Clazz.declarePackage("JV");
Clazz.load(null, "JV.ShapeManager", ["JU.BS", "$.P3", "J.api.Interface", "J.c.PAL", "$.VDW", "JU.BSUtil", "JV.JC"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.ms = null;
this.shapes = null;
this.vwr = null;
this.scaleText = null;
this.bsRenderableAtoms = null;
this.bsSlabbedInternal = null;
this.navMinMax = null;
Clazz.instantialize(this, arguments);}, JV, "ShapeManager", null);
Clazz.prepareFields (c$, function(){
this.navMinMax =  Clazz.newIntArray (4, 0);
});
Clazz.makeConstructor(c$, 
function(vwr){
this.vwr = vwr;
this.bsRenderableAtoms =  new JU.BS();
this.bsSlabbedInternal =  new JU.BS();
}, "JV.Viewer");
Clazz.defineMethod(c$, "findNearestShapeAtomIndex", 
function(x, y, closest, bsNot){
if (this.shapes != null) for (var i = 0; i < this.shapes.length && closest[0] == null; ++i) if (this.shapes[i] != null) this.shapes[i].findNearestAtomIndex(x, y, closest, bsNot);

}, "~N,~N,~A,JU.BS");
Clazz.defineMethod(c$, "getShapePropertyIndex", 
function(shapeID, propertyName, index){
if (this.shapes == null || this.shapes[shapeID] == null) return null;
this.vwr.setShapeErrorState(shapeID, "get " + propertyName);
var result = this.shapes[shapeID].getProperty(propertyName, index);
this.vwr.setShapeErrorState(-1, null);
return result;
}, "~N,~S,~N");
Clazz.defineMethod(c$, "getShapePropertyData", 
function(shapeID, propertyName, data){
if (this.shapes == null || this.shapes[shapeID] == null) return false;
this.vwr.setShapeErrorState(shapeID, "get " + propertyName);
var result = this.shapes[shapeID].getPropertyData(propertyName, data);
this.vwr.setShapeErrorState(-1, null);
return result;
}, "~N,~S,~A");
Clazz.defineMethod(c$, "getShapeIdFromObjectName", 
function(objectName){
if (this.shapes != null) for (var i = 16; i < 30; ++i) if (this.shapes[i] != null && this.shapes[i].getIndexFromName(objectName) >= 0) return i;

if (this.shapes[6] != null && this.shapes[6].getIndexFromName(objectName) >= 0) {
return 6;
}return -1;
}, "~S");
Clazz.defineMethod(c$, "loadDefaultShapes", 
function(newModelSet){
this.ms = newModelSet;
if (this.shapes != null) for (var i = 0; i < this.shapes.length; ++i) if (this.shapes[i] != null) this.shapes[i].setModelSet(newModelSet);

this.loadShape(0);
this.loadShape(1);
}, "JM.ModelSet");
Clazz.defineMethod(c$, "loadShape", 
function(shapeID){
if (this.shapes == null) return null;
if (this.shapes[shapeID] != null) return this.shapes[shapeID];
if (shapeID == 2 || shapeID == 3 || shapeID == 4) return null;
var className = JV.JC.getShapeClassName(shapeID, false);
var shape;
if ((shape = J.api.Interface.getInterface(className, this.vwr, "shape")) == null) return null;
this.vwr.setShapeErrorState(shapeID, "allocate");
shape.initializeShape(this.vwr, this.ms, shapeID);
this.vwr.setShapeErrorState(-1, null);
return this.shapes[shapeID] = shape;
}, "~N");
Clazz.defineMethod(c$, "notifyAtomPositionsChanged", 
function(baseModel, bs, mat){
var Imodel = Integer.$valueOf(baseModel);
var bsModelAtoms = this.vwr.getModelUndeletedAtomsBitSet(baseModel);
for (var i = 0; i < 37; i++) if (this.shapes[i] != null) this.setShapePropertyBs(i, "refreshTrajectories",  Clazz.newArray(-1, [Imodel, bs, mat]), bsModelAtoms);

