") >= 0) return "Obj";
if (line.indexOf("# object with") == 0) return "Nff";
if (line.indexOf("PRIMVEC") >= 0 || line.indexOf("BEGIN_DATAGRID_3D") >= 0 || line.indexOf("BEGIN_BANDGRID_3D") >= 0) return "Xsf";
if (line.indexOf("tiles in x, y") >= 0) return "Ras3D";
if (line.indexOf(" 0.00000e+00 0.00000e+00      0      0\n") >= 0) return "Uhbd";
line = br.readLineWithNewline();
if (line.indexOf("object 1 class gridpositions counts") == 0) return "Apbs";
var tokens = JU.PT.getTokens(line);
var line2 = br.readLineWithNewline();
if (tokens.length == 2 && JU.PT.parseInt(tokens[0]) == 3 && JU.PT.parseInt(tokens[1]) != -2147483648) {
tokens = JU.PT.getTokens(line2);
if (tokens.length == 3 && JU.PT.parseInt(tokens[0]) != -2147483648 && JU.PT.parseInt(tokens[1]) != -2147483648 && JU.PT.parseInt(tokens[2]) != -2147483648) return "PltFormatted";
}var line3 = br.readLineWithNewline();
if (line.startsWith("v ") && line2.startsWith("v ") && line3.startsWith("v ")) return "Obj";
var nAtoms = JU.PT.parseInt(line3);
if (nAtoms == -2147483648) return (line3.indexOf("+") == 0 ? "Jvxl+" : null);
tokens = JU.PT.getTokens(line3);
if (tokens[0].indexOf(".") > 0) return (line3.length >= 60 || tokens.length != 3 ? null : "VaspChgcar");
if (nAtoms >= 0) return (tokens.length == 4 || tokens.length == 5 && tokens[4].equals("1") ? "Cube" : null);
nAtoms = -nAtoms;
for (var i = 4 + nAtoms; --i >= 0; ) if ((line = br.readLineWithNewline()) == null) return null;

var nSurfaces = JU.PT.parseInt(line);
if (nSurfaces == -2147483648) return null;
return (nSurfaces < 0 ? "Jvxl" : "Cube");
}, "java.io.BufferedReader");
c$.getManifestScriptPath = Clazz.defineMethod(c$, "getManifestScriptPath", 
function(manifest){
if (manifest.indexOf("$SCRIPT_PATH$") >= 0) return "";
var ch = (manifest.indexOf('\n') >= 0 ? "\n" : "\r");
if (manifest.indexOf(".spt") >= 0) {
var s = JU.PT.split(manifest, ch);
for (var i = s.length; --i >= 0; ) if (s[i].indexOf(".spt") >= 0) return "|" + JU.PT.trim(s[i], "\r\n \t");

}return null;
}, "~S");
c$.getFileReferences = Clazz.defineMethod(c$, "getFileReferences", 
function(script, fileList, fileListUTF){
for (var ipt = 0; ipt < JV.FileManager.scriptFilePrefixes.length; ipt++) {
var tag = JV.FileManager.scriptFilePrefixes[ipt];
var i = -1;
while ((i = script.indexOf(tag, i + 1)) >= 0) {
var s = JU.PT.getQuotedStringAt(script, i);
if (s.indexOf("\\u") >= 0) s = JU.Escape.unescapeUnicode(s);
fileList.addLast(s);
if (fileListUTF != null) {
if (s.indexOf("\\u") >= 0) s = JU.Escape.unescapeUnicode(s);
fileListUTF.addLast(s);
}}
}
}, "~S,JU.Lst,JU.Lst");
c$.setScriptFileReferences = Clazz.defineMethod(c$, "setScriptFileReferences", 
function(script, localPath, remotePath, scriptPath){
if (localPath != null) script = JV.FileManager.setScriptFileRefs(script, localPath, true);
if (remotePath != null) script = JV.FileManager.setScriptFileRefs(script, remotePath, false);
script = JU.PT.rep(script, "\1\"", "\"");
if (scriptPath != null) {
while (scriptPath.endsWith("/")) scriptPath = scriptPath.substring(0, scriptPath.length - 1);

for (var ipt = 0; ipt < JV.FileManager.scriptFilePrefixes.length; ipt++) {
var tag = JV.FileManager.scriptFilePrefixes[ipt];
script = JU.PT.rep(script, tag + ".", tag + scriptPath);
}
}return script;
}, "~S,~S,~S,~S");
c$.setScriptFileRefs = Clazz.defineMethod(c$, "setScriptFileRefs", 
function(script, dataPath, isLocal){
