Clazz.declarePackage("J.adapter.readers.spartan");
Clazz.load(null, "J.adapter.readers.spartan.SpartanUtil", ["java.io.BufferedInputStream", "java.util.Hashtable", "$.StringTokenizer", "javajs.api.GenericZipInputStream", "JU.Lst", "$.PT", "$.Rdr", "$.SB", "J.api.Interface", "JU.Escape", "$.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.fm = null;
Clazz.instantialize(this, arguments);}, J.adapter.readers.spartan, "SpartanUtil", null);
/*LV!1824 unnec constructor*/Clazz.defineMethod(c$, "set", 
function(fm){
this.fm = fm;
return this;
}, "JV.FileManager");
Clazz.defineMethod(c$, "getFileList", 
function(name, isTypeCheckOnly){
var pt = name.lastIndexOf(".spardir");
var info = null;
if (name.endsWith(".spardir.zip")) {
info =  Clazz.newArray(-1, ["SpartanSmol", "Directory Entry ", name + "|output"]);
} else {
name = name.$replace('\\', '/');
if (!name.endsWith(".spardir") && name.indexOf(".spardir/") < 0) return null;
info = (name.lastIndexOf("/") > pt ?  Clazz.newArray(-1, ["SpartanSmol", "Directory Entry ", name + "/input", name + "/archive", name + "/parchive", name + "/Molecule:asBinaryString", name + "/proparc"]) :  Clazz.newArray(-1, ["SpartanSmol", "Directory Entry ", name + "/output"]));
}if (isTypeCheckOnly) return info;
var name00 = name;
var header = info[1];
var outputFileName = info[2];
var fileData =  new java.util.Hashtable();
if (info.length == 3) {
outputFileName = this.spartanGetObjectAsSections(outputFileName, header, fileData);
fileData.put("OUTPUT", outputFileName);
info = this.spartanFileList(name, fileData.get(outputFileName));
if (info.length == 3) {
outputFileName = this.spartanGetObjectAsSections(info[2], header, fileData);
fileData.put("OUTPUT", outputFileName);
info = this.spartanFileList(info[1], fileData.get(outputFileName));
}}var sb =  new JU.SB();
var s;
if (fileData.get("OUTPUT") != null) {
sb.append(fileData.get(fileData.get("OUTPUT")));
}for (var i = 2; i < info.length; i++) {
name = info[i];
name = this.spartanGetObjectAsSections(name, header, fileData);
JU.Logger.info("reading " + name);
s = fileData.get(name);
sb.append(s);
}
s = sb.toString();
if (this.fm.spardirCache == null) this.fm.spardirCache =  new java.util.Hashtable();
this.fm.spardirCache.put(name00.$replace('\\', '/'), s.getBytes());
return JU.Rdr.getBR(s);
}, "~S,~B");
Clazz.defineMethod(c$, "getData", 
function(is, zipDirectory){
var data =  new JU.SB();
data.append("Zip File Directory: ").append("\n").append(JU.Escape.eAS(zipDirectory, true)).append("\n");
var fileData =  new java.util.Hashtable();
this.getAllZipData(is,  Clazz.newArray(-1, []), "", "Molecule", "__MACOSX", fileData);
var prefix = "|";
var outputData = fileData.get(prefix + "output");
if (outputData == null) outputData = fileData.get((prefix = "|" + zipDirectory[1]) + "output");
data.append(outputData);
var files = this.getSpartanFileList(prefix, this.getSpartanDirs(outputData));
for (var i = 2; i < files.length; i++) {
var name = files[i];
if (fileData.containsKey(name)) data.append(fileData.get(name));
 else data.append(name + "\n");
}
return data;
}, "java.io.InputStream,~A");
Clazz.defineMethod(c$, "spartanFileList", 
function(name, outputFileData){
