Clazz.declarePackage("J.adapter.readers.xml");
Clazz.load(["J.adapter.readers.xml.XmlReader"], "J.adapter.readers.xml.XmlCmlReader", ["java.util.Hashtable", "$.Properties", "$.StringTokenizer", "JU.BS", "$.Lst", "$.PT", "J.adapter.smarter.Atom", "$.Bond", "J.api.JmolAdapter", "JU.BSUtil", "$.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.scalarDictRef = null;
this.scalarDictValue = null;
this.scalarTitle = null;
this.cellParameterType = null;
this.checkedSerial = false;
this.isSerial = false;
this.moleculeNesting = 0;
this.latticeVectorPtr = 0;
this.embeddedCrystal = false;
this.atomIdNames = null;
this.thisBond = null;
this.tokens = null;
this.aaLen = 0;
this.atomArray = null;
this.bondCount = 0;
this.bondArray = null;
this.tokenCount = 0;
this.moduleNestingLevel = 0;
this.haveMolecule = false;
this.localSpaceGroupName = null;
this.processing = true;
this.state = 0;
this.atomIndex0 = 0;
this.joinList = null;
this.mapRtoA = null;
this.deleteAtoms = null;
this.moleculeID = null;
this.htModelAtomMap = null;
this.optimize2d = false;
Clazz.instantialize(this, arguments);}, J.adapter.readers.xml, "XmlCmlReader", J.adapter.readers.xml.XmlReader);
Clazz.prepareFields (c$, function(){
this.tokens =  new Array(16);
this.atomArray =  new Array(100);
this.bondArray =  new Array(100);
});
Clazz.makeConstructor(c$, 
function(){
Clazz.superConstructor (this, J.adapter.readers.xml.XmlCmlReader, []);
});
Clazz.overrideMethod(c$, "processXml", 
function(parent, saxReader){
this.optimize2d = parent.checkFilterKey("2D");
this.processXml2(parent, saxReader);
if (this.optimize2d) this.set2D();
}, "J.adapter.readers.xml.XmlReader,~O");
Clazz.overrideMethod(c$, "processStartElement", 
function(name, nodeName){
if (!this.processing) return;
this.processStart2(name);
}, "~S,~S");
Clazz.defineMethod(c$, "processStart2", 
function(name){
name = name.toLowerCase();
var val;
switch (this.state) {
case 0:
switch (name) {
case "molecule":
this.moleculeID = this.atts.get("id");
this.state = 6;
this.haveMolecule = true;
if (this.moleculeNesting == 0) this.createNewAtomSet();
this.moleculeNesting++;
break;
case "crystal":
this.state = 2;
break;
case "symmetry":
this.state = 17;
if ((val = this.atts.get("spacegroup")) != null) {
this.localSpaceGroupName = val;
} else {
this.localSpaceGroupName = "P1";
this.parent.clearUnitCell();
}break;
case "module":
this.moduleNestingLevel++;
break;
case "latticevector":
this.state = 18;
this.setKeepChars(true);
break;
}
break;
case 2:
this.checkedSerial = true;
this.isSerial = false;
switch (name) {
case "scalar":
this.state = 3;
this.setKeepChars(true);
this.scalarTitle = this.atts.get("title");
this.getDictRefValue();
break;
case "symmetry":
this.state = 4;
if ((val = this.atts.get("spacegroup")) != null) {
this.localSpaceGroupName = val;
for (var i = 0; i < this.localSpaceGroupName.length; i++) if (this.localSpaceGroupName.charAt(i) == '_') this.localSpaceGroupName = this.localSpaceGroupName.substring(0, i) + this.localSpaceGroupName.substring((i--) + 1);

