Clazz.declarePackage("J.shapespecial");
Clazz.load(["J.shape.AtomShape", "JU.BS", "J.atomdata.RadiusData"], "J.shapespecial.Dots", ["java.util.Hashtable", "JU.M3", "$.SB", "J.c.VDW", "J.geodesic.EnvelopeCalculation", "JU.BSUtil", "$.C", "$.Escape"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.ec = null;
this.isSurface = false;
this.bsOn = null;
this.bsSelected = null;
this.bsIgnore = null;
this.thisAtom = 0;
this.thisRadius = 0;
this.thisArgb = 0;
this.rdLast = null;
Clazz.instantialize(this, arguments);}, J.shapespecial, "Dots", J.shape.AtomShape);
Clazz.prepareFields (c$, function(){
this.bsOn =  new JU.BS();
this.rdLast =  new J.atomdata.RadiusData(null, 0, null, null);
});
Clazz.defineMethod(c$, "initShape", 
function(){
Clazz.superCall(this, J.shapespecial.Dots, "initShape", []);
this.translucentAllowed = false;
this.ec =  new J.geodesic.EnvelopeCalculation().set(this.vwr, this.ms.ac, this.mads);
});
Clazz.overrideMethod(c$, "getSize", 
function(atomIndex){
return (this.mads != null ? this.mads[atomIndex] * 2 : this.bsOn.get(atomIndex) ? Clazz.doubleToInt(Math.floor(this.ec.getRadius(atomIndex) * 2000)) : 0);
}, "~N");
Clazz.overrideMethod(c$, "setProperty", 
function(propertyName, value, bs){
if ("init" === propertyName) {
this.initialize();
return;
}if ("translucency" === propertyName) {
if (!this.translucentAllowed) return;
}if ("ignore" === propertyName) {
this.bsIgnore = value;
return;
}if ("select" === propertyName) {
this.bsSelected = value;
return;
}if ("radius" === propertyName) {
this.thisRadius = (value).floatValue();
if (this.thisRadius > 16) this.thisRadius = 16.1;
return;
}if ("colorRGB" === propertyName) {
this.thisArgb = (value).intValue();
return;
}if ("atom" === propertyName) {
this.thisAtom = (value).intValue();
if (this.thisAtom >= this.ms.at.length) return;
this.ms.at[this.thisAtom].setShapeVisibility(this.vf, true);
this.ec.allocDotsConvexMaps(this.ms.ac);
return;
}if ("dots" === propertyName) {
var atoms = this.ms.at;
if (this.thisAtom >= atoms.length) return;
this.isActive = true;
this.ec.setFromBits(this.thisAtom, value);
atoms[this.thisAtom].setShapeVisibility(this.vf, true);
var ac = this.ms.ac;
if (this.mads == null) {
this.ec.setMads(null);
this.mads =  Clazz.newShortArray (ac, 0);
for (var i = 0; i < ac; i++) if (atoms[i] != null && atoms[i].isVisible(1 | this.vf)) try {
this.mads[i] = Clazz.floatToShort(this.ec.getAppropriateRadius(i) * 1000);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}