}, "~N,JU.BS,JU.M4");
Clazz.defineMethod(c$, "releaseShape", 
function(shapeID){
if (this.shapes != null) this.shapes[shapeID] = null;
}, "~N");
Clazz.defineMethod(c$, "setScale", 
function(){
if (this.scaleText != null) {
this.loadShape(31);
this.setShapePropertyBs(31, "%SCALE", this.scaleText, null);
this.scaleText = null;
}});
Clazz.defineMethod(c$, "resetShapes", 
function(cacheScale){
if (cacheScale) {
var data =  new Array(1);
this.getShapePropertyData(31, "%SCALE", data);
this.scaleText = data[0];
}this.shapes =  new Array(37);
}, "~B");
Clazz.defineMethod(c$, "setShapeProperties", 
function(shapeID, values){
this.vwr.setShapeErrorState(shapeID, "set properties");
this.loadShape(shapeID).setProperties(values);
this.vwr.setShapeErrorState(-1, null);
}, "~N,~A");
Clazz.defineMethod(c$, "setShapeSizeBs", 
function(shapeID, size, rd, bsSelected){
if (this.shapes == null) return;
if (bsSelected == null && (shapeID != 1 || size != 2147483647)) bsSelected = this.vwr.bsA();
if (rd != null && rd.value != 0 && rd.vdwType === J.c.VDW.TEMP) this.ms.getBfactor100Lo();
this.vwr.setShapeErrorState(shapeID, "set size");
if (rd == null ? size != 0 : rd.value != 0) this.loadShape(shapeID);
if (this.shapes[shapeID] != null) {
this.shapes[shapeID].setShapeSizeRD(size, rd, bsSelected);
}this.vwr.setShapeErrorState(-1, null);
}, "~N,~N,J.atomdata.RadiusData,JU.BS");
Clazz.defineMethod(c$, "setLabel", 
function(strLabel, bsSelection){
if (strLabel == null) {
if (this.shapes[5] == null) return;
} else {
this.loadShape(5);
this.setShapeSizeBs(5, 0, null, bsSelection);
}this.setShapePropertyBs(5, "label", strLabel, bsSelection);
}, "~O,JU.BS");
Clazz.defineMethod(c$, "setShapePropertyBs", 
function(shapeID, propertyName, value, bsSelected){
if (this.shapes == null || this.shapes[shapeID] == null) return;
if (bsSelected == null) bsSelected = this.vwr.bsA();
this.vwr.setShapeErrorState(shapeID, "set " + propertyName);
this.shapes[shapeID].setProperty(propertyName.intern(), value, bsSelected);
this.vwr.setShapeErrorState(-1, null);
}, "~N,~S,~O,JU.BS");
Clazz.defineMethod(c$, "checkFrankclicked", 
function(x, y){
var frankShape = this.shapes[36];
return (frankShape != null && frankShape.wasClicked(x, y));
}, "~N,~N");
Clazz.defineMethod(c$, "checkObjectClicked", 
function(x, y, modifiers, bsVisible, drawPicking){
var shape;
var map = null;
if (this.vwr.getPickingMode() == 2) {
return (this.shapes[5] == null ? null : this.shapes[5].checkObjectClicked(x, y, modifiers, bsVisible, false));
}if (modifiers != 0 && this.vwr.getBondsPickable() && (map = this.shapes[1].checkObjectClicked(x, y, modifiers, bsVisible, false)) != null) return map;
for (var i = 0; i < JV.ShapeManager.clickableMax; i++) if ((shape = this.shapes[JV.ShapeManager.hoverable[i]]) != null && (map = shape.checkObjectClicked(x, y, modifiers, bsVisible, drawPicking)) != null) return map;

return null;
}, "~N,~N,~N,JU.BS,~B");
Clazz.defineMethod(c$, "checkObjectDragged", 
function(prevX, prevY, x, y, modifiers, bsVisible, iShape){
var found = false;
var n = (iShape > 0 ? iShape + 1 : 37);
for (var i = iShape; !found && i < n; ++i) if (this.shapes[i] != null) found = this.shapes[i].checkObjectDragged(prevX, prevY, x, y, modifiers, bsVisible);

return found;
}, "~N,~N,~N,~N,~N,JU.BS,~N");
Clazz.defineMethod(c$, "checkObjectHovered", 
function(x, y, bsVisible, checkBonds){
var shape = this.shapes[1];
if (checkBonds && shape != null && shape.checkObjectHovered(x, y, bsVisible)) return true;
for (var i = 0; i < JV.ShapeManager.hoverable.length; i++) {
shape = this.shapes[JV.ShapeManager.hoverable[i]];
if (shape != null && shape.checkObjectHovered(x, y, bsVisible)) return true;
}
return false;
}, "~N,~N,JU.BS,~B");
Clazz.defineMethod(c$, "deleteShapeAtoms", 
function(value, bs){
if (this.shapes != null) for (var j = 0; j < 37; j++) if (this.shapes[j] != null) this.setShapePropertyBs(j, "deleteModelAtoms", value, bs);