}break;
case "cellparameter":
if ((val = this.atts.get("parametertype")) != null) {
this.cellParameterType = val;
this.setKeepChars(true);
}break;
}
break;
case 18:
this.setKeepChars(true);
break;
case 17:
case 3:
case 4:
switch (name) {
case "transform3":
this.state = 5;
this.setKeepChars(true);
break;
}
break;
case 5:
case 6:
switch (name) {
case "fragmentlist":
this.joinList =  new JU.Lst();
this.mapRtoA =  new java.util.Hashtable();
if (this.deleteAtoms == null) this.deleteAtoms =  new JU.BS();
break;
case "crystal":
this.state = 2;
this.embeddedCrystal = true;
break;
case "molecule":
this.state = 6;
this.moleculeNesting++;
break;
case "join":
var order = -1;
this.tokenCount = 0;
if ((val = this.atts.get("atomrefs2")) != null) {
this.breakOutTokens(val);
if ((val = this.atts.get("order")) != null) order = this.parseBondToken(val);
if (this.tokenCount == 2 && order > 0) this.joinList.addLast( Clazz.newArray(-1, [this.tokens[0], this.tokens[1], "" + order]));
}break;
case "bondarray":
this.state = 10;
this.bondCount = 0;
if ((val = this.atts.get("order")) != null) {
this.breakOutBondTokens(val);
for (var i = this.tokenCount; --i >= 0; ) this.bondArray[i].order = this.parseBondToken(this.tokens[i]);

}if ((val = this.atts.get("atomref1")) != null) {
this.breakOutBondTokens(val);
for (var i = this.tokenCount; --i >= 0; ) this.bondArray[i].atomIndex1 = this.getAtomIndex(this.tokens[i]);

}if ((val = this.atts.get("atomref2")) != null) {
this.breakOutBondTokens(val);
for (var i = this.tokenCount; --i >= 0; ) this.bondArray[i].atomIndex2 = this.getAtomIndex(this.tokens[i]);

}break;
case "atomarray":
this.state = 7;
this.aaLen = 0;
var coords3D = false;
if ((val = this.atts.get("atomid")) != null) {
this.breakOutAtomTokens(val);
for (var i = this.tokenCount; --i >= 0; ) this.atomArray[i].atomName = this.tokens[i];

}var is3d = (!this.optimize2d && (val = this.atts.get("x3")) != null);
if (is3d) {
is3d = true;
coords3D = true;
this.breakOutAtomTokens(val);
for (var i = this.tokenCount; --i >= 0; ) this.atomArray[i].x = this.parseFloatStr(this.tokens[i]);

if ((val = this.atts.get("y3")) != null) {
this.breakOutAtomTokens(val);
for (var i = this.tokenCount; --i >= 0; ) this.atomArray[i].y = this.parseFloatStr(this.tokens[i]);

}if ((val = this.atts.get("z3")) != null) {
this.breakOutAtomTokens(val);
for (var i = this.tokenCount; --i >= 0; ) this.atomArray[i].z = this.parseFloatStr(this.tokens[i]);

}} else {
if ((val = this.atts.get("x2")) != null) {
this.breakOutAtomTokens(val);
for (var i = this.tokenCount; --i >= 0; ) this.atomArray[i].x = this.parseFloatStr(this.tokens[i]);

}if ((val = this.atts.get("y2")) != null) {
this.breakOutAtomTokens(val);
for (var i = this.tokenCount; --i >= 0; ) this.atomArray[i].y = this.parseFloatStr(this.tokens[i]);

}}if ((val = this.atts.get("elementtype")) != null) {
this.breakOutAtomTokens(val);
for (var i = this.tokenCount; --i >= 0; ) this.atomArray[i].elementSymbol = this.tokens[i];

