Clazz.declarePackage("JU");
Clazz.load(["javajs.api.GenericCifDataParser", "java.util.Hashtable", "JU.SB"], "JU.CifDataParser", ["JU.Lst", "$.PT"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.reader = null;
this.br = null;
this.line = null;
this.str = null;
this.ich = 0;
this.cch = 0;
this.wasUnquoted = false;
this.cterm = '\0';
this.nullString = "\0";
this.asObject = false;
this.debugging = false;
this.strPeeked = null;
this.ichPeeked = 0;
this.columnCount = 0;
this.columnNames = null;
this.columnData = null;
this.isLoop = false;
this.haveData = false;
this.fileHeader = null;
this.isHeader = true;
this.skipToken = false;
Clazz.instantialize(this, arguments);}, JU, "CifDataParser", null, javajs.api.GenericCifDataParser);
Clazz.prepareFields (c$, function(){
this.columnData =  new Array(100);
this.fileHeader =  new JU.SB();
});
Clazz.makeConstructor(c$, 
function(){
});
Clazz.defineMethod(c$, "getVersion", 
function(){
return 1;
});
Clazz.defineMethod(c$, "setNullValue", 
function(nullString){
this.nullString = nullString;
}, "~S");
Clazz.overrideMethod(c$, "getColumnData", 
function(i){
return this.columnData[i];
}, "~N");
Clazz.overrideMethod(c$, "getColumnCount", 
function(){
return this.columnCount;
});
Clazz.overrideMethod(c$, "getColumnName", 
function(i){
return this.columnNames[i];
}, "~N");
Clazz.overrideMethod(c$, "set", 
function(reader, br, debugging){
this.reader = reader;
this.br = br;
this.debugging = debugging;
return this;
}, "javajs.api.GenericLineReader,java.io.BufferedReader,~B");
Clazz.overrideMethod(c$, "getFileHeader", 
function(){
return this.fileHeader.toString();
});
Clazz.overrideMethod(c$, "getAllCifData", 
function(){
return this.getAllCifDataType([]);
});
Clazz.defineMethod(c$, "getAllCifDataType", 
function(types){
if (types != null) {
if (types.length == 0) types = null;
 else for (var i = 0; i < types.length; i++) types[i] = this.fixKey(types[i]);

}this.line = "";
var key;
var data = null;
var data0 = null;
var allData =  new java.util.Hashtable();
var models =  new JU.Lst();
allData.put("models", models);
this.asObject = (this.getVersion() >= 2);
this.nullString = null;
var saveFrames =  new JU.Lst();
try {
while ((key = this.getNextToken()) != null) {
if (key.startsWith("global_") || key.startsWith("data_")) {
models.addLast(data0 = data =  new java.util.Hashtable());
data.put("name", key);
continue;
}if (key.startsWith("loop_")) {
this.getAllCifLoopData(data, types);
continue;
}if (key.startsWith("save_")) {
if (key.equals("save_")) {
var n = saveFrames.size();
if (n == 0) {
System.out.println("CIF ERROR ? save_ without corresponding save_xxxx");
data = data0;
} else {
data = saveFrames.removeItemAt(n - 1);
}} else {
saveFrames.addLast(data);
var d = data;
data =  new java.util.Hashtable();
d.put(key, data);
}continue;
}if (key.charAt(0) != '_') {
System.out.println("CIF ERROR ? should be an underscore: " + key);
} else {
var value = (this.asObject ? this.getNextTokenObject() : this.getNextToken());
if (value == null) {
System.out.println("CIF ERROR ? end of file; data missing: " + key);
} else {
key = this.fixKey(key);
if (types == null || this.checkKey(types, key)) data.put(key, value);
}}}
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
this.asObject = false;
try {
if (this.br != null) this.br.close();
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
this.nullString = "\0";
return allData;
}, "~A");
Clazz.defineMethod(c$, "getAllCifLoopData", 
function(data, types){
var key;
var keyWords =  new JU.Lst();
var o;
var skipping = false;
while ((o = this.peekToken()) != null && (typeof(o)=='string') && (o).charAt(0) == '_') {
key = this.fixKey(this.getTokenPeeked());
keyWords.addLast(key);
if (types == null || this.checkKey(types, key)) data.put(key,  new JU.Lst());
 else skipping = true;
}
this.columnCount = keyWords.size();
if (this.columnCount == 0) return;
this.isLoop = true;
if (skipping) this.skipLoop(false);
 else while (this.getData()) for (var i = 0; i < this.columnCount; i++) (data.get(keyWords.get(i))).addLast(this.columnData[i]);


