Clazz.declarePackage("J.shape");
Clazz.load(["J.shape.Shape", "JU.P3i"], "J.shape.MeshCollection", ["java.util.Hashtable", "JU.AU", "$.Lst", "$.P3", "$.PT", "$.SB", "JS.T", "J.shape.Mesh", "JU.C", "$.Escape", "$.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.jvxlData = null;
this.meshCount = 0;
this.meshes = null;
this.currentMesh = null;
this.isFixed = false;
this.nUnnamed = 0;
this.colix = 0;
this.explicitID = false;
this.previousMeshID = null;
this.linkedMesh = null;
this.modelIndex = 0;
this.displayWithinDistance2 = 0;
this.isDisplayWithinNot = false;
this.displayWithinPoints = null;
this.bsDisplay = null;
this.title = null;
this.pickedMesh = null;
this.pickedModel = 0;
this.pickedVertex = 0;
this.pickedPt = null;
this.connections = null;
this.htObjects = null;
this.color = 0;
this.ptXY = null;
this.keyXy = null;
Clazz.instantialize(this, arguments);}, J.shape, "MeshCollection", J.shape.Shape);
Clazz.prepareFields (c$, function(){
this.meshes =  new Array(4);
this.ptXY =  new JU.P3i();
});
Clazz.defineMethod(c$, "setMesh", 
function(thisID){
this.linkedMesh = null;
if (thisID == null || JU.PT.isWild(thisID)) {
if (thisID != null) this.previousMeshID = thisID;
this.currentMesh = null;
return null;
}this.currentMesh = this.getMesh(thisID);
if (this.currentMesh == null) {
this.allocMesh(thisID, null);
} else if (thisID.equals("+PREVIOUS_MESH+")) {
this.linkedMesh = this.currentMesh.linkedMesh;
}if (this.currentMesh.thisID == null) {
if (this.nUnnamed == 0 || this.getMesh(this.myType + this.nUnnamed) != null) this.nUnnamed++;
this.currentMesh.thisID = this.myType + this.nUnnamed;
if (this.htObjects != null) this.htObjects.put(this.currentMesh.thisID.toUpperCase(), this.currentMesh);
}this.previousMeshID = this.currentMesh.thisID;
return this.currentMesh;
}, "~S");
Clazz.defineMethod(c$, "allocMesh", 
function(thisID, m){
var index = this.meshCount++;
this.meshes = JU.AU.ensureLength(this.meshes, this.meshCount * 2);
this.currentMesh = this.meshes[index] = (m == null ?  new J.shape.Mesh().mesh1(this.vwr, thisID, this.colix, index) : m);
this.currentMesh.color = this.color;
this.currentMesh.index = index;
if (thisID != null && this.htObjects != null) this.htObjects.put(thisID.toUpperCase(), this.currentMesh);
this.previousMeshID = null;
}, "~S,J.shape.Mesh");
Clazz.defineMethod(c$, "merge", 
function(mc){
for (var i = 0; i < mc.meshCount; i++) {
if (mc.meshes[i] != null) {
var m = mc.meshes[i];
var m0 = this.getMesh(m.thisID);
if (m0 == null) {
this.allocMesh(m.thisID, m);
} else {
this.meshes[m0.index] = m;
m.index = m0.index;
}}}
this.previousMeshID = null;
this.currentMesh = null;
}, "J.shape.MeshCollection");
Clazz.overrideMethod(c$, "initShape", 
function(){
this.setMeshColor();
});
Clazz.defineMethod(c$, "setMeshColor", 
function(){
this.colix = 5;
this.color = 0xFFFFFFFF;
});
Clazz.defineMethod(c$, "setPropMC", 
function(propertyName, value, bs){
if ("init" === propertyName) {
this.title = null;
return;
}if ("link" === propertyName) {
if (this.meshCount >= 2 && this.currentMesh != null) this.currentMesh.linkedMesh = this.meshes[this.meshCount - 2];
return;
}if ("lattice" === propertyName) {
if (this.currentMesh != null) this.currentMesh.lattice = value;
return;
}if ("symops" === propertyName) {
if (this.currentMesh != null) {
this.currentMesh.symops = value;
if (this.currentMesh.symops == null) return;
var n = this.currentMesh.symops.length;
this.currentMesh.symopColixes =  Clazz.newShortArray (n, 0);
for (var i = n; --i >= 0; ) this.currentMesh.symopColixes[i] = JU.C.getColix(this.vwr.cm.ce.getArgbMinMax(i + 1, 1, n));

