Clazz.declarePackage("J.io");
Clazz.load(null, "J.io.JmolUtil", ["java.net.URL", "java.util.Hashtable", "JU.AU", "$.Lst", "$.OC", "$.PT", "$.Rdr", "J.adapter.smarter.AtomSetCollection", "J.api.Interface", "JU.Logger", "JV.FileManager", "$.Viewer"], function(){
var c$ = Clazz.declareType(J.io, "JmolUtil", null);
/*LV!1824 unnec constructor*/Clazz.defineMethod(c$, "getImage", 
function(vwr, fullPathNameOrBytes, echoName, forceSync){
var image = null;
var info = null;
var apiPlatform = vwr.apiPlatform;
var createImage = false;
var fullPathName = "" + fullPathNameOrBytes;
if ((typeof(fullPathNameOrBytes)=='string')) {
var isBMP = fullPathName.toUpperCase().endsWith("BMP");
if (forceSync || fullPathName.indexOf("|") > 0 || isBMP) {
var ret = vwr.fm.getFileAsBytes(fullPathName, null);
if (!JU.AU.isAB(ret)) return "" + ret;
if (JV.Viewer.isJS) info =  Clazz.newArray(-1, [echoName, fullPathNameOrBytes, ret]);
 else image = apiPlatform.createImage(ret);
} else if (JU.OC.urlTypeIndex(fullPathName) >= 0) {
if (JV.Viewer.isJS) info =  Clazz.newArray(-1, [echoName, fullPathNameOrBytes, null]);
 else try {
image = apiPlatform.createImage( new java.net.URL(Clazz.castNullAs("java.net.URL"), fullPathName, null));
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
return "bad URL: " + fullPathName;
} else {
throw e;
}
}
} else {
createImage = true;
}} else if (JV.Viewer.isJS) {
info =  Clazz.newArray(-1, [echoName, JU.Rdr.guessMimeTypeForBytes(fullPathNameOrBytes), fullPathNameOrBytes]);
} else {
createImage = true;
}if (createImage) image = apiPlatform.createImage("\1close".equals(fullPathNameOrBytes) ? "\1close" + echoName : fullPathNameOrBytes);
 else if (info != null) image = apiPlatform.createImage(info);
{
return image;
}}, "JV.Viewer,~O,~S,~B");
Clazz.defineMethod(c$, "getAtomSetCollectionOrBufferedReaderFromZip", 
function(vwr, is, fileName, zipDirectory, htParams, subFilePtr, asBufferedReader){
var adapter = vwr.getModelAdapter();
var doCombine = (subFilePtr == 1);
htParams.put("zipSet", fileName);
var subFileList = htParams.get("subFileList");
if (subFileList == null) subFileList = this.getSpartanSubfiles(zipDirectory);
var subFileName = (subFileList == null || subFilePtr >= subFileList.length ? htParams.get("SubFileName") : subFileList[subFilePtr]);
if (subFileName != null && (subFileName.startsWith("/") || subFileName.startsWith("\\"))) subFileName = subFileName.substring(1);
var selectedFile = 0;
if (subFileName == null && htParams.containsKey("modelNumber")) {
selectedFile = (htParams.get("modelNumber")).intValue();
if (selectedFile > 0 && doCombine) htParams.remove("modelNumber");
}var manifest = htParams.get("manifest");
var useFileManifest = (manifest == null);
if (useFileManifest) manifest = (zipDirectory.length > 0 ? zipDirectory[0] : "");
var haveManifest = (manifest.length > 0);
if (haveManifest) {
if (JU.Logger.debugging) JU.Logger.debug("manifest for  " + fileName + ":\n" + manifest);
}var ignoreErrors = (manifest.indexOf("IGNORE_ERRORS") >= 0);
var selectAll = (manifest.indexOf("IGNORE_MANIFEST") >= 0);
var exceptFiles = (manifest.indexOf("EXCEPT_FILES") >= 0);
if (selectAll || subFileName != null) haveManifest = false;
if (useFileManifest && haveManifest) {
var path = JV.FileManager.getManifestScriptPath(manifest);
if (path != null) {
return "NOTE: file recognized as a script file: " + fileName + path + "\n";
}}var vCollections =  new JU.Lst();
var htCollections = (haveManifest ?  new java.util.Hashtable() : null);
var nFiles = 0;
try {
var spartanData = (this.isSpartanZip(zipDirectory) ? vwr.fm.spartanUtil().getData(is, zipDirectory) : null);
var zpt = vwr.getJzt();
var ret;
if (spartanData != null) {
var reader = JU.Rdr.getBR(spartanData.toString());
