Clazz.declarePackage("JV");
Clazz.load(["JU.BS"], "JV.SelectionManager", ["JU.AU", "J.i18n.GT", "JU.BSUtil"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.vwr = null;
this.listeners = null;
this.bsHidden = null;
this.bsSelection = null;
this.bsFixed = null;
this.bsSubset = null;
this.bsDeleted = null;
this.noneSelected = null;
this.empty = 1;
this.hideNotSelected = false;
this.bsTemp = null;
Clazz.instantialize(this, arguments);}, JV, "SelectionManager", null);
Clazz.prepareFields (c$, function(){
this.listeners =  new Array(0);
this.bsHidden =  new JU.BS();
this.bsSelection =  new JU.BS();
this.bsFixed =  new JU.BS();
this.bsTemp =  new JU.BS();
});
Clazz.makeConstructor(c$, 
function(vwr){
this.vwr = vwr;
}, "JV.Viewer");
Clazz.defineMethod(c$, "processDeletedModelAtoms", 
function(bsAtoms){
JU.BSUtil.deleteBits(this.bsDeleted, bsAtoms);
JU.BSUtil.deleteBits(this.bsSubset, bsAtoms);
JU.BSUtil.deleteBits(this.bsFixed, bsAtoms);
JU.BSUtil.deleteBits(this.bsHidden, bsAtoms);
var bs = JU.BSUtil.copy(this.bsSelection);
JU.BSUtil.deleteBits(bs, bsAtoms);
this.setSelectionSet(bs, 0);
this.selectionChanged(false);
}, "JU.BS");
Clazz.defineMethod(c$, "clear", 
function(){
this.clearSelection(true);
this.setSelectionSubset(null);
this.hide(null, null, 0, true);
this.bsDeleted = null;
this.setMotionFixedAtoms(null);
});
Clazz.defineMethod(c$, "display", 
function(modelSet, bs, addRemove, isQuiet){
switch (addRemove) {
default:
var bsNotSubset = (this.bsSubset == null ? null : JU.BSUtil.andNot(JU.BSUtil.copy(this.bsHidden), this.bsSubset));
var bsAll = modelSet.getModelAtomBitSetIncludingDeleted(-1, false);
this.bsHidden.or(bsAll);
if (bsNotSubset != null) {
this.bsHidden.and(this.bsSubset);
this.bsHidden.or(bsNotSubset);
}case 1275069441:
if (bs != null) this.bsHidden.andNot(bs);
break;
case 1073742119:
if (bs != null) this.bsHidden.or(bs);
break;
}
JU.BSUtil.andNot(this.bsHidden, this.bsDeleted);
modelSet.setBsHidden(this.bsHidden);
if (!isQuiet) this.vwr.reportSelection(J.i18n.GT.i(J.i18n.GT.$("{0} atoms hidden"), this.bsHidden.cardinality()));
}, "JM.ModelSet,JU.BS,~N,~B");
Clazz.defineMethod(c$, "hide", 
function(modelSet, bs, addRemove, isQuiet){
var bsNotSubset = (addRemove == 0 || this.bsSubset == null ? null : JU.BSUtil.andNot(JU.BSUtil.copy(this.bsHidden), this.bsSubset));
JV.SelectionManager.setBitSet(this.bsHidden, bs, addRemove);
if (bsNotSubset != null) this.bsHidden.or(bsNotSubset);
if (modelSet != null) modelSet.setBsHidden(this.bsHidden);
if (!isQuiet) this.vwr.reportSelection(J.i18n.GT.i(J.i18n.GT.$("{0} atoms hidden"), this.bsHidden.cardinality()));
}, "JM.ModelSet,JU.BS,~N,~B");
Clazz.defineMethod(c$, "setSelectionSet", 
function(set, addRemove){
JV.SelectionManager.setBitSet(this.bsSelection, set, addRemove);
this.empty = -1;
}, "JU.BS,~N");
c$.setBitSet = Clazz.defineMethod(c$, "setBitSet", 
function(bsWhat, bs, addRemove){
switch (addRemove) {
default:
bsWhat.clearAll();
case 1275069441:
if (bs != null) bsWhat.or(bs);
break;
case 1073742119:
if (bs != null) bsWhat.andNot(bs);
break;
}
}, "JU.BS,JU.BS,~N");
Clazz.defineMethod(c$, "getHiddenSet", 
function(){
return this.bsHidden;
});
Clazz.defineMethod(c$, "getHideNotSelected", 
function(){
return this.hideNotSelected;
});
Clazz.defineMethod(c$, "setHideNotSelected", 
function(TF){
this.hideNotSelected = TF;
if (TF) this.selectionChanged(false);
}, "~B");
Clazz.defineMethod(c$, "isSelected", 
function(atomIndex){
return (atomIndex >= 0 && this.bsSelection.get(atomIndex));
}, "~N");
Clazz.defineMethod(c$, "select", 
function(bs, addRemove, isQuiet){
if (bs == null) {
this.selectAll(true);
if (!this.vwr.getBoolean(1612709900)) this.excludeSelectionSet(this.vwr.ms.getAtoms(1612709900, null));