this.ec.setMads(this.mads);
}this.mads[this.thisAtom] = Clazz.floatToShort(this.thisRadius * 1000);
if (this.colixes == null) this.checkColixLength(4, ac);
this.colixes[this.thisAtom] = JU.C.getColix(this.thisArgb);
this.bsOn.set(this.thisAtom);
return;
}if ("refreshTrajectories" === propertyName) {
bs = (value)[1];
var m4 = (value)[2];
if (m4 == null) return;
var m =  new JU.M3();
m4.getRotationScale(m);
this.ec.reCalculate(bs, m);
return;
}if (propertyName === "deleteModelAtoms") {
var firstAtomDeleted = ((value)[2])[1];
var nAtomsDeleted = ((value)[2])[2];
JU.BSUtil.deleteBits(this.bsOn, bs);
this.ec.deleteAtoms(firstAtomDeleted, nAtomsDeleted);
}this.setPropAS(propertyName, value, bs);
}, "~S,~O,JU.BS");
Clazz.defineMethod(c$, "initialize", 
function(){
this.bsSelected = null;
this.bsIgnore = null;
this.isActive = false;
if (this.ec == null) this.ec =  new J.geodesic.EnvelopeCalculation().set(this.vwr, this.ms.ac, this.mads);
});
Clazz.overrideMethod(c$, "setSizeRD", 
function(rd, bsSelected){
if (rd == null) rd =  new J.atomdata.RadiusData(null, 0, J.atomdata.RadiusData.EnumType.ABSOLUTE, null);
if (this.bsSelected != null) bsSelected = this.bsSelected;
var isVisible = true;
var setRadius = 3.4028235E38;
this.isActive = true;
switch (rd.factorType) {
case J.atomdata.RadiusData.EnumType.OFFSET:
break;
case J.atomdata.RadiusData.EnumType.ABSOLUTE:
if (rd.value == 0) isVisible = false;
setRadius = rd.value;
default:
rd.valueExtended = (this.vwr.getBoolean(603979948) ? this.vwr.getFloat(570425394) : 0);
}
var maxRadius;
switch (rd.vdwType) {
case J.c.VDW.ADPMIN:
case J.c.VDW.ADPMAX:
case J.c.VDW.HYDRO:
case J.c.VDW.TEMP:
maxRadius = setRadius;
break;
case J.c.VDW.BONDING:
maxRadius = this.ms.getMaxVanderwaalsRadius() * 2;
break;
default:
maxRadius = this.ms.getMaxVanderwaalsRadius();
}
var newSet = (this.rdLast.value != rd.value || this.rdLast.valueExtended != rd.valueExtended || this.rdLast.factorType !== rd.factorType || this.rdLast.vdwType !== rd.vdwType || this.ec.getDotsConvexMax() == 0);
if (isVisible) {
for (var i = bsSelected.nextSetBit(0); i >= 0; i = bsSelected.nextSetBit(i + 1)) if (!this.bsOn.get(i)) {
this.bsOn.set(i);
newSet = true;
}
} else {
var isAll = (bsSelected == null);
var i0 = (isAll ? this.ms.ac - 1 : bsSelected.nextSetBit(0));
for (var i = i0; i >= 0; i = (isAll ? i - 1 : bsSelected.nextSetBit(i + 1))) this.bsOn.setBitTo(i, false);

}var atoms = this.ms.at;
for (var i = this.ms.ac; --i >= 0; ) if (atoms[i] != null) atoms[i].setShapeVisibility(this.vf, this.bsOn.get(i));

if (!isVisible) return;
if (newSet) {
this.mads = null;
this.ec.newSet();
}var dotsConvexMaps = this.ec.getDotsConvexMaps();
if (dotsConvexMaps != null) {
for (var i = this.ms.ac; --i >= 0; ) if (atoms[i] != null && this.bsOn.get(i)) {
dotsConvexMaps[i] = null;
}
}if (dotsConvexMaps == null && (this.colixes == null || this.colixes.length != this.ms.ac)) this.checkColixLength(4, this.ms.ac);
this.ec.calculate(rd, maxRadius, this.bsOn, this.bsIgnore, !this.vwr.getBoolean(603979830), this.vwr.getBoolean(603979829), this.isSurface, true);
this.rdLast = rd;
}, "J.atomdata.RadiusData,JU.BS");
Clazz.overrideMethod(c$, "setAtomClickability", 
function(){
for (var i = this.ms.ac; --i >= 0; ) {
var atom = this.ms.at[i];
if (atom != null && ((atom.shapeVisibilityFlags & this.vf) == 0 || this.ms.isAtomHidden(i))) continue;
atom.setClickable(this.vf);
}
});
Clazz.overrideMethod(c$, "getShapeState", 
function(){
var dotsConvexMaps = this.ec.getDotsConvexMaps();
if (dotsConvexMaps == null || this.ec.getDotsConvexMax() == 0) return "";
var s =  new JU.SB();
var temp =  new java.util.Hashtable();
var ac = this.ms.ac;
var type = (this.isSurface ? "geoSurface " : "dots ");
for (var i = 0; i < ac; i++) {
if (!this.bsOn.get(i) || dotsConvexMaps[i] == null) continue;
if (this.bsColixSet != null && this.bsColixSet.get(i)) JU.BSUtil.setMapBitSet(temp, i, i, J.shape.Shape.getColorCommand(type, this.paletteIDs[i], this.colixes[i], this.translucentAllowed));
var bs = dotsConvexMaps[i];
if (!bs.isEmpty()) {
var r = this.ec.getAppropriateRadius(i);
J.shape.Shape.appendCmd(s, type + i + " radius " + r + " " + JU.Escape.eBS(bs));
}}
return s.append(this.vwr.getCommands(temp, null, "select")).toString();
});
c$.MAX_LEVEL = 3;
});
;//5.0.1-v7 Thu Jun 04 11:07:16 CDT 2026