if (asBufferedReader) return reader;
ret = adapter.getAtomSetCollectionFromReader(fileName, reader, htParams);
if ((typeof(ret)=='string')) return ret;
if (Clazz.instanceOf(ret,"J.adapter.smarter.AtomSetCollection")) {
var atomSetCollection = ret;
if (atomSetCollection.errorMessage != null) {
if (ignoreErrors) return null;
return atomSetCollection.errorMessage;
}return atomSetCollection;
}if (ignoreErrors) return null;
return "unknown reader error";
}if (Clazz.instanceOf(is,"java.io.BufferedInputStream")) is = JU.Rdr.getPngZipStream(is, true);
var zis = zpt.newZipInputStream(is);
var ze;
if (haveManifest) manifest = '|' + manifest.$replace('\r', '|').$replace('\n', '|') + '|';
while ((ze = zis.getNextEntry()) != null && (selectedFile <= 0 || vCollections.size() < selectedFile)) {
if (ze.isDirectory()) continue;
var thisEntry = ze.getName();
if (subFileName != null && !thisEntry.equals(subFileName)) continue;
if (subFileName != null) htParams.put("subFileName", subFileName);
if (thisEntry.startsWith("JmolManifest") || haveManifest && exceptFiles == manifest.indexOf("|" + thisEntry + "|") >= 0) continue;
var bytes = JU.Rdr.getLimitedStreamBytes(zis, ze.getSize());
if (JU.Rdr.isGzipB(bytes)) bytes = JU.Rdr.getLimitedStreamBytes(zpt.getUnGzippedInputStream(bytes), -1);
if (JU.Rdr.isZipB(bytes) || JU.Rdr.isPngZipB(bytes)) {
var bis = JU.Rdr.getBIS(bytes);
var zipDir2 = zpt.getZipDirectoryAndClose(bis, "JmolManifest");
bis = JU.Rdr.getBIS(bytes);
var atomSetCollections = this.getAtomSetCollectionOrBufferedReaderFromZip(vwr, bis, fileName + "|" + thisEntry, zipDir2, htParams, ++subFilePtr, asBufferedReader);
if ((typeof(atomSetCollections)=='string')) {
if (ignoreErrors) continue;
return atomSetCollections;
} else if (Clazz.instanceOf(atomSetCollections,"J.adapter.smarter.AtomSetCollection") || Clazz.instanceOf(atomSetCollections,"JU.Lst")) {
if (haveManifest && !exceptFiles) htCollections.put(thisEntry, atomSetCollections);
 else vCollections.addLast(atomSetCollections);
} else if (Clazz.instanceOf(atomSetCollections,"java.io.BufferedReader")) {
if (doCombine) zis.close();
return atomSetCollections;
} else {
if (ignoreErrors) continue;
zis.close();
return "unknown zip reader error";
}} else if (JU.Rdr.isPickleB(bytes)) {
var bis = JU.Rdr.getBIS(bytes);
if (doCombine) zis.close();
return bis;
} else {
var sData;
if (JU.Rdr.isCompoundDocumentB(bytes)) {
var jd = J.api.Interface.getInterface("JU.CompoundDocument", vwr, "file");
jd.setDocStream(zpt, JU.Rdr.getBIS(bytes));
sData = jd.getAllDataFiles("Molecule", "Input").toString();
} else {
sData = JU.Rdr.fixUTF(bytes);
}var reader = JU.Rdr.getBR(sData);
if (asBufferedReader) {
if (doCombine) zis.close();
return reader;
}var fname = fileName + "|" + ze.getName();
ret = adapter.getAtomSetCollectionFromReader(fname, reader, htParams);
if (!(Clazz.instanceOf(ret,"J.adapter.smarter.AtomSetCollection"))) {
if (ignoreErrors) continue;
zis.close();
return "" + ret;
}if (haveManifest && !exceptFiles) htCollections.put(thisEntry, ret);
 else vCollections.addLast(ret);
var a = ret;
if (a.errorMessage != null) {
if (ignoreErrors) continue;
zis.close();
return a.errorMessage;
}}}
if (doCombine) zis.close();
if (haveManifest && !exceptFiles) {
var list = JU.PT.split(manifest, "|");
for (var i = 0; i < list.length; i++) {
var file = list[i];
if (file.length == 0 || file.indexOf("#") == 0) continue;
if (htCollections.containsKey(file)) vCollections.addLast(htCollections.get(file));
 else if (JU.Logger.debugging) JU.Logger.debug("manifested file " + file + " was not found in " + fileName);
}
}if (!doCombine) return vCollections;