}return;
}if ("thisID" === propertyName) {
var id = value;
this.setMesh(id);
this.checkExplicit(id);
return;
}if ("title" === propertyName) {
this.setTitle(value);
return;
}if ("delete" === propertyName) {
this.deleteMesh();
return;
}if ("reset" === propertyName) {
var thisID = value;
if (this.setMesh(thisID) == null) return;
this.setMesh(thisID);
return;
}if ("color" === propertyName) {
if (value == null) return;
this.colix = JU.C.getColixO(value);
this.color = (value).intValue();
if (this.currentMesh != null) {
this.currentMesh.color = this.color;
}this.setTokenProperty(1765808134, false, false);
return;
}if ("translucency" === propertyName) {
this.setTokenProperty(1111490588, ((value).equals("translucent")), false);
return;
}if ("hidden" === propertyName) {
value = Integer.$valueOf((value).booleanValue() ? 1073742334 : 1073742335);
propertyName = "token";
}if ("token" === propertyName) {
var tok = (value).intValue();
var tok2 = 0;
var test = true;
switch (tok) {
case 1610625028:
case 1073742335:
case 1073742072:
case 1073741958:
case 1073741861:
case 1073741964:
case 1112150019:
case 1073741938:
case 1073741862:
case 1073742182:
case 1073741960:
break;
case 1073742334:
test = false;
tok = 1073742335;
break;
case 1073741898:
tok2 = 1073742018;
break;
case 1073742039:
test = false;
tok = 1073741898;
tok2 = 1073742018;
break;
case 1073742018:
tok2 = 1073741898;
break;
case 1073742052:
test = false;
tok = 1073742018;
tok2 = 1073741898;
break;
case 1073742042:
test = false;
tok = 1112150019;
break;
case 1073742046:
test = false;
tok = 1073741938;
break;
case 1073742057:
test = false;
tok = 1073741862;
break;
case 1073742060:
test = false;
tok = 1073742182;
break;
case 1073742058:
test = false;
tok = 1073741960;
break;
default:
JU.Logger.error("PROBLEM IN MESHCOLLECTION: token? " + JS.T.nameOf(tok));
}
this.setTokenProperty(tok, test, false);
if (tok2 != 0) this.setTokenProperty(tok2, test, true);
return;
}this.setPropS(propertyName, value, bs);
}, "~S,~O,JU.BS");
Clazz.defineMethod(c$, "setTitle", 
function(value){
if ((typeof(value)=='string')) {
var nLine = 1;
var lines = value;
if (lines.length > 0) {
for (var i = lines.length; --i >= 0; ) if (lines.charAt(i) == '|') nLine++;

this.title =  new Array(nLine);
nLine = 0;
var i0 = -1;
for (var i = 0; i < lines.length; i++) if (lines.charAt(i) == '|') {
this.title[nLine++] = lines.substring(i0 + 1, i);
i0 = i;
}
this.title[nLine] = lines.substring(i0 + 1);
return this.title;
}value = null;
}return (this.title = (value == null ? null : value));
}, "~O");
Clazz.defineMethod(c$, "checkExplicit", 
function(id){
if (this.explicitID) return;
this.explicitID = (id != null && !id.equals("+PREVIOUS_MESH+"));
if (this.explicitID) this.previousMeshID = id;
}, "~S");
Clazz.defineMethod(c$, "setTokenProperty", 
function(tokProp, bProp, testD){
if (tokProp == 1073742072) {
if (this.meshCount == 0) return;
for (var i = 0; i < this.meshCount; i++) this.meshes[i].visible = false;

tokProp = 1073742335;
}if (this.currentMesh == null) {
var key = (this.explicitID && JU.PT.isWild(this.previousMeshID) ? this.previousMeshID : null);
var list = this.getMeshList(key, false);
for (var i = list.size(); --i >= 0; ) this.setMeshTokenProperty(list.get(i), tokProp, bProp, testD);