this.isLoop = false;
}, "java.util.Map,~A");
Clazz.defineMethod(c$, "checkKey", 
function(types, key){
for (var i = 0; i < types.length; i++) if (key.startsWith(types[i])) return true;

return false;
}, "~A,~S");
Clazz.overrideMethod(c$, "readLine", 
function(){
try {
this.line = (this.reader == null ? this.br.readLine() : this.reader.readNextLine());
if (this.line == null) return null;
if (this.isHeader) {
if (this.line.startsWith("#")) {
this.fileHeader.append(this.line).appendC('\n');
} else if (this.line.length > 0) {
this.isHeader = false;
}}return this.line;
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
return null;
} else {
throw e;
}
}
});
Clazz.overrideMethod(c$, "getData", 
function(){
if (this.isLoop) {
for (var i = 0; i < this.columnCount; ++i) if ((this.columnData[i] = this.getNextDataToken()) == null) return false;

} else if (this.haveData) {
this.haveData = false;
} else {
return false;
}return (this.columnCount > 0);
});
Clazz.overrideMethod(c$, "skipLoop", 
function(doReport){
var str;
var ret = (doReport ?  new JU.SB() : null);
var n = 0;
while ((str = this.peekToken()) != null && str.charAt(0) == '_') {
if (ret != null) ret.append(str).append("\n");
this.getTokenPeeked();
n++;
}
if (n == 0) n = this.columnCount;
var m = 0;
while ((str = this.getNextDataToken()) != null) {
if (ret == null) continue;
ret.append(str).append(" ");
if ((++m % n) == 0) ret.append("\n");
}
return (ret == null ? null : ret.toString());
}, "~B");
Clazz.overrideMethod(c$, "getNextToken", 
function(){
this.wasUnquoted = true;
return this.getNextTokenProtected();
});
Clazz.defineMethod(c$, "getNextTokenObject", 
function(){
this.wasUnquoted = true;
return this.getNextTokenProtected();
});
Clazz.defineMethod(c$, "getNextTokenProtected", 
function(){
return (this.getNextLine() ? this.nextStrToken() : null);
});
Clazz.overrideMethod(c$, "getNextDataToken", 
function(){
var o = this.peekToken();
if (o == null) return null;
if (this.wasUnquoted && (typeof(o)=='string')) {
var str = o;
if (str.charAt(0) == '_' || str.startsWith("loop_") || str.startsWith("data_") || str.startsWith("save_") || str.startsWith("stop_") || str.startsWith("global_")) return null;
}return this.getTokenPeeked();
});
Clazz.overrideMethod(c$, "peekToken", 
function(){
if (!this.getNextLine()) return null;
var ich = this.ich;
this.strPeeked = this.nextStrToken();
this.ichPeeked = this.ich;
this.ich = ich;
return this.strPeeked;
});
Clazz.defineMethod(c$, "getNextLine", 
function(){
while (!this.strHasMoreTokens()) if (this.prepareNextLine() == null) return false;