}for (var i = this.aaLen; --i >= 0; ) {
var atom = this.atomArray[i];
if (!coords3D) atom.z = 0;
this.addAtom(atom);
}
break;
case "formula":
this.state = 13;
break;
case "association":
this.state = 19;
}
break;
case 10:
switch (name) {
case "bond":
this.state = 11;
var order = -1;
this.tokenCount = 0;
if ((val = this.atts.get("atomrefs2")) != null) this.breakOutTokens(val);
if ((val = this.atts.get("order")) != null) order = this.parseBondToken(val);
if (this.tokenCount == 2 && order > 0) {
this.addNewBond(this.tokens[0], this.tokens[1], order);
}break;
}
break;
case 7:
switch (name) {
case "atom":
this.state = 8;
this.thisAtom =  new J.adapter.smarter.Atom();
this.parent.setFractionalCoordinates(false);
var id = this.atts.get("id");
if ((val = this.atts.get("name")) != null) this.thisAtom.atomName = val;
 else if ((val = this.atts.get("title")) != null) this.thisAtom.atomName = val;
 else if ((val = this.atts.get("label")) != null) this.thisAtom.atomName = val;
 else this.thisAtom.atomName = id;
if (!this.checkedSerial) {
this.isSerial = (id != null && id.length > 1 && id.startsWith("a") && JU.PT.parseInt(id.substring(1)) != -2147483648);
this.checkedSerial = true;
}if (this.isSerial) this.thisAtom.atomSerial = JU.PT.parseInt(id.substring(1));
if ((val = this.atts.get("xfract")) != null && (this.parent.iHaveUnitCell || !this.atts.containsKey("x3"))) {
this.parent.setFractionalCoordinates(true);
this.thisAtom.set(this.parseFloatStr(val), this.parseFloatStr(this.atts.get("yfract")), this.parseFloatStr(this.atts.get("zfract")));
} else if ((val = this.atts.get("x3")) != null) {
this.thisAtom.set(this.parseFloatStr(val), this.parseFloatStr(this.atts.get("y3")), this.parseFloatStr(this.atts.get("z3")));
} else if ((val = this.atts.get("x2")) != null) {
this.thisAtom.set(this.parseFloatStr(val), this.parseFloatStr(this.atts.get("y2")), 0);
}if ((val = this.atts.get("elementtype")) != null) {
var sym = val;
if ((val = this.atts.get("isotope")) != null) this.thisAtom.elementNumber = ((this.parseIntStr(val) << 7) + J.api.JmolAdapter.getElementNumber(sym));
this.thisAtom.elementSymbol = sym;
}if ((val = this.atts.get("formalcharge")) != null) this.thisAtom.formalCharge = this.parseIntStr(val);
break;
}
break;
case 11:
if ((val = this.atts.get("builtin")) != null) {
this.setKeepChars(true);
this.state = 15;
this.scalarDictValue = val;
} else if (name.equals("bondstereo")) {
this.state = 12;
}break;
case 12:
this.setKeepChars(true);
this.state = 12;
break;
case 8:
if (name.equals("scalar")) {
this.state = 9;
this.setKeepChars(true);
this.scalarTitle = this.atts.get("title");
this.getDictRefValue();
} else if ((val = this.atts.get("builtin")) != null) {
this.setKeepChars(true);
this.state = 14;
this.scalarDictValue = val;
}break;
case 9:
break;
case 13:
break;
case 14:
break;
case 15:
break;
}
}, "~S");
Clazz.defineMethod(c$, "getAtomIndex", 
function(label){
return this.asc.getAtomIndex(this.isSerial ? label.substring(1) : label);
}, "~S");
Clazz.overrideMethod(c$, "processEndElement", 
function(name){
if (!this.processing) return;
this.processEnd2(name);
}, "~S");
Clazz.defineMethod(c$, "processEnd2", 
function(name){
name = name.toLowerCase();
switch (this.state) {
case 0:
if (name.equals("module")) {
if (--this.moduleNestingLevel == 0) {
if (this.parent.iHaveUnitCell) this.applySymmetryAndSetTrajectory();
this.setAtomNames();
}}break;
case 19:
if (name.equals("association")) this.state = 6;
break;
case 2:
if (name.equals("crystal")) {
if (this.embeddedCrystal) {
this.state = 6;
this.embeddedCrystal = false;
} else {
this.state = 0;
}} else if (name.equals("cellparameter") && this.keepChars) {
var tokens = JU.PT.getTokens(this.chars.toString());
this.setKeepChars(false);
if (tokens.length != 3 || this.cellParameterType == null) {
} else if (this.cellParameterType.equals("length")) {
for (var i = 0; i < 3; i++) this.parent.setUnitCellItem(i, this.parseFloatStr(tokens[i]));

break;
} else if (this.cellParameterType.equals("angle")) {
for (var i = 0; i < 3; i++) this.parent.setUnitCellItem(i + 3, this.parseFloatStr(tokens[i]));