if (dataPath == null) return script;
var noPath = (dataPath.length == 0);
var fileNames =  new JU.Lst();
JV.FileManager.getFileReferences(script, fileNames, null);
var oldFileNames =  new JU.Lst();
var newFileNames =  new JU.Lst();
var nFiles = fileNames.size();
for (var iFile = 0; iFile < nFiles; iFile++) {
var name0 = fileNames.get(iFile);
var name = name0;
var pt = name.indexOf("::");
var type = "";
if (pt >= 0) {
type = name.substring(pt + 2);
name = name.substring(pt + 2);
}if (isLocal == JU.OC.isLocal(name)) {
pt = (noPath ? -1 : name.indexOf("/" + dataPath + "/"));
if (pt >= 0) {
name = name.substring(pt + 1);
} else {
pt = name.lastIndexOf("/");
if (pt < 0 && !noPath) name = "/" + name;
if (pt < 0 || noPath) pt++;
name = dataPath + name.substring(pt);
}}name = type + name;
JU.Logger.info("FileManager substituting " + name0 + " --> " + name);
oldFileNames.addLast("\"" + name0 + "\"");
newFileNames.addLast("\1\"" + name + "\"");
}
return JU.PT.replaceStrings(script, oldFileNames, newFileNames);
}, "~S,~S,~B");
Clazz.defineMethod(c$, "cachePut", 
function(key, data){
key = JV.FileManager.fixDOSName(key);
if (JU.Logger.debugging) JU.Logger.debug("cachePut " + key);
if (data == null || "".equals(data)) {
this.cache.remove(key);
return;
}this.cache.put(key, data);
this.getCachedPngjBytes(key);
}, "~S,~O");
Clazz.defineMethod(c$, "cacheGet", 
function(key, bytesOnly){
key = JV.FileManager.fixDOSName(key);
var pt = key.indexOf("|");
if (pt >= 0 && !key.endsWith("##JmolSurfaceInfo##")) key = key.substring(0, pt);
key = this.getFilePath(key, true, false);
var data = null;
{
(data = Jmol.Cache.get(key)) || (data = this.cache.get(key));
}return (bytesOnly && ((typeof(data)=='string')) ? null : data);
}, "~S,~B");
Clazz.defineMethod(c$, "cacheClear", 
function(){
JU.Logger.info("cache cleared");
this.cache.clear();
if (this.pngjCache == null) return;
this.pngjCache = null;
JU.Logger.info("PNGJ cache cleared");
});
Clazz.defineMethod(c$, "cacheFileByNameAdd", 
function(fileName, isAdd){
if (fileName == null || !isAdd && fileName.equalsIgnoreCase("")) {
this.cacheClear();
return -1;
}var data;
if (isAdd) {
fileName = JV.JC.fixProtocol(this.vwr.resolveDatabaseFormat(fileName));
data = this.getFileAsBytes(fileName, null);
if ((typeof(data)=='string')) return 0;
this.cachePut(fileName, data);
} else {
if (fileName.endsWith("*")) return JU.AU.removeMapKeys(this.cache, fileName.substring(0, fileName.length - 1));
data = this.cache.remove(JV.FileManager.fixDOSName(fileName));
}return (data == null ? 0 : (typeof(data)=='string') ? (data).length : (data).length);
}, "~S,~B");
Clazz.defineMethod(c$, "cacheList", 
function(){
var map =  new java.util.Hashtable();
for (var entry, $entry = this.cache.entrySet().iterator (); $entry.hasNext()&& ((entry = $entry.next ()) || true);) map.put(entry.getKey(), Integer.$valueOf(JU.AU.isAB(entry.getValue()) ? (entry.getValue()).length : entry.getValue().toString().length));

return map;
});
Clazz.defineMethod(c$, "getCanonicalName", 
function(pathName){
var names = this.getClassifiedName(pathName, true);
return (names == null ? pathName : names[2]);
}, "~S");
Clazz.defineMethod(c$, "recachePngjBytes", 
function(fileName, bytes){
if (this.pngjCache == null || !this.pngjCache.containsKey(fileName)) return;
this.pngjCache.put(fileName, bytes);
JU.Logger.info("PNGJ recaching " + fileName + " (" + bytes.length + ")");
