Clazz.declarePackage("J.io");
Clazz.load(null, "J.io.FileReader", ["java.io.BufferedReader", "JU.AU", "$.PT", "$.Rdr", "J.api.Interface", "JU.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.vwr = null;
this.fileNameIn = null;
this.fullPathNameIn = null;
this.nameAsGivenIn = null;
this.fileTypeIn = null;
this.atomSetCollection = null;
this.readerOrDocument = null;
this.htParams = null;
this.isAppend = false;
this.bytesOrStream = null;
Clazz.instantialize(this, arguments);}, J.io, "FileReader", null);
Clazz.makeConstructor(c$, 
function(vwr, fileName, fullPathName, nameAsGiven, type, reader, htParams, isAppend){
this.vwr = vwr;
this.fileNameIn = (fileName == null ? fullPathName : fileName);
this.fullPathNameIn = (fullPathName == null ? this.fileNameIn : fullPathName);
this.nameAsGivenIn = (nameAsGiven == null ? this.fileNameIn : nameAsGiven);
this.fileTypeIn = type;
if (reader != null) {
if (JU.AU.isAB(reader) || Clazz.instanceOf(reader,"java.io.BufferedInputStream")) {
this.bytesOrStream = reader;
reader = null;
} else if (Clazz.instanceOf(reader,"java.io.Reader") && !(Clazz.instanceOf(reader,"java.io.BufferedReader"))) {
reader =  new java.io.BufferedReader(reader);
}}this.readerOrDocument = reader;
this.htParams = htParams;
this.isAppend = isAppend;
}, "JV.Viewer,~S,~S,~S,~S,~O,java.util.Map,~B");
Clazz.defineMethod(c$, "run", 
function(){
if (!this.isAppend && this.vwr.displayLoadErrors) this.vwr.zap(false, true, false);
var errorMessage = null;
var t = null;
if (this.fullPathNameIn.contains("#_DOCACHE_")) this.readerOrDocument = J.io.FileReader.getChangeableReader(this.vwr, this.nameAsGivenIn, this.fullPathNameIn);
if (this.readerOrDocument == null) {
t = this.vwr.fm.getUnzippedReaderOrStreamFromName(this.fullPathNameIn, this.bytesOrStream, true, false, false, true, this.htParams);
if (t == null || (typeof(t)=='string')) {
errorMessage = (t == null ? "error opening:" + this.nameAsGivenIn : t);
if (!errorMessage.startsWith("NOTE:")) JU.Logger.error("file ERROR: " + this.fullPathNameIn + "\n" + errorMessage);
this.atomSetCollection = errorMessage;
return;
}if (Clazz.instanceOf(t,"java.io.BufferedReader")) {
this.readerOrDocument = t;
} else if (Clazz.instanceOf(t,"javajs.api.ZInputStream")) {
var name = this.fullPathNameIn;
var subFileList = null;
name = name.$replace('\\', '/');
if (name.indexOf("|") >= 0 && !name.endsWith(".zip")) {
subFileList = JU.PT.split(name, "|");
name = subFileList[0];
}if (subFileList != null) this.htParams.put("subFileList", subFileList);
var zis = t;
var zipDirectory = this.vwr.fm.getZipDirectory(name, true, true);
this.atomSetCollection = t = this.vwr.fm.getJzu().getAtomSetCollectionOrBufferedReaderFromZip(this.vwr, zis, name, zipDirectory, this.htParams, 1, false);
try {
zis.close();
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
}}if (Clazz.instanceOf(t,"java.io.BufferedInputStream")) this.readerOrDocument = (J.api.Interface.getInterface("JU.BinaryDocument", this.vwr, "file")).setStream(t, !this.htParams.containsKey("isLittleEndian"));
if (this.readerOrDocument != null) {
this.atomSetCollection = this.vwr.getModelAdapter().getAtomSetCollectionReader(this.fullPathNameIn, this.fileTypeIn, this.readerOrDocument, this.htParams);
if (!((typeof(this.atomSetCollection)=='string'))) this.atomSetCollection = this.vwr.getModelAdapter().getAtomSetCollection(this.atomSetCollection);
try {
if (Clazz.instanceOf(this.readerOrDocument,"java.io.BufferedReader")) (this.readerOrDocument).close();
 else if (Clazz.instanceOf(this.readerOrDocument,"javajs.api.GenericBinaryDocument")) (this.readerOrDocument).close();
} catch (e) {
if (Clazz.exceptionOf(e,"java.io.IOException")){
} else {
throw e;
}
}
}if ((typeof(this.atomSetCollection)=='string')) return;
if (!this.isAppend && !this.vwr.displayLoadErrors) this.vwr.zap(false, true, false);
this.vwr.fm.setFileInfo( Clazz.newArray(-1, [this.fullPathNameIn, this.fileNameIn, this.nameAsGivenIn]));
});
c$.getChangeableReader = Clazz.defineMethod(c$, "getChangeableReader", 
function(vwr, nameAsGivenIn, fullPathNameIn){
return JU.Rdr.getBR(vwr.getLigandModel(nameAsGivenIn, fullPathNameIn, "_file", null));
}, "JV.Viewer,~S,~S");
Clazz.defineMethod(c$, "getAtomSetCollection", 
function(){
return this.atomSetCollection;
});
});
;//5.0.1-v7 Wed Jun 03 09:22:38 CDT 2026
