Clazz.declarePackage("J.shape");
Clazz.load(["JU.MeshSurface"], "J.shape.Mesh", ["java.util.Hashtable", "JU.AU", "$.BS", "$.M3", "$.M4", "$.Measure", "$.P3", "$.PT", "$.SB", "$.V3", "JS.T", "JU.BSUtil", "$.C", "$.Escape", "$.Normix"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.title = null;
this.hoverLabel = null;
this.meshColix = 0;
this.normixes = null;
this.lineData = null;
this.thisID = null;
this.isValid = true;
this.scriptCommand = null;
this.colorCommand = null;
this.lattice = null;
this.symops = null;
this.symopNormixes = null;
this.visible = true;
this.lighting = 1073741958;
this.colorType = 0;
this.reverseColor = false;
this.haveXyPoints = false;
this.diameter = 0;
this.width = 0;
this.ptCenter = null;
this.linkedMesh = null;
this.vAB = null;
this.vTemp = null;
this.color = 0;
this.useColix = true;
this.unitCell = null;
this.scale3d = 0;
this.index = 0;
this.atomIndex = -1;
this.modelIndex = -1;
this.visibilityFlags = 0;
this.insideOut = false;
this.checkByteCount = 0;
this.normalsInverted = false;
this.showContourLines = false;
this.showPoints = false;
this.drawTriangles = false;
this.fillTriangles = true;
this.showTriangles = false;
this.frontOnly = false;
this.isShell = false;
this.isTwoSided = true;
this.havePlanarContours = false;
this.bsTemp = null;
this.colorDensity = false;
this.cappingObject = null;
this.slabbingObject = null;
this.volumeRenderPointSize = 0.15;
this.connectedAtoms = null;
this.isModelConnected = false;
this.recalcAltVertices = false;
this.symopColixes = null;
this.hasTranslucentVertices = false;
Clazz.instantialize(this, arguments);}, J.shape, "Mesh", JU.MeshSurface);
Clazz.defineMethod(c$, "setVisibilityFlags", 
function(n){
this.visibilityFlags = n;
}, "~N");
Clazz.defineMethod(c$, "mesh1", 
function(vwr, thisID, colix, index){
if ("+PREVIOUS_MESH+".equals(thisID)) thisID = null;
this.vwr = vwr;
this.thisID = thisID;
this.colix = colix;
this.index = index;
this.ptCenter =  new JU.P3();
this.vAB =  new JU.V3();
this.vTemp =  new JU.V3();
return this;
}, "JV.Viewer,~S,~N,~N");
Clazz.defineMethod(c$, "clear", 
function(meshType){
this.clearMesh(meshType);
}, "~S");
Clazz.defineMethod(c$, "clearMesh", 
function(meshType){
this.altVertices = null;
this.bsDisplay = null;
this.bsSlabDisplay = null;
this.bsSlabGhost = null;
this.symops = null;
this.symopColixes = null;
this.cappingObject = null;
this.colix = 23;
this.colorDensity = false;
this.connectedAtoms = null;
this.diameter = 0;
this.drawTriangles = false;
this.fillTriangles = true;
this.frontOnly = false;
this.isShell = false;
this.havePlanarContours = false;
this.haveXyPoints = false;
this.isModelConnected = false;
this.isDrawPolygon = false;
this.isTwoSided = false;
this.lattice = null;
this.mat4 = null;
this.normixes = null;
this.pis = null;
this.scale3d = 0;
this.showContourLines = false;
this.showPoints = false;
this.showTriangles = false;
this.slabbingObject = null;
this.slabOptions = null;
this.oabc = null;
this.symopNormixes = null;
this.title = null;
this.unitCell = null;
this.useColix = true;
this.vertexCount0 = this.polygonCount0 = this.vc = this.pc = 0;
this.vs = null;
this.vertexSource = null;
this.volumeRenderPointSize = 0.15;
this.meshType = meshType;
}, "~S");
Clazz.defineMethod(c$, "initialize", 
function(lighting, vertices, plane){
if (vertices == null) vertices = this.vs;
var normals = this.getNormals(vertices, plane);
this.setNormixes(normals);
this.lighting = 1073741958;
if (this.insideOut) this.invertNormixes();
if (this.isShell && !this.isTwoSided) this.invertNormixes();
this.setLighting(lighting);
}, "~N,~A,JU.P4");
Clazz.defineMethod(c$, "setNormixes", 
function(normals){
if (normals == null) return (this.normixes = null);
this.normixes =  Clazz.newShortArray (this.normixCount, 0);
if (this.bsTemp == null) this.bsTemp = JU.Normix.newVertexBitSet();
if (this.haveXyPoints) for (var i = this.normixCount; --i >= 0; ) this.normixes[i] = 9999;