}, "~A,JU.BS");
Clazz.defineMethod(c$, "deleteVdwDependentShapes", 
function(bs){
if (bs == null) bs = this.vwr.bsA();
this.setShapeAtomsSafely(24, "deleteVdw", bs);
this.setShapeAtomsSafely(25, "deleteVdw", bs);
}, "JU.BS");
Clazz.defineMethod(c$, "setShapeAtomsSafely", 
function(i, key, bs){
if (this.shapes[i] != null) this.shapes[i].setProperty(key, null, bs);
}, "~N,~S,JU.BS");
Clazz.defineMethod(c$, "notifyAtoms", 
function(prop, atomsAndModels){
switch (prop) {
case "atomslabeled":
this.vwr.setModelkitPropertySafely("updatemodelkeys", atomsAndModels);
break;
case "atomsDeleted":
this.setShapeAtomsSafely(6, prop, atomsAndModels[0]);
this.vwr.setModelkitPropertySafely("updatemodelkeys", atomsAndModels);
break;
case "atomsMoved":
if (this.getShape(22) != null) this.vwr.setModelkitPropertySafely(prop, atomsAndModels[0]);
break;
}
}, "~S,~A");
Clazz.defineMethod(c$, "getAtomShapeValue", 
function(tok, group, atomIndex){
var iShape = JV.JC.shapeTokenIndex(tok);
if (iShape < 0 || this.shapes[iShape] == null) return 0;
var mad = this.shapes[iShape].getSize(atomIndex);
if (mad == 0) {
if ((group.shapeVisibilityFlags & this.shapes[iShape].vf) == 0) return 0;
mad = this.shapes[iShape].getSizeG(group);
}return mad / 2000;
}, "~N,JM.Group,~N");
Clazz.defineMethod(c$, "replaceGroup", 
function(g0, g1){
if (this.shapes == null) return;
for (var i = 9; i < 16; i++) if (this.shapes[i] != null) this.shapes[i].replaceGroup(g0, g1);

}, "JM.Group,JM.Group");
Clazz.defineMethod(c$, "getObjectMap", 
function(map, withDollar){
if (this.shapes == null) return;
var bDollar = Boolean.$valueOf(withDollar);
for (var i = 16; i < 30; ++i) this.getShapePropertyData(i, "getNames",  Clazz.newArray(-1, [map, bDollar]));

}, "java.util.Map,~B");
Clazz.defineMethod(c$, "getProperty", 
function(paramInfo){
if (paramInfo.equals("getShapes")) return this.shapes;
return null;
}, "~O");
Clazz.defineMethod(c$, "getShape", 
function(i){
return (this.shapes == null ? null : this.shapes[i]);
}, "~N");
Clazz.defineMethod(c$, "resetBioshapes", 
function(bsAllAtoms){
if (this.shapes == null) return;
for (var i = 0; i < this.shapes.length; ++i) if (this.shapes[i] != null && this.shapes[i].isBioShape) {
this.shapes[i].setModelSet(this.ms);
this.shapes[i].setShapeSizeRD(0, null, bsAllAtoms);
this.shapes[i].setProperty("color", J.c.PAL.NONE, bsAllAtoms);
}
}, "JU.BS");
Clazz.defineMethod(c$, "setAtomLabel", 
function(strLabel, i){
if (this.shapes != null) {
this.shapes[5].setProperty("label:" + strLabel, Integer.$valueOf(i), null);
if (this.vwr.getModelkitPropertySafely(null) === Boolean.TRUE) this.notifyAtoms("atomslabeled",  Clazz.newArray(-1, [null, JU.BSUtil.newAndSetBit(this.vwr.ms.at[i].mi)]));
}}, "~S,~N");
Clazz.defineMethod(c$, "setModelVisibility", 
function(bs){
var shapes = this.shapes;
if (shapes == null || shapes[0] == null) return;
if (bs == null) bs = this.vwr.getVisibleFramesBitSet();
if (shapes[8] != null) shapes[8].setProperty("highlight", null, null);
for (var i = 8; i < 33; i++) if (shapes[i] != null) shapes[i].setModelVisibilityFlags(bs);