break;
}JU.Logger.error("bad cellParameter information: parameterType=" + this.cellParameterType + " data=" + this.chars);
this.parent.setFractionalCoordinates(false);
}break;
case 3:
if (name.equals("scalar")) {
this.state = 2;
if (this.scalarTitle != null) this.checkUnitCellItem(J.adapter.readers.xml.XmlCmlReader.unitCellParamTags, this.scalarTitle);
 else if (this.scalarDictRef != null) this.checkUnitCellItem(J.api.JmolAdapter.cellParamNames, (this.scalarDictValue.startsWith("_") ? this.scalarDictValue : "_" + this.scalarDictValue));
}this.setKeepChars(false);
this.scalarTitle = null;
this.scalarDictRef = null;
break;
case 5:
if (name.equals("transform3")) {
this.setKeepChars(false);
this.state = 4;
}break;
case 18:
var values = J.adapter.smarter.AtomSetCollectionReader.getTokensFloat(this.chars.toString(), null, 3);
this.parent.addExplicitLatticeVector(this.latticeVectorPtr, values, 0);
this.latticeVectorPtr = (this.latticeVectorPtr + 1) % 3;
this.setKeepChars(false);
this.state = 0;
break;
case 4:
case 17:
if (name.equals("symmetry")) this.state = (this.state == 4 ? 2 : 0);
if (this.moduleNestingLevel == 0 && this.parent.iHaveUnitCell && !this.embeddedCrystal) this.applySymmetryAndSetTrajectory();
break;
case 6:
if (name.equals("fragmentlist")) {
for (var i = this.joinList.size(); --i >= 0; ) {
var join = this.joinList.get(i);
var r1 = this.asc.getAtomFromName(this.fixSerialName(join[0]));
var r2 = this.asc.getAtomFromName(this.fixSerialName(join[1]));
if (r1 != null && r2 != null) {
this.deleteAtoms.set(r1.index);
this.deleteAtoms.set(r2.index);
this.addNewBond(this.mapRtoA.get(r1), this.mapRtoA.get(r2), this.parseIntStr(join[2]));
}}
this.joinList = null;
this.mapRtoA = null;
}if (name.equals("molecule")) {
if (--this.moleculeNesting == 0) {
this.applySymmetryAndSetTrajectory();
this.setAtomNames();
this.state = 0;
} else {
this.state = 6;
}}break;
case 10:
if (name.equals("bondarray")) {
this.state = 6;
for (var i = 0; i < this.bondCount; ++i) this.addBond(this.bondArray[i]);