 else for (var i = this.normixCount; --i >= 0; ) this.normixes[i] = JU.Normix.getNormixV(normals[i], this.bsTemp);

return this.normixes;
}, "~A");
Clazz.defineMethod(c$, "getNormals", 
function(vertices, plane){
this.normixCount = (this.isDrawPolygon ? this.pc : this.vc);
if (this.normixCount < 0) return null;
var normals =  new Array(this.normixCount);
for (var i = this.normixCount; --i >= 0; ) normals[i] =  new JU.V3();

if (plane == null) {
this.sumVertexNormals(vertices, normals);
} else {
var normal = JU.V3.new3(plane.x, plane.y, plane.z);
for (var i = this.normixCount; --i >= 0; ) normals[i] = normal;

}if (!this.isDrawPolygon) for (var i = this.normixCount; --i >= 0; ) {
normals[i].normalize();
}
return normals;
}, "~A,JU.P4");
Clazz.defineMethod(c$, "setLighting", 
function(lighting){
this.isTwoSided = (lighting == 1073741964);
if (lighting == this.lighting) return;
this.flipLighting(this.lighting);
this.flipLighting(this.lighting = lighting);
}, "~N");
Clazz.defineMethod(c$, "flipLighting", 
function(lighting){
if (lighting == 1073741964) for (var i = this.normixCount; --i >= 0; ) this.normixes[i] = ~this.normixes[i];

 else if ((lighting == 1073741958) == this.insideOut) this.invertNormixes();
}, "~N");
Clazz.defineMethod(c$, "invertNormixes", 
function(){
JU.Normix.setInverseNormixes();
this.normalsInverted = !this.normalsInverted;
for (var i = this.normixCount; --i >= 0; ) this.normixes[i] = JU.Normix.getInverseNormix(this.normixes[i]);

});
Clazz.defineMethod(c$, "setTranslucent", 
function(isTranslucent, iLevel){
this.colix = JU.C.getColixTranslucent3(this.colix, isTranslucent, iLevel);
}, "~B,~N");
Clazz.defineMethod(c$, "sumVertexNormals", 
function(vertices, normals){
J.shape.Mesh.sumVertexNormals2(this, vertices, normals);
}, "~A,~A");
c$.sumVertexNormals2 = Clazz.defineMethod(c$, "sumVertexNormals2", 
function(m, vertices, normals){
var adjustment = m.checkByteCount;
var min = m.getMinDistance2ForVertexGrouping();
for (var i = m.pc; --i >= 0; ) {
try {
var face = m.setABC(i);
if (face == null) continue;
var vA = vertices[face[0]];
var vB = vertices[face[1]];
var vC = vertices[face[2]];
if (vA.distanceSquared(vB) < min || vB.distanceSquared(vC) < min || vA.distanceSquared(vC) < min) continue;
JU.Measure.calcNormalizedNormal(vA, vB, vC, m.vTemp, m.vAB);
if (m.isDrawPolygon) {
normals[i].setT(m.vTemp);
} else {
var l = m.vTemp.length();
if (l > 0.9 && l < 1.1) for (var j = face.length - adjustment; --j >= 0; ) {
var k = face[j];
normals[k].add(m.vTemp);
}
}} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
System.out.println(e);
} else {
throw e;
}
}
}
}, "J.shape.Mesh,~A,~A");
Clazz.defineMethod(c$, "getMinDistance2ForVertexGrouping", 
function(){
return 1e-8;
});
Clazz.defineMethod(c$, "getState", 
function(type){
var s =  new JU.SB();
if (this.isValid) {
s.append(type);
if (!type.equals("mo") && !type.equals("nbo")) s.append(" ID ").append(JU.PT.esc(this.thisID));
if (this.lattice != null) s.append(" lattice ").append(JU.Escape.eP(this.lattice));
if (this.meshColix != 0) s.append(" color mesh ").append(JU.C.getHexCode(this.meshColix));
s.append(this.getRendering());
if (!this.visible) s.append(" hidden");
if (this.bsDisplay != null) {
s.append(";\n  ").append(type);
if (!type.equals("mo") && !type.equals("nbo")) s.append(" ID ").append(JU.PT.esc(this.thisID));
s.append(" display " + JU.Escape.eBS(this.bsDisplay));
}}return s.toString();
}, "~S");
Clazz.defineMethod(c$, "getRendering", 
function(){
var s =  new JU.SB();
s.append(this.fillTriangles ? " fill" : " noFill");
s.append(this.drawTriangles ? " mesh" : " noMesh");
s.append(this.showPoints ? " dots" : " noDots");
s.append(this.frontOnly ? " frontOnly" : " notFrontOnly");
if (this.showContourLines) s.append(" contourlines");
if (this.showTriangles) s.append(" triangles");
s.append(" ").append(JS.T.nameOf(this.lighting));
if (this.isShell && !this.isTwoSided) s.append(" backshell");
return s.toString();
});
Clazz.defineMethod(c$, "getOffsetVertices", 
function(thePlane){
if (this.altVertices != null && !this.recalcAltVertices) return this.altVertices;
this.altVertices =  new Array(this.vc);
for (var i = 0; i < this.vc; i++) this.altVertices[i] = JU.P3.newP(this.vs[i]);