if (list.size() == 1) this.currentMesh = list.get(0);
} else {
this.setMeshTokenProperty(this.currentMesh, tokProp, bProp, testD);
if (this.linkedMesh != null) this.setMeshTokenProperty(this.linkedMesh, tokProp, bProp, testD);
}}, "~N,~B,~B");
Clazz.defineMethod(c$, "setMeshTokenProperty", 
function(m, tokProp, bProp, testD){
if (testD && (!m.havePlanarContours || m.drawTriangles == m.showContourLines)) return;
switch (tokProp) {
case 1610625028:
m.bsDisplay = this.bsDisplay;
if (this.bsDisplay == null && this.displayWithinPoints != null) m.setShowWithin(this.displayWithinPoints, this.displayWithinDistance2, this.isDisplayWithinNot);
return;
case 1073742335:
m.visible = bProp;
return;
case 1765808134:
m.colix = this.colix;
return;
case 1111490588:
m.setTranslucent(bProp, this.translucentLevel);
if (bProp && m.bsSlabGhost != null) m.resetSlab();
return;
default:
m.setTokenProperty(tokProp, bProp);
}
}, "J.shape.Mesh,~N,~B,~B");
Clazz.defineMethod(c$, "getPropDataMC", 
function(property, data){
if (property === "keys") {
var keys = (Clazz.instanceOf(data[1],"JU.Lst") ? data[1] :  new JU.Lst());
data[1] = keys;
keys.addLast("count");
keys.addLast("getCenter");
}if (property === "getNames") {
var map = data[0];
var withDollar = (data[1]).booleanValue();
for (var i = this.meshCount; --i >= 0; ) if (this.meshes[i] != null && this.meshes[i].vc != 0) map.put((withDollar ? "$" : "") + this.meshes[i].thisID, JS.T.tokenOr);

return true;
}if (property === "getVertices") {
var m = this.getMesh(data[0]);
if (m == null) return false;
data[1] = m.vs;
data[2] = m.getVisibleVertexBitSet();
return true;
}if (property === "points") {
var m = this.getMesh(data[0]);
if (m == null) return false;
var bs = m.getVisibleVertexBitSet();
var pts =  new Array(bs.cardinality());
for (var p = 0, i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
pts[p++] = m.vs[i];
}
data[1] = pts;
return true;
}if (property === "checkID") {
var key = data[0];
var list = this.getMeshList(key, true);
var m;
if (list.size() == 0 || (m = list.get(0)) == null) return false;
data[1] = m.thisID;
return true;
}if (property === "index") {
var m = this.getMesh(data[0]);
data[1] = Integer.$valueOf(m == null ? -1 : m.index);
return true;
}if (property === "getCenter") {
var id = data[0];
var index = (data[1]).intValue();
var m;
if ((m = this.getMesh(id)) == null || m.vs == null) return false;
if (index == 2147483647) data[2] = JU.P3.new3(m.index + 1, this.meshCount, m.vc);
 else data[2] = m.vs[m.getVertexIndexFromNumber(index)];
return true;
}return this.getPropShape(property, data);
}, "~S,~A");
Clazz.defineMethod(c$, "getMeshList", 
function(key, justOne){
var list =  new JU.Lst();
if (key != null) key = (key.length == 0 ? null : key.toUpperCase());
var isWild = JU.PT.isWild(key);
var id;
for (var i = this.meshCount; --i >= 0; ) {
if (key == null || (id = this.meshes[i].thisID.toUpperCase()).equals(key) || isWild && JU.PT.isMatch(id, key, true, true)) {
list.addLast(this.meshes[i]);
if (justOne) break;
}}
return list;
}, "~S,~B");
Clazz.defineMethod(c$, "getPropMC", 
function(property, index){
var m = this.currentMesh;
if (index >= 0 && (index >= this.meshCount || (m = this.meshes[index]) == null)) return null;
if (property === "count") {
var n = 0;
for (var i = 0; i < this.meshCount; i++) if ((m = this.meshes[i]) != null && m.vc > 0) n++;