this.parent.applySymmetryToBonds = true;
}break;
case 7:
if (name.equals("atomarray")) {
this.state = 6;
}break;
case 11:
if (name.equals("bond")) {
this.state = 10;
}break;
case 8:
if (name.equals("atom")) {
this.state = 7;
this.addAtom(this.thisAtom);
this.thisAtom = null;
}break;
case 9:
if (name.equals("scalar")) {
this.state = 8;
if ("jmol:charge".equals(this.scalarDictRef)) {
this.thisAtom.partialCharge = this.parseFloatStr(this.chars.toString());
} else if (this.scalarDictRef != null && "_atom_site_label".equals(this.scalarDictValue)) {
if (this.atomIdNames == null) this.atomIdNames =  new java.util.Properties();
this.atomIdNames.put(this.thisAtom.atomName, this.chars.toString());
}}this.setKeepChars(false);
this.scalarTitle = null;
this.scalarDictRef = null;
break;
case 14:
this.state = 8;
if (this.scalarDictValue.equals("x3")) this.thisAtom.x = this.parseFloatStr(this.chars.toString());
 else if (this.scalarDictValue.equals("y3")) this.thisAtom.y = this.parseFloatStr(this.chars.toString());
 else if (this.scalarDictValue.equals("z3")) this.thisAtom.z = this.parseFloatStr(this.chars.toString());
 else if (this.scalarDictValue.equals("elementType")) this.thisAtom.elementSymbol = this.chars.toString();
this.setKeepChars(false);
break;
case 12:
var stereo = this.chars.toString();
if (this.thisBond.order == 1) this.thisBond.order = (stereo.equals("H") ? 1041 : 1025);
this.setKeepChars(false);
this.state = 11;
break;
case 15:
this.state = 11;
if (this.scalarDictValue.equals("atomRef")) {
if (this.tokenCount == 0) this.tokens =  new Array(2);
if (this.tokenCount < 2) this.tokens[this.tokenCount++] = this.chars.toString();
} else if (this.scalarDictValue.equals("order")) {
var order = this.parseBondToken(this.chars.toString());
if (order > 0 && this.tokenCount == 2) this.addNewBond(this.tokens[0], this.tokens[1], order);
}this.setKeepChars(false);
break;
case 13:
this.state = 6;
break;
}
}, "~S");
Clazz.defineMethod(c$, "addBond", 
function(bond){
var a1 = this.asc.atoms[bond.atomIndex1];
var a2 = this.asc.atoms[bond.atomIndex2];
if (this.joinList != null && !this.checkBondToR(a1.atomName, a2.atomName)) this.asc.addBond(bond);
}, "J.adapter.smarter.Bond");
Clazz.defineMethod(c$, "checkBondToR", 
function(a1name, a2name){
var a1 = this.asc.getAtomFromName(a1name);
var a2 = this.asc.getAtomFromName(a2name);
if (a1 == null || a2 == null) return true;
if ("R".equals(a1.elementSymbol)) {
this.mapRtoA.put(a1, a2.atomName);
return true;
} else if ("R".equals(a2.elementSymbol)) {
this.mapRtoA.put(a2, a1.atomName);
return true;
}return false;
}, "~S,~S");
Clazz.defineMethod(c$, "setAtomNames", 
function(){
if (this.atomIdNames == null) return;
var s;
var atoms = this.asc.atoms;
for (var i = this.atomIndex0; i < this.asc.ac; i++) if ((s = this.atomIdNames.getProperty(atoms[i].atomName)) != null) atoms[i].atomName = s;

this.atomIdNames = null;
this.atomIndex0 = this.asc.ac;
});
Clazz.defineMethod(c$, "addNewBond", 
function(a1, a2, order){
if (a1 == null || a2 == null) return;
this.parent.applySymmetryToBonds = true;
a1 = this.fixSerialName(a1);
a2 = this.fixSerialName(a2);
if (this.joinList == null || !this.checkBondToR(a1, a2)) {
this.asc.addNewBondFromNames(a1, a2, order);
this.thisBond = this.asc.bonds[this.asc.bondCount - 1];
}}, "~S,~S,~N");
Clazz.defineMethod(c$, "fixSerialName", 
function(a){
return (this.isSerial ? a.substring(1) : a);
}, "~S");
Clazz.defineMethod(c$, "getDictRefValue", 
function(){
this.scalarDictRef = this.atts.get("dictref");
if (this.scalarDictRef != null) {
var iColon = this.scalarDictRef.indexOf(":");
this.scalarDictValue = this.scalarDictRef.substring(iColon + 1);
}});
Clazz.defineMethod(c$, "checkUnitCellItem", 
function(tags, value){
for (var i = tags.length; --i >= 0; ) if (value.equals(tags[i])) {
this.parent.setUnitCellItem(i, this.parseFloatStr(this.chars.toString()));
return;
}
}, "~A,~S");
Clazz.defineMethod(c$, "addAtom", 
function(atom){
if ((atom.elementSymbol == null && atom.elementNumber < 0) || Float.isNaN(atom.z)) return;
this.parent.setAtomCoord(atom);
if (this.htModelAtomMap != null) this.htModelAtomMap.put(this.moleculeID + atom.atomName, atom);
if (this.isSerial) this.asc.addAtomWithMappedSerialNumber(atom);
 else this.asc.addAtomWithMappedName(atom);
}, "J.adapter.smarter.Atom");
Clazz.defineMethod(c$, "parseBondToken", 
function(str){
var floatOrder = this.parseFloatStr(str);
if (Float.isNaN(floatOrder) && str.length >= 1) {
str = str.toUpperCase();
switch ((str.charAt(0)).charCodeAt(0)) {
case 49:
case 83:
return 1;
case 50:
case 68:
return 2;
case 51:
case 84:
return 3;
case 65:
return 515;
case 80:
return 66;
}
return this.parseIntStr(str);
}if (floatOrder == 1.5) return 515;
if (floatOrder == 2) return 2;
if (floatOrder == 3) return 3;
return 1;
}, "~S");
Clazz.defineMethod(c$, "breakOutTokens", 
function(str){
var st =  new java.util.StringTokenizer(str);
this.tokenCount = st.countTokens();
if (this.tokenCount > this.tokens.length) this.tokens =  new Array(this.tokenCount);
for (var i = 0; i < this.tokenCount; ++i) {
try {
this.tokens[i] = st.nextToken();
} catch (nsee) {
if (Clazz.exceptionOf(nsee,"java.util.NoSuchElementException")){
this.tokens[i] = null;
} else {
throw nsee;
}
}
}
}, "~S");
Clazz.defineMethod(c$, "breakOutAtomTokens", 
function(str){
this.breakOutTokens(str);
this.checkAtomArrayLength(this.tokenCount);
}, "~S");
Clazz.defineMethod(c$, "checkAtomArrayLength", 
function(newAtomCount){
if (this.aaLen == 0) {
if (newAtomCount > this.atomArray.length) this.atomArray =  new Array(newAtomCount);
for (var i = newAtomCount; --i >= 0; ) this.atomArray[i] =  new J.adapter.smarter.Atom();