}, "~S,~A");
Clazz.defineMethod(c$, "getPngjOrDroppedBytes", 
function(fullName, name){
var bytes = this.getCachedPngjBytes(fullName);
return (bytes == null ? this.cacheGet(name, true) : bytes);
}, "~S,~S");
Clazz.defineMethod(c$, "getCachedPngjBytes", 
function(pathName){
return (pathName == null || this.pngjCache == null || pathName.indexOf(".png") < 0 ? null : this.getJzu().getCachedPngjBytes(this, pathName));
}, "~S");
Clazz.overrideMethod(c$, "postByteArray", 
function(fileName, bytes){
if (fileName.startsWith("cache://")) {
this.cachePut(fileName, bytes);
return "OK " + bytes.length + "cached";
}var ret = this.getBufferedInputStreamOrErrorMessageFromName(fileName, null, false, false, bytes, false, true);
if ((typeof(ret)=='string')) return ret;
try {
ret = JU.Rdr.getStreamAsBytes(ret, null);
} catch (e) {
if (Clazz.exceptionOf(e,"java.io.IOException")){
try {
(ret).close();
} catch (e1) {
if (Clazz.exceptionOf(e1,"java.io.IOException")){
} else {
throw e1;
}
}
} else {
throw e;
}
}
return (ret == null ? "" : JU.Rdr.fixUTF(ret));
}, "~S,~A");
c$.isJmolType = Clazz.defineMethod(c$, "isJmolType", 
function(type){
return (type.equals("PNG") || type.equals("PNGJ") || type.equals("JMOL") || type.equals("ZIP") || type.equals("ZIPALL"));
}, "~S");
c$.isEmbeddable = Clazz.defineMethod(c$, "isEmbeddable", 
function(type){
var pt = type.lastIndexOf('.');
if (pt >= 0) type = type.substring(pt + 1);
type = type.toUpperCase();
return (JV.FileManager.isJmolType(type) || JU.PT.isOneOf(type, ";JPG;JPEG;POV;IDTF;"));
}, "~S");
Clazz.defineMethod(c$, "getEmbeddedFileState", 
function(fileName, allowCached, sptName){
if (!JV.FileManager.isEmbeddable(fileName)) return "";
var dir = this.getZipDirectory(fileName, false, allowCached);
if (dir.length == 0) {
var state = this.vwr.getFileAsString4(fileName, -1, false, true, false, "file");
return (state.indexOf("**** Jmol Embedded Script ****") < 0 ? "" : JV.FileManager.getEmbeddedScript(state));
}for (var i = 0; i < dir.length; i++) if (dir[i].indexOf(sptName) >= 0) {
var data =  Clazz.newArray(-1, [fileName + "|" + dir[i], null]);
this.getFileDataAsString(data, -1, false, false, false);
return data[1];
}
return "";
}, "~S,~B,~S");
c$.stripTypePrefix = Clazz.defineMethod(c$, "stripTypePrefix", 
function(fileName){
var pt = fileName.indexOf("::");
return (pt < 0 || pt >= 20 ? fileName : fileName.substring(pt + 2));
}, "~S");
c$.getEmbeddedScript = Clazz.defineMethod(c$, "getEmbeddedScript", 
function(s){
if (s == null) return s;
var pt = s.indexOf("**** Jmol Embedded Script ****");
if (pt < 0) return s;
var pt1 = s.lastIndexOf("/*", pt);
var pt2 = s.indexOf((s.charAt(pt1 + 2) == '*' ? "*" : "") + "*/", pt);
if (pt1 >= 0 && pt2 >= pt) s = s.substring(pt + "**** Jmol Embedded Script ****".length, pt2) + "\n";
while ((pt1 = s.indexOf(" #Jmol...\u0000")) >= 0) s = s.substring(0, pt1) + s.substring(pt1 + " #Jmol...\u0000".length + 4);

if (JU.Logger.debugging) JU.Logger.debug(s);
return s;
}, "~S");
Clazz.defineMethod(c$, "isZipStream", 
function(br){
return this.vwr.getJzt().isZipStream(br);
}, "~O");
Clazz.defineMethod(c$, "openFileAsync", 
function(fname, flags, type){
var scriptOnly = ((flags & 32) != 0);
if (!scriptOnly && (flags & 64) != 0 && JV.FileManager.isEmbeddable(fname)) this.checkResize(fname);
var noScript = ((flags & 2) != 0);
var noAutoPlay = ((flags & 8) != 0);