var dirNums = this.getSpartanDirs(outputFileData);
if (dirNums.length == 0) {
if (name.endsWith(".spardir")) return this.getSpartanFileList(name,  Clazz.newArray(-1, ["M0001"]));
if (name.endsWith(".spardir.zip")) {
if (outputFileData.indexOf(".zip|output") >= 0) {
var sname = name.$replace('\\', '/');
var pt = name.lastIndexOf(".spardir");
pt = sname.lastIndexOf("/");
sname = name + "|" + JU.PT.rep(name.substring(pt + 1, name.length - 4), "DROP_", "");
return  Clazz.newArray(-1, ["SpartanSmol", sname, sname + "/output"]);
}}}return this.getSpartanFileList(name, dirNums);
}, "~S,~S");
Clazz.defineMethod(c$, "getSpartanDirs", 
function(outputFileData){
if (outputFileData == null) return  Clazz.newArray(-1, []);
var v =  new JU.Lst();
var token;
var lastToken = "";
if (outputFileData.startsWith("java.io.FileNotFoundException") || outputFileData.startsWith("FILE NOT FOUND") || outputFileData.indexOf("<html") >= 0) return  new Array(0);
try {
var tokens =  new java.util.StringTokenizer(outputFileData, " \t\r\n");
while (tokens.hasMoreTokens()) {
if ((token = tokens.nextToken()).equals(")")) v.addLast(lastToken);
 else if (token.equals("Start-") && tokens.nextToken().equals("Molecule")) v.addLast(JU.PT.split(tokens.nextToken(), "\"")[1]);
 else if (token.equals("Molecules")) {
var n = JU.PT.parseInt(lastToken);
for (var i = 1; i <= n; i++) {
var s = "0000" + i;
v.addLast("M" + s.substring(s.length - 4));
}
}lastToken = token;
}
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
return (v.size() == 0 ?  Clazz.newArray(-1, ["M0001"]) : v.toArray( new Array(v.size())));
}, "~S");
Clazz.defineMethod(c$, "getSpartanFileList", 
function(name, dirNums){
var files =  new Array(2 + dirNums.length * 6);
files[0] = "SpartanSmol";
files[1] = "Directory Entry ";
var pt = 2;
name = name.$replace('\\', '/');
if (name.endsWith("/")) name = name.substring(0, name.length - 1);
var sep = (name.equals("|") ? "" : name.endsWith(".zip") ? "|" : "/");
for (var i = 0; i < dirNums.length; i++) {
var path = name + sep;
var s = dirNums[i];
path += (JU.PT.isDigit(s.charAt(0)) ? "Profile." + s : s) + "/";
files[pt++] = path + "#JMOL_MODEL " + dirNums[i];
files[pt++] = path + "input";
files[pt++] = path + "archive";
files[pt++] = path + "parchive";
files[pt++] = path + "Molecule:asBinaryString";
files[pt++] = path + "proparc";
}
return files;
}, "~S,~A");
Clazz.defineMethod(c$, "spartanGetObjectAsSections", 
function(name, header, fileData){
if (name == null) return null;
var subFileList = null;
var asBinaryString = false;
var path = name.$replace('\\', '/');
if (name.indexOf(":asBinaryString") >= 0) {
asBinaryString = true;
name = name.substring(0, name.indexOf(":asBinaryString"));
}var sb = null;
if (fileData.containsKey(path)) return path;
if (path.indexOf("#JMOL_MODEL ") >= 0) {
fileData.put(path, path + "\n");
return path;
}var fullName = name;
if (name.indexOf("|") >= 0) {
subFileList = JU.PT.split(name, "|");
name = subFileList[0];
}var bis = null;
try {
var t = this.fm.getBufferedInputStreamOrErrorMessageFromName(name, fullName, false, false, null, false, true);
if ((typeof(t)=='string')) {
fileData.put(path, t + "\n");
return path;
}name = name.$replace('\\', '/');
bis = t;