return Integer.$valueOf(n);
}if (property === "bsVertices") {
if (m == null) return null;
var lst =  new JU.Lst();
lst.addLast(m.vs);
lst.addLast(m.getVisibleVBS());
return lst;
}if (property === "ID") return (m == null ? null : m.thisID);
if (property.startsWith("list")) {
this.clean();
var sb =  new JU.SB();
var k = 0;
var isNamed = property.length > 5;
var id = (property.equals("list") ? null : isNamed ? property.substring(5) : m == null ? null : m.thisID);
for (var i = 0; i < this.meshCount; i++) {
m = this.meshes[i];
if (id != null && !id.equalsIgnoreCase(m.thisID)) continue;
sb.appendI((++k)).append(" id:" + m.thisID).append("; model:" + this.vwr.getModelNumberDotted(m.modelIndex)).append("; vertices:" + m.vc).append("; polygons:" + m.pc).append("; visible:" + m.visible);
var range = this.getProperty("dataRange", 0);
if (range != null) sb.append("; dataRange:").append(JU.Escape.eAF(range));
if (m.title != null) {
var s = "";
for (var j = 0; j < m.title.length; j++) s += (j == 0 ? "; title:" : " | ") + m.title[j];

if (s.length > 10000) s = s.substring(0, 10000) + "...";
sb.append(s);
}sb.appendC('\n');
if (isNamed) {
var info = this.getProperty("jvxlFileInfo", 0);
if (info != null) sb.append(info).appendC('\n');
}}
return sb.toString();
}if (property === "values") return this.getValues(m);
if (property === "vertices") return this.getVertices(m);
if (property === "info") {
if (m == null) return null;
var info = m.getInfo(false);
if (info != null && this.jvxlData != null) {
var ss = this.jvxlData.jvxlFileTitle;
if (ss != null) info.put("jvxlFileTitle", ss.trim());
ss = this.jvxlData.jvxlFileSource;
if (ss != null) info.put("jvxlFileSource", ss);
ss = this.jvxlData.jvxlFileMessage;
if (ss != null) info.put("jvxlFileMessage", ss.trim());
}return info;
}if (property === "data") return (m == null ? null : m.getInfo(true));
return null;
}, "~S,~N");
Clazz.defineMethod(c$, "getValues", 
function(mesh){
return (mesh == null ? null : mesh.vvs);
}, "J.shape.Mesh");
Clazz.defineMethod(c$, "getVertices", 
function(mesh){
return (mesh == null ? null : mesh.vs);
}, "J.shape.Mesh");
Clazz.defineMethod(c$, "clean", 
function(){
for (var i = this.meshCount; --i >= 0; ) if (this.meshes[i] == null || this.meshes[i].vc == 0) this.deleteMeshI(i);

});
Clazz.defineMethod(c$, "deleteMesh", 
function(){
if (this.explicitID && this.currentMesh != null) this.deleteMeshI(this.currentMesh.index);
 else this.deleteMeshKey(this.explicitID && this.previousMeshID != null && JU.PT.isWild(this.previousMeshID) ? this.previousMeshID : null);
this.currentMesh = null;
});
Clazz.defineMethod(c$, "deleteMeshKey", 
function(key){
if (key == null || key.length == 0) {
for (var i = this.meshCount; --i >= 0; ) this.meshes[i] = null;

this.meshCount = 0;
this.nUnnamed = 0;
if (this.htObjects != null) this.htObjects.clear();
} else {
var list = this.getMeshList(key, false);
var n = list.size();
for (var i = 0; i < n; i++) this.deleteMeshI(list.get(i).index);

}}, "~S");
Clazz.defineMethod(c$, "deleteMeshI", 
function(i){
if (this.htObjects != null) this.htObjects.remove(this.meshes[i].thisID.toUpperCase());
for (var j = i + 1; j < this.meshCount; ++j) this.meshes[--this.meshes[j].index] = this.meshes[j];