return true;
});
Clazz.overrideMethod(c$, "getTokenPeeked", 
function(){
this.ich = this.ichPeeked;
return this.strPeeked;
});
Clazz.overrideMethod(c$, "fullTrim", 
function(str){
var pt0 = -1;
var pt1 = str.length;
while (++pt0 < pt1 && JU.PT.isWhitespace(str.charAt(pt0))) {
}
while (--pt1 > pt0 && JU.PT.isWhitespace(str.charAt(pt1))) {
}
return str.substring(pt0, pt1 + 1);
}, "~S");
Clazz.overrideMethod(c$, "toUnicode", 
function(data){
var pt;
try {
while ((pt = data.indexOf('\\')) >= 0) {
var c = (data.charAt(pt + 1)).charCodeAt(0);
var ch = (c >= 65 && c <= 90 ? "ABX\u0394E\u03a6\u0393HI_K\u039bMNO\u03a0\u0398P\u03a3TY_\u03a9\u039e\u03a5Z".substring(c - 65, c - 64) : c >= 97 && c <= 122 ? "\u03b1\u03b2\u03c7\u03a4\u03a5\u03c6\u03b3\u03b7\u03b9_\u03ba\u03bb\u03bc\u03bd\u03bf\u03c0\u03b8\u03c1\u03c3\u03c4\u03c5_\u03c9\u03be\u03c5\u03b6".substring(c - 97, c - 96) : "_");
data = data.substring(0, pt) + ch + data.substring(pt + 2);
}
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
return data;
}, "~S");
Clazz.overrideMethod(c$, "parseDataBlockParameters", 
function(fields, key, data, key2col, col2key){
this.isLoop = (key == null);
var o;
var s;
if (fields == null) {
this.columnNames =  new Array(100);
} else {
if (!JU.CifDataParser.htFields.containsKey(fields[0])) for (var i = fields.length; --i >= 0; ) JU.CifDataParser.htFields.put(fields[i], Integer.$valueOf(i));

for (var i = fields.length; --i >= 0; ) key2col[i] = -1;

}this.columnCount = 0;
var pt;
var i;
if (this.isLoop) {
while (true) {
o = this.peekToken();
if (o == null) {
this.columnCount = 0;
break;
}if (!((typeof(o)=='string')) || (o).charAt(0) != '_') break;
pt = this.columnCount++;
s = this.fixKey(this.getTokenPeeked());
if (fields == null) {
this.columnNames[col2key[pt] = key2col[pt] = pt] = s;
continue;
}var iField = JU.CifDataParser.htFields.get(s);
i = (iField == null ? -1 : iField.intValue());
if ((col2key[pt] = i) != -1) key2col[i] = pt;
}
} else {
pt = key.indexOf(".");
var str0 = (pt < 0 ? key : key.substring(0, pt + 1));
while (true) {
pt = this.columnCount++;
if (key == null) {
key = this.getTokenPeeked();
data = this.getNextToken();
}var iField = JU.CifDataParser.htFields.get(this.fixKey(key));
i = (iField == null ? -1 : iField.intValue());
if ((col2key[pt] = i) == -1) this.columnData[pt] = "";
 else this.columnData[key2col[i] = pt] = data;
if ((o = this.peekToken()) == null || !((typeof(o)=='string')) || !(o).startsWith(str0)) break;
key = null;
}
this.haveData = (this.columnCount > 0);
}}, "~A,~S,~S,~A,~A");
Clazz.overrideMethod(c$, "fixKey", 
function(key){
return (key.startsWith("_magnetic") ? key.substring(9) : key.startsWith("_jana") ? key.substring(5) : key).$replace('.', '_').toLowerCase();
}, "~S");
Clazz.defineMethod(c$, "setString", 
function(str){
this.str = this.line = str;
this.cch = (str == null ? 0 : str.length);
this.ich = 0;
return str;
}, "~S");
Clazz.defineMethod(c$, "prepareNextLine", 
function(){
this.setString(this.readLine());
if (this.line == null || this.line.length == 0) return this.line;
if (this.line.charAt(0) == ';') return this.preprocessString();
if (this.str.startsWith("###non-st#")) this.ich = 10;
return this.line;
});
Clazz.defineMethod(c$, "preprocessString", 
function(){
return this.setString(this.preprocessSemiString());
});
Clazz.defineMethod(c$, "preprocessSemiString", 
function(){
this.ich = 1;
var str = '\1' + this.line.substring(1) + '\n';
while (this.readLine() != null) {
if (this.line.startsWith(";")) {
str = str.substring(0, str.length - 1) + '\1' + this.line.substring(1);
break;
} else if (!this.skipToken) {
str += this.line + '\n';
}}
return str;
});
Clazz.defineMethod(c$, "strHasMoreTokens", 
function(){
if (this.str == null) return false;
var ch = '#';
while (this.ich < this.cch && ((ch = this.str.charAt(this.ich)) == ' ' || ch == '\t')) ++this.ich;