var cmd = null;
fname = fname.trim().$replace('\\', '/');
var isCached = fname.startsWith("cache://");
if (this.vwr.isApplet && fname.indexOf("://") < 0) fname = "file://" + (fname.startsWith("/") ? "" : "/") + fname;
try {
if (scriptOnly) {
cmd = "script " + JU.PT.esc(fname);
return;
}if (fname.endsWith(".pse")) {
cmd = (isCached ? "" : "zap;") + "load SYNC " + JU.PT.esc(fname) + (this.vwr.isApplet ? "" : " filter 'DORESIZE'");
return;
}if (fname.endsWith(".jvxl")) {
cmd = "isosurface ";
} else if (!fname.toLowerCase().endsWith(".spt")) {
if (type == null) type = this.getDragDropFileTypeName(fname);
 else if (!type.endsWith("::")) type += "::";
if (type == null) {
try {
var bis = this.vwr.getBufferedInputStream(fname);
type = JV.FileManager.determineSurfaceFileType(JU.Rdr.getBufferedReader(bis, "ISO-8859-1"));
if (type == null) {
cmd = "script " + JU.PT.esc(fname);
return;
}} catch (e) {
if (Clazz.exceptionOf(e,"java.io.IOException")){
return;
} else {
throw e;
}
}
if (type === "MENU") {
cmd = "load MENU " + JU.PT.esc(fname);
} else {
cmd = "if (_filetype == 'Pdb') { isosurface sigma 1.0 within 2.0 {*} " + JU.PT.esc(fname) + " mesh nofill }; else; { isosurface " + JU.PT.esc(fname) + "}";
}return;
}if (type.equals("spt::")) {
cmd = "script " + JU.PT.esc((fname.startsWith("spt::") ? fname.substring(5) : fname));
return;
}if (type.equals("dssr")) {
cmd = "model {visible} property dssr ";
} else if (type.equals("Jmol")) {
cmd = "script ";
} else if (type.equals("Cube::")) {
cmd = (this.vwr.ms.ac == 0 ? "load " + JU.PT.esc(fname) + ";" : "");
cmd += "isosurface sign red blue ";
} else if (!type.equals("spt")) {
if ((flags & 16) != 0) {
flags = (flags & -17) | 1;
switch (this.vwr.ms.ac == 0 ? 0 : this.vwr.confirm(J.i18n.GT.$("Would you like to replace the current model with the selected model?"), J.i18n.GT.$("Would you like to append?"))) {
case 2:
return;
case 0:
break;
default:
flags |= 4;
break;
}
}var isAppend = ((flags & 4) != 0);
var pdbCartoons = ((flags & 1) != 0 && !isAppend);
if (type.endsWith("::")) {
var pt = type.indexOf("|");
if (pt >= 0) {
fname += type.substring(pt, type.length - 2);
type = "";
}fname = type + fname;
}cmd = this.vwr.g.defaultDropScript;
if (cmd.equals("zap; load SYNC \"%FILE\";if (%ALLOWCARTOONS && _loadScript == \'\' && defaultLoadScript == \'\' && _filetype == \'Pdb\') {if ({(protein or nucleic)&*/1.1} && {*/1.1}[1].groupindex != {*/1.1}[0].groupindex){select protein or nucleic;cartoons only;}if ({visible && cartoons > 0}){color structure}else{wireframe -0.1};if (!{visible}){select !visible;wireframe 0.15;color none;select !visible;spacefill 23%};select *}")) {
if (!JV.JC.isLikelyPDB(type) || !pdbCartoons) {
var pt = cmd.indexOf("if (");
if (pt >= 0) {
cmd = cmd.substring(0, pt).trim();
}}}cmd = JU.PT.rep(cmd, "%FILE", fname);
cmd = JU.PT.rep(cmd, "%ALLOWCARTOONS", "" + pdbCartoons);
if (cmd.toLowerCase().startsWith("zap") && (isCached || isAppend)) cmd = cmd.substring(3);
if (isAppend) {
cmd = JU.PT.rep(cmd, "load SYNC", "load append");
}return;
}}if (cmd == null && !noScript && this.vwr.scriptEditorVisible) this.vwr.showEditor( Clazz.newArray(-1, [fname, this.vwr.getFileAsString3(fname, true, null)]));
 else cmd = (cmd == null ? "script " : cmd) + JU.PT.esc(fname);
} finally {
if (cmd != null) this.vwr.evalString(cmd + (noAutoPlay ? "#!NOAUTOPLAY" : ""));
}
}, "~S,~N,~S");