this.meshes[--this.meshCount] = null;
}, "~N");
Clazz.defineMethod(c$, "resetObjects", 
function(){
this.htObjects.clear();
for (var i = 0; i < this.meshCount; i++) {
var m = this.meshes[i];
m.index = i;
this.htObjects.put(m.thisID.toUpperCase(), m);
}
});
Clazz.defineMethod(c$, "getMesh", 
function(thisID){
var i = this.getIndexFromName(thisID);
return (i < 0 ? null : this.meshes[i]);
}, "~S");
Clazz.overrideMethod(c$, "getIndexFromName", 
function(id){
if ("+PREVIOUS_MESH+".equals(id)) return (this.previousMeshID == null ? this.meshCount - 1 : this.getIndexFromName(this.previousMeshID));
if (JU.PT.isWild(id)) {
var list = this.getMeshList(id, true);
return (list.size() == 0 ? -1 : list.get(0).index);
}if (this.htObjects != null) {
var m = this.htObjects.get(id.toUpperCase());
return (m == null ? -1 : m.index);
}for (var i = this.meshCount; --i >= 0; ) {
if (this.meshes[i] != null && this.meshes[i].vc != 0 && id.equalsIgnoreCase(this.meshes[i].thisID)) return i;
}
return -1;
}, "~S");
Clazz.overrideMethod(c$, "setModelVisibilityFlags", 
function(bsModels){
var bsDeleted = this.vwr.slm.bsDeleted;
for (var i = this.meshCount; --i >= 0; ) {
var mesh = this.meshes[i];
mesh.setVisibilityFlags(mesh.visible && mesh.isValid && (mesh.modelIndex < 0 || bsModels.get(mesh.modelIndex) && (mesh.atomIndex < 0 || !this.ms.isAtomHidden(mesh.atomIndex) && !(bsDeleted != null && bsDeleted.get(mesh.atomIndex)))) ? this.vf : 0);
}
}, "JU.BS");
Clazz.defineMethod(c$, "setStatusPicked", 
function(flag, v, map){
this.vwr.setStatusAtomPicked(flag, "[\"" + this.myType + "\"," + JU.PT.esc(this.pickedMesh.thisID) + "," + +this.pickedModel + "," + this.pickedVertex + "," + v.x + "," + v.y + "," + v.z + "," + (this.pickedMesh.title == null ? "\"\"" : JU.PT.esc(this.pickedMesh.title[0])) + "]", map, false);
}, "~N,JU.T3,java.util.Map");
Clazz.defineMethod(c$, "getPickedPoint", 
function(v, modelIndex){
var map =  new java.util.Hashtable();
if (v != null) {
map.put("pt", v);
map.put("modelIndex", Integer.$valueOf(modelIndex));
map.put("model", this.vwr.getModelNumberDotted(modelIndex));
map.put("id", this.pickedMesh.thisID);
map.put("vertex", Integer.$valueOf(this.pickedVertex + 1));
map.put("type", this.myType);
}return map;
}, "JU.T3,~N");
Clazz.overrideMethod(c$, "checkObjectClicked", 
function(x, y, action, bsVisible, drawPicking){
if (!drawPicking) return null;
if (!this.vwr.isBound(action, 18)) return null;
var dmin2 = 100;
if (this.vwr.gdata.isAntialiased()) {
x <<= 1;
y <<= 1;
dmin2 <<= 1;
}var imesh = -1;
var maxz = -2147483648;
var minz = 2147483647;
for (var i = 0; i < this.meshCount; i++) {
var m = this.meshes[i];
if (!this.isPickable(m, bsVisible)) continue;
var centers = m.vs;
if (centers == null) continue;
for (var j = centers.length; --j >= 0; ) {
var v = centers[j];
if (v == null) continue;
var d2 = this.coordinateInRange(x, y, v, dmin2, this.ptXY);
if (d2 >= 0) {
if (this.ptXY.z < minz) {
imesh = i;
minz = this.ptXY.z;
}if (this.ptXY.z > maxz) {
maxz = this.ptXY.z;
}}}
}
if (imesh < 0) return null;
this.pickedMesh = this.meshes[imesh];
this.setPropertySuper("thisID", this.pickedMesh.thisID, null);
var ptRet =  new JU.P3();
ptRet.setT(this.pickedMesh.vs[this.pickedVertex]);
this.pickedModel = this.pickedMesh.modelIndex;
var map = this.getPickedPoint(ptRet, this.pickedModel);
this.setStatusPicked(-4, ptRet, map);
return map;
}, "~N,~N,~N,JU.BS,~B");
Clazz.defineMethod(c$, "setPropertySuper", 
function(propertyName, value, bs){
this.setPropMC(propertyName, value, bs);
}, "~S,~O,JU.BS");
Clazz.defineMethod(c$, "isPickable", 
function(m, bsVisible){
return m.visibilityFlags != 0 && (m.modelIndex < 0 || bsVisible.get(m.modelIndex)) && !JU.C.isColixTranslucent(m.colix);
}, "J.shape.Mesh,JU.BS");
});
;//5.0.1-v7 Thu Jun 04 11:20:16 CDT 2026
