Clazz.declarePackage ("J.adapter.readers.simple");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.simple.JSONReader", ["JU.P3", "$.PT", "J.adapter.smarter.Bond", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.scale = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.simple, "JSONReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "initializeReader", 
function () {
this.asc.setCollectionName ("JSON");
this.asc.newAtomSet ();
var s = "";
while (this.rd () != null) s += this.line;

s = JU.PT.replaceAllCharacters (s, "\" \t", "").$replace (',', ':');
if (s.contains ("_is2D:true")) this.set2D ();
if (s.contains ("_scale:")) this.getScaling (this.getSection (s, "_scale", false));
s = JU.PT.replaceAllCharacters (s, "}", "").$replace (',', ':');
if (s.indexOf ("atomArray:[") >= 0) {
this.readAtomArray (this.getSection (s, "atomArray", true));
this.readBondArray (this.getSection (s, "bondArray", true));
} else {
this.readAtoms (this.getSection (s, "a", true));
this.readBonds (this.getSection (s, "b", true));
}this.continuing = false;
});
Clazz.defineMethod (c$, "getScaling", 
 function (s) {
var xyz = JU.PT.split (s[0], ":");
this.scale = JU.P3.new3 (1, 1, 1);
for (var j = 0; j < xyz.length; j += 2) if (xyz[j].length == 1) switch (xyz[j].charAt (0)) {
case 'x':
this.scale.x = this.parseFloatStr (xyz[j + 1]);
break;
case 'y':
this.scale.y = this.parseFloatStr (xyz[j + 1]);
break;
case 'z':
this.scale.z = this.parseFloatStr (xyz[j + 1]);
break;
}

JU.Logger.info ("scale set to " + this.scale);
}, "~A");
Clazz.defineMethod (c$, "getSection", 
 function (json, key, isArray) {
var a = JU.PT.split (json, key + ":" + (isArray ? "[" : "") + "{");
if (a.length < 2) return a;
var data = a[1];
data = data.substring (0, data.indexOf ((isArray ? "]" : "}"))) + ":";
return JU.PT.split (data, "{");
}, "~S,~S,~B");
Clazz.defineMethod (c$, "readAtoms", 
 function (atoms) {
for (var i = 0; i < atoms.length; ++i) {
var lxyz = JU.PT.split (atoms[i], ":");
var atom = this.asc.addNewAtom ();
var x = 0;
var y = 0;
var z = 0;
var l = "C";
for (var j = 0; j < lxyz.length; j += 2) if (lxyz[j].length == 1) switch (lxyz[j].charAt (0)) {
case 'x':
x = this.parseFloatStr (lxyz[j + 1]);
break;
case 'y':
y = this.parseFloatStr (lxyz[j + 1]);
break;
case 'z':
z = this.parseFloatStr (lxyz[j + 1]);
break;
case 'l':
l = lxyz[j + 1];
break;
}

if (this.scale != null) {
x /= this.scale.x;
y /= this.scale.y;
z /= this.scale.z;
}this.setAtomCoordXYZ (atom, x, y, z);
atom.elementSymbol = l;
}
}, "~A");
Clazz.defineMethod (c$, "readBonds", 
 function (bonds) {
for (var i = 0; i < bonds.length; ++i) {
var beo = JU.PT.split (bonds[i], ":");
var b = 0;
var e = 0;
var order = 1;
for (var j = 0; j < beo.length; j += 2) if (beo[j].length == 1) switch (beo[j].charAt (0)) {
case 'b':
b = this.parseIntStr (beo[j + 1]);
break;
case 'e':
e = this.parseIntStr (beo[j + 1]);
break;
case 'o':
var o = Clazz.floatToInt (this.parseFloatStr (beo[j + 1]) * 2);
switch (o) {
case 0:
continue;
case 2:
case 4:
case 6:
case 8:
order = Clazz.doubleToInt (o / 2);
break;
case 1:
order = 33;
break;
case 3:
order = 66;
break;
case 5:
order = 97;
break;
default:
order = 1;
break;
}
break;
}

this.asc.addBond ( new J.adapter.smarter.Bond (b, e, order));
}
}, "~A");
Clazz.defineMethod (c$, "readAtomArray", 
 function (atoms) {
for (var i = 0; i < atoms.length; ++i) {
var lxyz = JU.PT.split (atoms[i], ":");
var atom = this.asc.addNewAtom ();
var x = 0;
var y = 0;
var z = 0;
var l = "C";
for (var j = 0; j < lxyz.length; j += 2) {
switch (lxyz[j].charAt (0)) {
case 'x':
x = this.parseFloatStr (lxyz[j + 1]);
break;
case 'y':
y = this.parseFloatStr (lxyz[j + 1]);
break;
case 'z':
z = this.parseFloatStr (lxyz[j + 1]);
break;
case 'e':
l = lxyz[j + 1];
break;
}
}
if (this.scale != null) {
x /= this.scale.x;
y /= this.scale.y;
z /= this.scale.z;
}this.setAtomCoordXYZ (atom, x, y, z);
atom.elementSymbol = l;
}
}, "~A");
Clazz.defineMethod (c$, "readBondArray", 
 function (bonds) {
for (var i = 0; i < bonds.length; ++i) {
var beo = JU.PT.split (bonds[i], ":");
var b = 0;
var e = 0;
var order = 1;
for (var j = 0; j < beo.length; j += 2) {
if (beo[j].length > 1) {
switch (beo[j].charAt (1)) {
case '1':
b = this.parseIntStr (beo[j + 1]) - 1;
break;
case '2':
e = this.parseIntStr (beo[j + 1]) - 1;
break;
case 'y':
var type = beo[j + 1];
switch (type.charAt (0)) {
case 'D':
order = 2;
break;
case 'A':
order = 1;
break;
case 'S':
default:
order = 1;
break;
}
break;
}
} else {
System.err.println ("JSONReader error bond tag " + beo[j]);
}}
if (b >= this.asc.ac || e >= this.asc.ac) System.err.println ("JSONReader error bond referencing atoms " + b + " " + e + " atomCount=" + this.asc.ac + " for " + this.fileName);
 else this.asc.addBond ( new J.adapter.smarter.Bond (b, e, order));
}
}, "~A");
});
