Clazz.declarePackage("J.adapter.writers");
Clazz.load(["J.api.JmolWriter"], "J.adapter.writers.CMLWriter", ["JU.BS", "$.PT", "$.SB", "JU.Edge"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.vwr = null;
this.oc = null;
this.atomsMax = 0;
this.addBonds = false;
this.doTransform = false;
this.allTrajectories = false;
Clazz.instantialize(this, arguments);}, J.adapter.writers, "CMLWriter", null, J.api.JmolWriter);
/*LV!1824 unnec constructor*/Clazz.overrideMethod(c$, "set", 
function(viewer, out, data){
this.vwr = viewer;
this.oc = (this.oc == null ? this.vwr.getOutputChannel(null, null) : this.oc);
this.atomsMax = (data[0]).intValue();
this.addBonds = (data[1]).booleanValue();
this.doTransform = (data[2]).booleanValue();
this.allTrajectories = (data[3]).booleanValue();
}, "JV.Viewer,JU.OC,~A");
Clazz.overrideMethod(c$, "write", 
function(bs){
var sb =  new JU.SB();
var nAtoms = bs.cardinality();
if (nAtoms == 0) return "";
J.adapter.writers.CMLWriter.openTag(sb, "molecule");
J.adapter.writers.CMLWriter.openTag(sb, "atomArray");
var bsAtoms =  new JU.BS();
var atoms = this.vwr.ms.at;
for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
if (--this.atomsMax < 0) break;
var atom = atoms[i];
var name = atom.getAtomName();
JU.PT.rep(name, "\"", "''");
bsAtoms.set(atom.i);
J.adapter.writers.CMLWriter.appendEmptyTag(sb, "atom",  Clazz.newArray(-1, ["id", "a" + (atom.i + 1), "title", atom.getAtomName(), "elementType", atom.getElementSymbol(), "x3", "" + atom.x, "y3", "" + atom.y, "z3", "" + atom.z]));
}
J.adapter.writers.CMLWriter.closeTag(sb, "atomArray");
if (this.addBonds) {
J.adapter.writers.CMLWriter.openTag(sb, "bondArray");
var bondCount = this.vwr.ms.bondCount;
var bonds = this.vwr.ms.bo;
for (var i = 0; i < bondCount; i++) {
var bond = bonds[i];
if (bond == null) continue;
var a1 = bond.atom1;
var a2 = bond.atom2;
if (!bsAtoms.get(a1.i) || !bsAtoms.get(a2.i)) continue;
var order = JU.Edge.getCmlBondOrder(bond.order);
if (order == null) continue;
J.adapter.writers.CMLWriter.appendEmptyTag(sb, "bond",  Clazz.newArray(-1, ["atomRefs2", "a" + (bond.atom1.i + 1) + " a" + (bond.atom2.i + 1), "order", order]));
}
J.adapter.writers.CMLWriter.closeTag(sb, "bondArray");
}J.adapter.writers.CMLWriter.closeTag(sb, "molecule");
this.oc.append(sb.toString());
return this.toString();
}, "JU.BS");
c$.openDocument = Clazz.defineMethod(c$, "openDocument", 
function(sb){
sb.append("<?xml version=\"1.0\"?>\n");
}, "JU.SB");
c$.openTag = Clazz.defineMethod(c$, "openTag", 
function(sb, name){
sb.append("<").append(name).append(">\n");
}, "JU.SB,~S");
c$.startOpenTag = Clazz.defineMethod(c$, "startOpenTag", 
function(sb, name){
sb.append("<").append(name);
}, "JU.SB,~S");
c$.terminateTag = Clazz.defineMethod(c$, "terminateTag", 
function(sb){
sb.append(">\n");
}, "JU.SB");
c$.terminateEmptyTag = Clazz.defineMethod(c$, "terminateEmptyTag", 
function(sb){
sb.append("/>\n");
}, "JU.SB");
c$.appendEmptyTag = Clazz.defineMethod(c$, "appendEmptyTag", 
function(sb, name, attributes){
J.adapter.writers.CMLWriter.startOpenTag(sb, name);
J.adapter.writers.CMLWriter.addAttributes(sb, attributes);
J.adapter.writers.CMLWriter.terminateEmptyTag(sb);
}, "JU.SB,~S,~A");
c$.addAttributes = Clazz.defineMethod(c$, "addAttributes", 
function(sb, attributes){
for (var i = 0; i < attributes.length; i++) {
J.adapter.writers.CMLWriter.addAttribute(sb, attributes[i], attributes[++i]);
}
}, "JU.SB,~A");
c$.addAttribute = Clazz.defineMethod(c$, "addAttribute", 
function(sb, key, val){
sb.append(" ").append(key).append("=").append(JU.PT.esc(val));
}, "JU.SB,~S,~S");
c$.closeTag = Clazz.defineMethod(c$, "closeTag", 
function(sb, name){
sb.append("</").append(name).append(">\n");
}, "JU.SB,~S");
Clazz.overrideMethod(c$, "toString", 
function(){
return (this.oc == null ? "" : this.oc.toString());
});
});
;//5.0.1-v4 Thu Feb 20 12:29:54 CST 2025