var result = (vCollections.size() == 1 && Clazz.instanceOf(vCollections.get(0),"J.adapter.smarter.AtomSetCollection") ? vCollections.get(0) :  new J.adapter.smarter.AtomSetCollection("Array", null, null, vCollections));
if (result.errorMessage != null) {
if (ignoreErrors) return null;
return result.errorMessage;
}if (nFiles == 1) selectedFile = 1;
if (selectedFile > 0 && selectedFile <= vCollections.size()) return vCollections.get(selectedFile - 1);
return result;
} catch (e$$) {
if (Clazz.exceptionOf(e$$, Exception)){
var e = e$$;
{
if (ignoreErrors) return null;
JU.Logger.error("" + e);
return "" + e;
}
} else if (Clazz.exceptionOf(e$$, Error)){
var er = e$$;
{
JU.Logger.errorEx(null, er);
return "" + er;
}
} else {
throw e$$;
}
}
}, "JV.Viewer,java.io.InputStream,~S,~A,java.util.Map,~N,~B");
Clazz.defineMethod(c$, "getCachedPngjBytes", 
function(fm, pathName){
if (pathName.startsWith("file:///")) pathName = "file:" + pathName.substring(7);
JU.Logger.info("JmolUtil checking PNGJ cache for " + pathName);
var shortName = this.shortSceneFilename(pathName);
if (fm.pngjCache == null && !this.clearAndCachePngjFile(fm,  Clazz.newArray(-1, [pathName, null]))) return null;
var cache = fm.pngjCache;
var isMin = (pathName.indexOf(".min.") >= 0);
if (!isMin) {
var cName = fm.getCanonicalName(JU.Rdr.getZipRoot(pathName));
if (!cache.containsKey(cName) && !this.clearAndCachePngjFile(fm,  Clazz.newArray(-1, [pathName, null]))) return null;
if (pathName.indexOf("|") < 0) shortName = cName;
}if (cache.containsKey(shortName)) {
JU.Logger.info("FileManager using memory cache " + shortName);
return fm.pngjCache.get(shortName);
}if (!isMin || !this.clearAndCachePngjFile(fm,  Clazz.newArray(-1, [pathName, null]))) return null;
JU.Logger.info("FileManager using memory cache " + shortName);
return cache.get(shortName);
}, "JV.FileManager,~S");
Clazz.defineMethod(c$, "clearAndCachePngjFile", 
function(fm, data){
fm.pngjCache =  new java.util.Hashtable();
if (data == null || data[0] == null) return false;
data[0] = JU.Rdr.getZipRoot(data[0]);
var shortName = this.shortSceneFilename(data[0]);
var cache = fm.pngjCache;
try {
data[1] = fm.vwr.getJzt().cacheZipContents(JU.Rdr.getPngZipStream(fm.getBufferedInputStreamOrErrorMessageFromName(data[0], null, false, false, null, false, true), true), shortName, cache, false);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
return false;
} else {
throw e;
}
}
if (data[1] == null) return false;
var bytes = data[1].getBytes();
cache.put(fm.getCanonicalName(data[0]), bytes);
if (shortName.indexOf("_scene_") >= 0) {
cache.put(this.shortSceneFilename(data[0]), bytes);
bytes = cache.remove(shortName + "|state.spt");
if (bytes != null) cache.put(this.shortSceneFilename(data[0] + "|state.spt"), bytes);
}return true;
}, "JV.FileManager,~A");
Clazz.defineMethod(c$, "shortSceneFilename", 
function(pathName){
var pt = pathName.indexOf("_scene_") + 7;
if (pt < 7) return pathName;
var s = "";
if (pathName.endsWith("|state.spt")) {
var pt1 = pathName.indexOf('.', pt);
if (pt1 < 0) return pathName;
s = pathName.substring(pt, pt1);
}var pt2 = pathName.lastIndexOf("|");
return pathName.substring(0, pt) + s + (pt2 > 0 ? pathName.substring(pt2) : "");
}, "~S");
Clazz.defineMethod(c$, "getSpartanSubfiles", 
function(zipDirectory){
var name = (zipDirectory.length < 2 ? null : zipDirectory[1]);
return (name == null || zipDirectory.length != 2 || !name.endsWith(".spardir/") ? null :  Clazz.newArray(-1, ["", JU.PT.trim(name, "/")]));
}, "~A");
Clazz.defineMethod(c$, "isSpartanZip", 
function(zipDirectory){
for (var i = 1; i < zipDirectory.length; i++) if (zipDirectory[i].endsWith(".spardir/") || zipDirectory[i].indexOf("_spartandir") >= 0) return true;

return false;
}, "~A");
});
;//5.0.1-v7 Mon Aug 17 10:07:10 MDT 2026