var showHydrogens = this.vwr.getBoolean(603979922);
var bsDeleted = this.vwr.slm.bsDeleted;
var atoms = this.ms.at;
this.ms.clearVisibleSets();
if (atoms.length > 0) {
for (var i = this.ms.ac; --i >= 0; ) {
var atom = atoms[i];
if (atom != null) atom.shapeVisibilityFlags &= -64;
if (bsDeleted != null && bsDeleted.get(i)) continue;
if (bs.get(atom.mi)) {
var f = 1;
if (!this.ms.isAtomHidden(i) && (showHydrogens || atom.getElementNumber() != 1)) {
f |= 8;
if (atom.madAtom != 0) f |= 16;
atom.setShapeVisibility(f, true);
}}}
}this.setShapeVis();
}, "JU.BS");
Clazz.defineMethod(c$, "setShapeVis", 
function(){
for (var i = 0; i < 37; ++i) {
var shape = this.shapes[i];
if (shape != null) shape.setAtomClickability();
}
});
Clazz.defineMethod(c$, "finalizeAtoms", 
function(bsTranslateSelected, finalizeParams){
var vwr = this.vwr;
var tm = vwr.tm;
if (finalizeParams) vwr.finalizeTransformParameters();
if (bsTranslateSelected != null) {
var ptCenter = this.ms.getAtomSetCenter(bsTranslateSelected);
var pt =  new JU.P3();
tm.transformPt3fSafe(ptCenter, pt);
pt.add(tm.ptOffset);
tm.unTransformPoint(pt, pt);
pt.sub(ptCenter);
vwr.setAtomCoordsRelative(pt, bsTranslateSelected);
tm.ptOffset.set(0, 0, 0);
tm.bsSelectedAtoms = null;
}var bsOK = this.bsRenderableAtoms;
this.ms.getAtomsInFrame(bsOK);
var vibrationVectors = this.ms.vibrations;
var vibsOn = (vibrationVectors != null && tm.vibrationOn);
var checkOccupancy = (this.ms.bsModulated != null && this.ms.occupancies != null);
var atoms = this.ms.at;
var occ;
var occMax = vwr.getInt(553648159);
var haveMods = false;
var bsSlabbed = this.bsSlabbedInternal;
bsSlabbed.clearAll();
for (var i = bsOK.nextSetBit(0); i >= 0; i = bsOK.nextSetBit(i + 1)) {
var atom = atoms[i];
var screen = (vibsOn && atom.hasVibration() ? tm.transformPtVibSafe(atom, vibrationVectors[i]) : tm.transformPtSafe(atom));
if (screen.z == 1 && tm.internalSlab && tm.xyzIsSlabbedInternal(atom)) {
bsSlabbed.set(i);
}atom.sX = screen.x;
atom.sY = screen.y;
atom.sZ = screen.z;
var d = Math.abs(atom.madAtom);
if (d == 32200) d = Clazz.floatToInt(vwr.getFloat(1153433601) * 2000);
atom.sD = Clazz.floatToInt(vwr.tm.scaleToScreen(screen.z, d));
if (checkOccupancy && vibrationVectors[i] != null && (occ = vibrationVectors[i].getOccupancy100(vibsOn)) != -2147483648) {
haveMods = true;
atom.setShapeVisibility(2, false);
if (occ >= 0 && occ < occMax) atom.setShapeVisibility(24, false);
 else atom.setShapeVisibility(8 | (atom.madAtom > 0 ? 16 : 0), true);
this.ms.occupancies[atom.i] = Math.abs(occ);
}}
if (haveMods) this.setShapeVis();
var gdata = vwr.gdata;
if (tm.slabEnabled) {
var slabByMolecule = vwr.getBoolean(603979940);
var slabByAtom = vwr.getBoolean(603979939);
var minZ = gdata.slab;
var maxZ = gdata.depth;
if (slabByMolecule) {
var molecules = this.ms.getMolecules();
var moleculeCount = this.ms.getMoleculeCountInModel(-1);
for (var i = 0; i < moleculeCount; i++) {
var m = molecules[i];
var j = 0;
var pt = m.firstAtomIndex;
if (!bsOK.get(pt)) continue;
for (; j < m.ac; j++, pt++) if (gdata.isClippedZ(atoms[pt].sZ - (atoms[pt].sD >> 1))) break;

