Clazz.declarePackage("J.shape");
Clazz.load(null, "J.shape.Shape", ["J.c.PAL", "JU.C", "$.Logger", "JV.JC"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.myType = null;
this.vwr = null;
this.ms = null;
this.shapeID = 0;
this.vf = 0;
this.translucentLevel = 0;
this.translucentAllowed = true;
this.isBioShape = false;
this.bsSizeSet = null;
this.bsColixSet = null;
Clazz.instantialize(this, arguments);}, J.shape, "Shape", null);
Clazz.defineMethod(c$, "initializeShape", 
function(vwr, modelSet, shapeID){
this.vwr = vwr;
this.shapeID = shapeID;
this.vf = JV.JC.getShapeVisibilityFlag(shapeID);
this.setModelSet(modelSet);
this.initShape();
}, "JV.Viewer,JM.ModelSet,~N");
Clazz.defineMethod(c$, "setModelVisibilityFlags", 
function(bsModels){
}, "JU.BS");
Clazz.defineMethod(c$, "getSize", 
function(atomIndex){
return 0;
}, "~N");
Clazz.defineMethod(c$, "getSizeG", 
function(group){
return 0;
}, "JM.Group");
Clazz.defineMethod(c$, "replaceGroup", 
function(g0, g1){
}, "JM.Group,JM.Group");
Clazz.defineMethod(c$, "setModelSet", 
function(modelSet){
this.ms = modelSet;
this.initModelSet();
}, "JM.ModelSet");
Clazz.defineMethod(c$, "initModelSet", 
function(){
});
Clazz.defineMethod(c$, "setShapeSizeRD", 
function(size, rd, bsSelected){
if (rd == null) this.setSize(size, bsSelected);
 else this.setSizeRD(rd, bsSelected);
}, "~N,J.atomdata.RadiusData,JU.BS");
Clazz.defineMethod(c$, "setSize", 
function(size, bsSelected){
}, "~N,JU.BS");
Clazz.defineMethod(c$, "setSizeRD", 
function(rd, bsSelected){
}, "J.atomdata.RadiusData,JU.BS");
Clazz.defineMethod(c$, "setPropS", 
function(propertyName, value, bsSelected){
if (propertyName === "setProperties") {
this.setProperties(value);
return;
}if (propertyName === "translucentLevel") {
this.translucentLevel = (value).floatValue();
return;
}if (propertyName === "refreshTrajectories") {
return;
}JU.Logger.warn("unassigned " + JV.JC.shapeClassBases[this.shapeID] + " + shape setProperty:" + propertyName + ":" + value);
}, "~S,~O,JU.BS");
Clazz.defineMethod(c$, "setProperties", 
function(value){
var bsSelected = this.vwr.bsA();
if (Clazz.instanceOf(value,"JU.Lst")) {
var propertyList = value;
while (propertyList.size() > 0) {
var data = propertyList.removeItemAt(0);
this.setProperty((data[0]).intern(), data[1], bsSelected);
}
} else {
var data = (value);
for (var i = 0, n = data.length; i < n; i++) {
this.setProperty((data[i][0]).intern(), data[i][1], bsSelected);
}
}}, "~O");
Clazz.defineMethod(c$, "getPropertyData", 
function(property, data){
return this.getPropShape(property, data);
}, "~S,~A");
Clazz.defineMethod(c$, "getPropShape", 
function(property, data){
if (Clazz.instanceOf(data[1], Integer)) {
var index = (data[1]).intValue();
data[1] = this.getProperty(property, index);
return (data[1] != null);
}return false;
}, "~S,~A");
Clazz.defineMethod(c$, "getProperty", 
function(property, index){
return null;
}, "~S,~N");
Clazz.defineMethod(c$, "getIndexFromName", 
function(thisID){
return -1;
}, "~S");
Clazz.defineMethod(c$, "wasClicked", 
function(x, y){
return false;
}, "~N,~N");