var normal = null;
var val = 0;
if (this.scale3d != 0 && this.vvs != null && thePlane != null) {
normal = JU.V3.new3(thePlane.x, thePlane.y, thePlane.z);
normal.normalize();
normal.scale(this.scale3d);
if (this.mat4 != null) {
var m3 =  new JU.M3();
this.mat4.getRotationScale(m3);
m3.rotate(normal);
}}for (var i = 0; i < this.vc; i++) {
if (this.vvs != null && Float.isNaN(val = this.vvs[i])) continue;
var pt = this.altVertices[i];
if (this.mat4 != null) this.mat4.rotTrans(pt);
if (normal != null && val != 0) pt.scaleAdd2(val, normal, pt);
}
this.initialize(this.lighting, this.altVertices, null);
this.recalcAltVertices = false;
return this.altVertices;
}, "JU.P4");
Clazz.defineMethod(c$, "setShowWithin", 
function(showWithinPoints, showWithinDistance2, isWithinNot){
if (showWithinPoints.size() == 0) {
this.bsDisplay = (isWithinNot ? JU.BSUtil.newBitSet2(0, this.vc) : null);
return;
}this.bsDisplay =  new JU.BS();
for (var i = 0; i < this.vc; i++) if (J.shape.Mesh.checkWithin(this.vs[i], showWithinPoints, showWithinDistance2, isWithinNot)) this.bsDisplay.set(i);

}, "JU.Lst,~N,~B");
c$.checkWithin = Clazz.defineMethod(c$, "checkWithin", 
function(pti, withinPoints, withinDistance2, isWithinNot){
if (withinPoints.size() != 0) for (var i = withinPoints.size(); --i >= 0; ) if (pti.distanceSquared(withinPoints.get(i)) <= withinDistance2) return !isWithinNot;