this.aaLen = newAtomCount;
} else if (newAtomCount != this.aaLen) {
throw  new IndexOutOfBoundsException("bad atom attribute length");
}}, "~N");
Clazz.defineMethod(c$, "breakOutBondTokens", 
function(str){
this.breakOutTokens(str);
this.checkBondArrayLength(this.tokenCount);
}, "~S");
Clazz.defineMethod(c$, "checkBondArrayLength", 
function(newBondCount){
if (this.bondCount == 0) {
if (newBondCount > this.bondArray.length) this.bondArray =  new Array(newBondCount);
for (var i = newBondCount; --i >= 0; ) this.bondArray[i] =  new J.adapter.smarter.Bond(-1, -1, 1);

this.bondCount = newBondCount;
} else if (newBondCount != this.bondCount) {
throw  new IndexOutOfBoundsException("bad bond attribute length");
}}, "~N");
Clazz.defineMethod(c$, "createNewAtomSet", 
function(){
this.asc.newAtomSet();
var val;
if (this.htModelAtomMap != null) this.htModelAtomMap.put("" + this.asc.iSet, "" + this.moleculeID);
var collectionName = ((val = this.atts.get("title")) != null || (val = this.atts.get("id")) != null ? val : null);
if (collectionName != null) {
this.asc.setAtomSetName(collectionName);
}});
Clazz.defineMethod(c$, "applySymmetryAndSetTrajectory", 
function(){
if (this.moduleNestingLevel > 0 || !this.haveMolecule || this.localSpaceGroupName == null) return;
this.parent.setSpaceGroupName(this.localSpaceGroupName);
this.parent.iHaveSymmetryOperators = this.iHaveSymmetryOperators;
if (this.parent === this) Clazz.superCall(this, J.adapter.readers.xml.XmlCmlReader, "applySymmetryAndSetTrajectory", []);
 else this.parent.applySymmetryAndSetTrajectory();
});
Clazz.overrideMethod(c$, "endDocument", 
function(){
if (this.deleteAtoms != null) {
var bs = (this.asc.bsAtoms == null ? this.asc.bsAtoms = JU.BSUtil.newBitSet2(0, this.asc.ac) : this.asc.bsAtoms);
bs.andNot(this.deleteAtoms);
}});
c$.unitCellParamTags =  Clazz.newArray(-1, ["a", "b", "c", "alpha", "beta", "gamma"]);
});
;//5.0.1-v7 Tue Jul 22 18:14:29 CDT 2025