if (JU.Rdr.isCompoundDocumentS(bis)) {
var doc = J.api.Interface.getInterface("JU.CompoundDocument", this.fm.vwr, "file");
doc.setDocStream(this.fm.vwr.getJzt(), bis);
doc.getAllDataMapped(name, "Molecule", fileData);
} else if (JU.Rdr.isZipS(bis)) {
this.getAllZipData(bis, subFileList, name, "Molecule", "__MACOSX", fileData);
} else if (asBinaryString) {
var bd = J.api.Interface.getInterface("JU.BinaryDocument", this.fm.vwr, "file");
bd.setStream(bis, false);
sb =  new JU.SB();
if (header != null) sb.append("BEGIN Directory Entry " + path + "\n");
try {
while (true) sb.append(Integer.toHexString(bd.readByte() & 0xFF)).appendC(' ');

} catch (e1) {
if (Clazz.exceptionOf(e1, Exception)){
sb.appendC('\n');
} else {
throw e1;
}
}
if (header != null) sb.append("\nEND Directory Entry " + path + "\n");
fileData.put(path, sb.toString());
} else {
var br = JU.Rdr.getBufferedReader(JU.Rdr.isGzipS(bis) ?  new java.io.BufferedInputStream(this.fm.vwr.getJzt().newGZIPInputStream(bis)) : bis, null);
var line;
sb =  new JU.SB();
if (header != null) sb.append("BEGIN Directory Entry " + path + "\n");
while ((line = br.readLine()) != null) {
sb.append(line);
sb.appendC('\n');
}
br.close();
if (header != null) sb.append("\nEND Directory Entry " + path + "\n");
fileData.put(path, sb.toString());
}} catch (ioe) {
if (Clazz.exceptionOf(ioe, Exception)){
fileData.put(path, ioe.toString());
} else {
throw ioe;
}
}
if (bis != null) try {
bis.close();
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
if (!fileData.containsKey(path)) fileData.put(path, "FILE NOT FOUND: " + path + "\n");
return path;
}, "~S,~S,java.util.Map");
Clazz.defineMethod(c$, "getAllZipData", 
function(is, subfileList, name0, binaryFileList, exclude, fileData){
var zis =  new javajs.api.GenericZipInputStream(Clazz.instanceOf(is,"java.io.BufferedInputStream") ? is :  new java.io.BufferedInputStream(is));
var ze;
var listing =  new JU.SB();
binaryFileList = "|" + binaryFileList + "|";
var prefix = JU.PT.join(subfileList, '/', 1);
var prefixd = null;
if (prefix != null) {
prefixd = prefix.substring(0, prefix.indexOf("/") + 1);
if (prefixd.length == 0) prefixd = null;
}try {
while ((ze = zis.getNextEntry()) != null) {
var name = ze.getName();
if (prefix != null && prefixd != null && !(name.equals(prefix) || name.startsWith(prefixd)) || exclude != null && name.contains(exclude)) continue;
listing.append(name).appendC('\n');
var sname = "|" + name.substring(name.lastIndexOf("/") + 1) + "|";
var asBinaryString = (binaryFileList.indexOf(sname) >= 0);
var bytes = JU.Rdr.getLimitedStreamBytes(zis, ze.getSize());
var str;
if (asBinaryString) {
var ret =  new JU.SB();
for (var i = 0; i < bytes.length; i++) ret.append(Integer.toHexString(bytes[i] & 0xFF)).appendC(' ');

str = ret.toString();
name += ":asBinaryString";
} else {
str = JU.Rdr.fixUTF(bytes);
}str = "BEGIN Directory Entry " + name + "\n" + str + "\nEND Directory Entry " + name + "\n";
var key = name0 + "|" + name;
fileData.put(key, str);
}
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
fileData.put("#Directory_Listing", listing.toString());
}, "java.io.InputStream,~A,~S,~S,~S,java.util.Map");
});
;//5.0.1-v7 Tue Feb 10 09:16:45 CST 2026