return isWithinNot;
}, "JU.T3,JU.Lst,~N,~B");
Clazz.defineMethod(c$, "getVertexIndexFromNumber", 
function(vertexIndex){
if (--vertexIndex < 0) vertexIndex = this.vc + vertexIndex;
return (this.vc <= vertexIndex ? this.vc - 1 : vertexIndex < 0 ? 0 : vertexIndex);
}, "~N");
Clazz.defineMethod(c$, "getVisibleVertexBitSet", 
function(){
return this.getVisibleVBS();
});
Clazz.defineMethod(c$, "getVisibleVBS", 
function(){
var bs =  new JU.BS();
if (this.pc == 0 && this.bsSlabDisplay != null) JU.BSUtil.copy2(this.bsSlabDisplay, bs);
 else for (var i = this.pc; --i >= 0; ) if (this.bsSlabDisplay == null || this.bsSlabDisplay.get(i)) {
var vertexIndexes = this.pis[i];
if (vertexIndexes == null) continue;
bs.set(vertexIndexes[0]);
bs.set(vertexIndexes[1]);
bs.set(vertexIndexes[2]);
}
return bs;
});
Clazz.defineMethod(c$, "setTokenProperty", 
function(tokProp, bProp){
switch (tokProp) {
case 1073742058:
case 1073741960:
this.frontOnly = (tokProp == 1073741960 ? bProp : !bProp);
return;
case 1073742057:
case 1073741862:
if (!this.isTwoSided && this.isShell != (tokProp == 1073741862 ? bProp : !bProp)) {
this.isShell = !this.isShell;
this.invertNormixes();
}return;
case 1073741958:
case 1073741861:
case 1073741964:
this.setLighting(tokProp);
return;
case 1073742042:
case 1112150019:
this.showPoints = (tokProp == 1112150019 ? bProp : !bProp);
return;
case 1073742052:
case 1073742018:
this.drawTriangles = (tokProp == 1073742018 ? bProp : !bProp);
return;
case 1073742046:
case 1073741938:
this.fillTriangles = (tokProp == 1073741938 ? bProp : !bProp);
return;
case 1073742060:
case 1073742182:
this.showTriangles = (tokProp == 1073742182 ? bProp : !bProp);
return;
case 1073742039:
case 1073741898:
this.showContourLines = (tokProp == 1073741898 ? bProp : !bProp);
return;
}
}, "~N,~B");
Clazz.defineMethod(c$, "getInfo", 
function(isAll){
var info =  new java.util.Hashtable();
info.put("id", this.thisID);
info.put("vertexCount", Integer.$valueOf(this.vc));
info.put("haveQuads", Boolean.$valueOf(this.haveQuads));
info.put("haveValues", Boolean.$valueOf(this.vvs != null));
var np = this.pc;
if (isAll) {
if (this.vc > 0) {
info.put("vertices", JU.AU.arrayCopyPt(this.vs, this.vc));
if (this.bsSlabDisplay != null) info.put("bsVertices", this.getVisibleVBS());
}if (this.vvs != null) {
info.put("vertexValues", JU.AU.arrayCopyF(this.vvs, this.vc));
}if (np > 0) {
var ii = J.shape.Mesh.nonNull(this.pis, np);
info.put("polygons", ii);
np = ii.length;
if (this.bsSlabDisplay != null) {
var bs = (ii.length == this.pc ? JU.BS.copy(this.bsSlabDisplay) : J.shape.Mesh.nonNullBS(this.bsSlabDisplay, this.pis, this.pc));
info.put("bsPolygons", bs);
np = bs.cardinality();
}}}info.put("polygonCount", Integer.$valueOf(np));
return info;
}, "~B");
c$.nonNullBS = Clazz.defineMethod(c$, "nonNullBS", 
function(bsSlabDisplay, pis, pc){
var bs =  new JU.BS();
for (var pt = 0, i = 0; i < pc; i++) {
if (pis[i] != null) {
if (bsSlabDisplay.get(i)) bs.set(pt);
pt++;
}}
return bs;
}, "JU.BS,~A,~N");
c$.nonNull = Clazz.defineMethod(c$, "nonNull", 
function(pis, pc){
var n = 0;
for (var i = pc; --i >= 0; ) if (pis[i] != null) {
n++;
}
var ii =  Clazz.newIntArray (n, 0);
if (n > 0) for (var pt = 0, i = 0; i < pc; i++) if (pis[i] != null) ii[pt++] = pis[i];

return ii;
}, "~A,~N");
Clazz.defineMethod(c$, "getBoundingBox", 
function(){
return null;
});
Clazz.defineMethod(c$, "getUnitCell", 
function(){
return null;
});
Clazz.defineMethod(c$, "rotateTranslate", 
function(q, offset, isAbsolute){
if (q == null && offset == null) {
this.mat4 = null;
return;
}var m3 =  new JU.M3();
var v =  new JU.V3();
if (this.mat4 == null) this.mat4 = JU.M4.newM4(null);
this.mat4.getRotationScale(m3);
this.mat4.getTranslation(v);
if (q == null) {
if (isAbsolute) v.setT(offset);
 else v.add(offset);
} else {
m3.mul(q.getMatrix());
}this.mat4 = JU.M4.newMV(m3, v);
this.recalcAltVertices = true;
}, "JU.Quat,JU.T3,~B");
Clazz.defineMethod(c$, "getNormalsTemp", 
function(){
return (this.normalsTemp == null ? (this.normalsTemp = this.getNormals(this.vs, null)) : this.normalsTemp);
});
Clazz.overrideMethod(c$, "toString", 
function(){
return this.meshType + "." + this.thisID;
});
});
;//5.0.1-v7 Wed Jun 03 09:22:38 CDT 2026