Clazz.defineMethod(c$, "getDragDropFileTypeName", 
function(fileName){
var pt = fileName.indexOf("::");
if (pt >= 0) return fileName.substring(0, pt + 2);
if (fileName.startsWith("=")) return "pdb";
if (fileName.endsWith(".dssr")) return "dssr";
var br = this.getUnzippedReaderOrStreamFromName(fileName, null, true, false, true, true, null);
var modelType = null;
if (this.isZipStream(br)) {
var zipDirectory = this.vwr.getZipDirectoryAsString(fileName);
if (zipDirectory.indexOf("JmolManifest") >= 0) return "Jmol";
modelType = this.getFileTypeName(JU.Rdr.getBR(zipDirectory));
} else if (Clazz.instanceOf(br,"java.io.BufferedReader") || Clazz.instanceOf(br,"java.io.BufferedInputStream")) {
modelType = this.getFileTypeName(br);
}if (modelType != null) return modelType + "::";
if (JU.AU.isAS(br)) {
return (br)[0];
}return null;
}, "~S");
Clazz.defineMethod(c$, "checkResize", 
function(fname){
try {
var data = this.getEmbeddedFileState(fname, false, "state.spt");
if (data.indexOf("preferredWidthHeight") >= 0) this.vwr.sm.resizeInnerPanelString(data);
} catch (e) {
}
}, "~S");
Clazz.defineMethod(c$, "getJmolDataReader", 
function(){
if (this.staticJmolDataReader == null) {
this.staticJmolDataReader = J.adapter.smarter.Resolver.getReader("JmolData", null);
this.staticJmolDataReader.vwr = this.vwr;
}return this.staticJmolDataReader;
});
Clazz.defineMethod(c$, "readCifData", 
function(fnameOrCifData, type){
var isData = (fnameOrCifData != null && fnameOrCifData.indexOf("#CIF") >= 0);
var keys = null;
var pt = (fnameOrCifData == null ? -1 : fnameOrCifData.indexOf(";keys="));
if (pt >= 0) {
keys = fnameOrCifData.substring(pt + 6).$plit(",");
fnameOrCifData = fnameOrCifData.substring(0, pt);
}if (type == null && fnameOrCifData != null && fnameOrCifData.toUpperCase().indexOf("BCIF") >= 0) {
var is = this.getBufferedInputStream(fnameOrCifData);
try {
return (J.api.Interface.getInterface("JU.MessagePackReader", this.vwr, "script")).getMapForStream(is);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
e.printStackTrace();
return  new java.util.Hashtable();
} else {
throw e;
}
}
}var data = (isData ? fnameOrCifData : fnameOrCifData == null || fnameOrCifData.length == 0 ? this.vwr.getCurrentFileAsString("script") : this.getAsciiFileOrNull(fnameOrCifData));
if (data == null || data.length < 2) return null;
var rdr = JU.Rdr.getBR(data);
if (type == null) type = this.getFileTypeName(rdr);
return (type == null ? null : this.readCifDataKey(rdr, type, keys));
}, "~S,~S");
Clazz.defineMethod(c$, "readCifDataKey", 
function(rdrOrStringData, type, keys){
var rdr = (Clazz.instanceOf(rdrOrStringData,"java.io.BufferedReader") ? rdrOrStringData : JU.Rdr.getBR(rdrOrStringData));
return JU.Rdr.readCifData(J.api.Interface.getInterface(("Cif2".equals(type) ? "J.adapter.readers.cif.Cif2DataParser" : "JU.CifDataParser"), this.vwr, "script"), rdr, keys);
}, "~O,~S,~A");
Clazz.defineMethod(c$, "getAsciiFileOrNull", 
function(name){
var data =  Clazz.newArray(-1, [name, null]);
return (this.getFileDataAsString(data, -1, false, false, false) ? data[1] : null);
}, "~S");
Clazz.defineMethod(c$, "getFileTypeName", 
function(br){
return this.vwr.getModelAdapter().getFileTypeName(br);
}, "~O");
c$.SIMULATION_PROTOCOL = "http://SIMULATION/";
c$.scriptFilePrefixes =  Clazz.newArray(-1, ["/*file*/\"", "FILE0=\"", "FILE1=\""]);
});
;//5.0.1-v7 Mon Aug 17 10:07:10 MDT 2026