Clazz.defineMethod(c$, "findNearestAtomIndex", 
function(xMouse, yMouse, closest, bsNot){
}, "~N,~N,~A,JU.BS");
Clazz.defineMethod(c$, "checkBoundsMinMax", 
function(pointMin, pointMax){
}, "JU.P3,JU.P3");
Clazz.defineMethod(c$, "setAtomClickability", 
function(){
});
Clazz.defineMethod(c$, "checkObjectClicked", 
function(x, y, modifiers, bsVisible, drawPicking){
return null;
}, "~N,~N,~N,JU.BS,~B");
Clazz.defineMethod(c$, "checkObjectHovered", 
function(x, y, bsVisible){
return false;
}, "~N,~N,JU.BS");
Clazz.defineMethod(c$, "checkObjectDragged", 
function(prevX, prevY, x, y, dragAction, bsVisible){
return false;
}, "~N,~N,~N,~N,~N,JU.BS");
Clazz.defineMethod(c$, "coordinateInRange", 
function(x, y, vertex, dmin2, ptXY){
this.vwr.tm.transformPtScrSafe(vertex, ptXY);
var d2 = (x - ptXY.x) * (x - ptXY.x) + (y - ptXY.y) * (y - ptXY.y);
return (d2 <= dmin2 ? d2 : -1);
}, "~N,~N,JU.T3,~N,JU.P3i");
Clazz.defineMethod(c$, "getColixI", 
function(colix, paletteID, atomIndex){
return this.getColixA(colix, paletteID, this.ms.at[atomIndex]);
}, "~N,~N,~N");
Clazz.defineMethod(c$, "getColixA", 
function(colix, paletteID, atom){
return (colix == 2 ? this.vwr.cm.getColixAtomPalette(atom, paletteID) : colix);
}, "~N,~N,JM.Atom");
Clazz.defineMethod(c$, "getColixB", 
function(colix, pid, bond){
return (colix == 2 ? this.vwr.cm.getColixBondPalette(bond, pid) : colix);
}, "~N,~N,JM.Bond");
Clazz.defineMethod(c$, "getShapeDetail", 
function(){
return null;
});
c$.getColix = Clazz.defineMethod(c$, "getColix", 
function(colixes, i, atom){
return JU.C.getColixInherited((colixes == null || i >= colixes.length ? 0 : colixes[i]), atom.colixAtom);
}, "~A,~N,JM.Atom");
c$.getFontCommand = Clazz.defineMethod(c$, "getFontCommand", 
function(type, font){
if (font == null) return "";
return "font " + type + " " + font.getInfo();
}, "~S,JU.Font");
c$.getColorCommandUnk = Clazz.defineMethod(c$, "getColorCommandUnk", 
function(type, colix, translucentAllowed){
return J.shape.Shape.getColorCommand(type, J.c.PAL.UNKNOWN.id, colix, translucentAllowed);
}, "~S,~N,~B");
c$.getColorCommand = Clazz.defineMethod(c$, "getColorCommand", 
function(type, pid, colix, translucentAllowed){
if (pid == J.c.PAL.UNKNOWN.id && colix == 0) return "";
var s = (pid == J.c.PAL.UNKNOWN.id && colix == 0 ? "" : (translucentAllowed ? J.shape.Shape.getTranslucentLabel(colix) + " " : "") + (pid != J.c.PAL.UNKNOWN.id && !J.c.PAL.isPaletteVariable(pid) ? J.c.PAL.getPaletteName(pid) : J.shape.Shape.encodeColor(colix)));
return "color " + type + " " + s;
}, "~S,~N,~N,~B");
c$.encodeColor = Clazz.defineMethod(c$, "encodeColor", 
function(colix){
return (JU.C.isColixColorInherited(colix) ? "none" : JU.C.getHexCode(colix));
}, "~N");
c$.getTranslucentLabel = Clazz.defineMethod(c$, "getTranslucentLabel", 
function(colix){
return (JU.C.isColixTranslucent(colix) ? JU.C.getColixTranslucencyLabel(colix) : "opaque");
}, "~N");
c$.appendCmd = Clazz.defineMethod(c$, "appendCmd", 
function(s, cmd){
if (cmd.length == 0) return;
s.append("  ").append(cmd).append(";\n");
}, "JU.SB,~S");
});
;//5.0.1-v7 Thu Jun 04 11:07:16 CDT 2026