return (this.ich < this.cch && ch != '#');
});
Clazz.defineMethod(c$, "nextStrToken", 
function(){
if (this.ich == this.cch) return null;
var ch = this.str.charAt(this.ich);
if (this.isQuote(ch)) {
this.wasUnquoted = false;
return this.getQuotedStringOrObject(ch);
}var ichStart = this.ich;
this.wasUnquoted = true;
while (this.ich < this.cch && !this.isTerminator(ch = this.str.charAt(this.ich))) ++this.ich;

if (this.ich == ichStart + 1) if (this.nullString != null && (this.str.charAt(ichStart) == '.' || this.str.charAt(ichStart) == '?')) return this.nullString;
var s = this.str.substring(ichStart, this.ich);
return this.unquoted(s);
});
Clazz.defineMethod(c$, "unquoted", 
function(s){
return s;
}, "~S");
Clazz.defineMethod(c$, "isTerminator", 
function(c){
return c == ' ' || c == '\t' || c == this.cterm;
}, "~S");
Clazz.defineMethod(c$, "isQuote", 
function(ch){
switch ((ch).charCodeAt(0)) {
case 39:
case 34:
case 1:
case 91:
case 93:
return true;
}
return false;
}, "~S");
Clazz.defineMethod(c$, "getQuotedStringOrObject", 
function(ch){
switch ((ch).charCodeAt(0)) {
case 91:
try {
return this.readList();
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
System.out.println("exception in CifDataParser ; " + e);
} else {
throw e;
}
}
return "[";
case 93:
this.ich++;
return "]";
}
var ichStart = this.ich;
var chClosingQuote = ch;
var wasQuote = false;
while (++this.ich < this.cch) {
ch = this.str.charAt(this.ich);
if (wasQuote && (ch == ' ' || ch == '\t')) break;
wasQuote = (ch == chClosingQuote);
}
var pt1 = ichStart + 1;
var pt2 = this.ich - 1;
if (this.ich == this.cch && !wasQuote) {
pt1--;
pt2++;
} else {
++this.ich;
}return this.str.substring(pt1, pt2);
}, "~S");
Clazz.defineMethod(c$, "readList", 
function(){
this.ich++;
var cterm0 = this.cterm;
this.cterm = ']';
var ns = this.nullString;
this.nullString = null;
var lst = (this.asObject ?  new JU.Lst() : null);
var n = 0;
var str = "";
while (true) {
var value = (this.asObject ? this.getNextTokenObject() : this.getNextToken());
if (value == null || value.equals("]")) break;
if (this.asObject) {
lst.addLast(value);
} else {
if (n++ > 0) str += ",";
str += value;
}}
this.cterm = cterm0;
this.nullString = ns;
return (this.asObject ? lst : "[" + str + "]");
});
Clazz.overrideMethod(c$, "skipNextToken", 
function(){
this.skipToken = true;
this.getNextToken();
this.skipToken = false;
return "<skipped>";
});
c$.htFields =  new java.util.Hashtable();
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