if (j != m.ac) {
pt = m.firstAtomIndex;
for (var k = 0; k < m.ac; k++) {
bsOK.clear(pt);
atoms[pt++].sZ = 0;
}
}}
}for (var i = bsOK.nextSetBit(0); i >= 0; i = bsOK.nextSetBit(i + 1)) {
var atom = atoms[i];
if (gdata.isClippedZ(atom.sZ - (slabByAtom ? atoms[i].sD >> 1 : 0))) {
atom.setClickable(0);
var r = Clazz.doubleToInt((slabByAtom ? -1 : 1) * atom.sD / 2);
if (atom.sZ + r < minZ || atom.sZ - r > maxZ || !gdata.isInDisplayRange(atom.sX, atom.sY)) {
bsOK.clear(i);
}}}
}if (this.ms.ac == 0 || !vwr.getShowNavigationPoint()) return null;
var minX = 2147483647;
var maxX = -2147483648;
var minY = 2147483647;
var maxY = -2147483648;
for (var i = bsOK.nextSetBit(0); i >= 0; i = bsOK.nextSetBit(i + 1)) {
var atom = atoms[i];
if (atom.sX < minX) minX = atom.sX;
if (atom.sX > maxX) maxX = atom.sX;
if (atom.sY < minY) minY = atom.sY;
if (atom.sY > maxY) maxY = atom.sY;
}
this.navMinMax[0] = minX;
this.navMinMax[1] = maxX;
this.navMinMax[2] = minY;
this.navMinMax[3] = maxY;
return this.navMinMax;
}, "JU.BS,~B");
Clazz.defineMethod(c$, "setModelSet", 
function(modelSet){
this.ms = modelSet;
}, "JM.ModelSet");
Clazz.defineMethod(c$, "checkInheritedShapes", 
function(){
if (this.shapes[24] == null) return;
this.setShapePropertyBs(24, "remapInherited", null, null);
});
Clazz.defineMethod(c$, "restrictSelected", 
function(isBond, doInvert){
var bsSelected = this.vwr.slm.getSelectedAtomsNoSubset();
if (doInvert) {
this.vwr.slm.invertSelection();
var bsSubset = this.vwr.slm.bsSubset;
if (bsSubset != null) {
bsSelected = this.vwr.slm.getSelectedAtomsNoSubset();
bsSelected.and(bsSubset);
this.vwr.selectStatus(bsSelected, false, 0, true, false);
JU.BSUtil.invertInPlace(bsSelected, this.vwr.ms.ac);
bsSelected.and(bsSubset);
}}JU.BSUtil.andNot(bsSelected, this.vwr.slm.bsDeleted);
var bondmode = this.vwr.getBoolean(603979812);
if (!isBond) this.vwr.setBooleanProperty("bondModeOr", true);
this.setShapeSizeBs(1, 0, null, null);
this.setShapePropertyBs(1, "type", Integer.$valueOf(32768), null);
this.setShapeSizeBs(1, 0, null, null);
this.setShapePropertyBs(1, "type", Integer.$valueOf(1023), null);
var bs = this.vwr.bsA();
for (var iShape = 21; --iShape >= 0; ) if (iShape != 6 && this.getShape(iShape) != null) this.setShapeSizeBs(iShape, 0, null, bs);

if (this.getShape(21) != null) this.setShapePropertyBs(21, "off", bs, null);
this.setLabel(null, bs);
if (!isBond) this.vwr.setBooleanProperty("bondModeOr", bondmode);
this.vwr.selectStatus(bsSelected, false, 0, true, false);
}, "~B,~B");
c$.hoverable =  Clazz.newIntArray(-1, [31, 20, 25, 24, 22, 36]);
c$.clickableMax = JV.ShapeManager.hoverable.length - 1;
});
;//5.0.1-v7 Tue Feb 10 12:29:49 CST 2026