if (!this.vwr.getBoolean(1612709894)) this.excludeSelectionSet(this.vwr.ms.getAtoms(1612709894, null));
} else {
this.setSelectionSet(bs, addRemove);
if (!this.vwr.getBoolean(1612709900)) this.excludeSelectionSet(this.vwr.ms.getAtoms(1612709900, null));
if (!this.vwr.getBoolean(1612709894)) this.excludeSelectionSet(this.vwr.ms.getAtoms(1612709894, null));
}this.selectionChanged(false);
var reportChime = this.vwr.getBoolean(603979879);
if (!reportChime && isQuiet) return;
var n = this.getSelectionCount();
if (reportChime) this.vwr.getChimeMessenger().reportSelection(n);
 else if (!isQuiet) this.vwr.reportSelection(J.i18n.GT.i(J.i18n.GT.$("{0} atoms selected"), n));
}, "JU.BS,~N,~B");
Clazz.defineMethod(c$, "selectAll", 
function(isQuiet){
var count = this.vwr.ms.ac;
this.empty = (count == 0) ? 1 : 0;
for (var i = count; --i >= 0; ) this.bsSelection.set(i);

JU.BSUtil.andNot(this.bsSelection, this.bsDeleted);
this.selectionChanged(isQuiet);
}, "~B");
Clazz.defineMethod(c$, "clearSelection", 
function(isQuiet){
this.setHideNotSelected(false);
this.bsSelection.clearAll();
this.empty = 1;
this.selectionChanged(isQuiet);
}, "~B");
Clazz.defineMethod(c$, "isAtomSelected", 
function(atomIndex){
return ((this.bsSubset == null || this.bsSubset.get(atomIndex)) && this.bsDeleted == null || !this.bsDeleted.get(atomIndex)) && this.bsSelection.get(atomIndex);
}, "~N");
Clazz.defineMethod(c$, "setSelectedAtom", 
function(atomIndex, TF){
if (atomIndex < 0) {
this.selectionChanged(true);
return;
}if (this.bsSubset != null && !this.bsSubset.get(atomIndex) || this.bsDeleted != null && this.bsDeleted.get(atomIndex)) return;
this.bsSelection.setBitTo(atomIndex, TF);
if (TF) this.empty = 0;
 else this.empty = -1;
}, "~N,~B");
Clazz.defineMethod(c$, "setSelectionSubset", 
function(bs){
this.bsSubset = bs;
}, "JU.BS");
Clazz.defineMethod(c$, "isInSelectionSubset", 
function(atomIndex){
return (atomIndex < 0 || this.bsSubset == null || this.bsSubset.get(atomIndex));
}, "~N");
Clazz.defineMethod(c$, "invertSelection", 
function(){
JU.BSUtil.invertInPlace(this.bsSelection, this.vwr.ms.ac);
this.empty = (this.bsSelection.length() > 0 ? 0 : 1);
this.selectionChanged(false);
});
Clazz.defineMethod(c$, "excludeSelectionSet", 
function(setExclude){
if (setExclude == null || this.empty == 1) return;
this.bsSelection.andNot(setExclude);
this.empty = -1;
}, "JU.BS");
Clazz.defineMethod(c$, "getSelectionCount", 
function(){
if (this.empty == 1) return 0;
this.empty = 1;
var bs;
if (this.bsSubset == null) {
bs = this.bsSelection;
} else {
this.bsTemp.clearAll();
this.bsTemp.or(this.bsSubset);
this.bsTemp.and(this.bsSelection);
bs = this.bsTemp;
}var count = bs.cardinality();
if (count > 0) this.empty = 0;
return count;
});
Clazz.defineMethod(c$, "addListener", 
function(listener){
for (var i = this.listeners.length; --i >= 0; ) if (this.listeners[i] === listener) {
this.listeners[i] = null;
break;
}
var len = this.listeners.length;
for (var i = len; --i >= 0; ) if (this.listeners[i] == null) {
this.listeners[i] = listener;
return;
}
if (this.listeners.length == 0) this.listeners =  new Array(1);
 else this.listeners = JU.AU.doubleLength(this.listeners);
this.listeners[len] = listener;
}, "J.api.JmolSelectionListener");
Clazz.defineMethod(c$, "selectionChanged", 
function(isQuiet){
if (this.hideNotSelected) this.hide(this.vwr.ms, JU.BSUtil.copyInvert(this.bsSelection, this.vwr.ms.ac), 0, isQuiet);
if (isQuiet || this.listeners.length == 0) return;
for (var i = this.listeners.length; --i >= 0; ) if (this.listeners[i] != null) this.listeners[i].selectionChanged(this.bsSelection);

}, "~B");
Clazz.defineMethod(c$, "deleteAtoms", 
function(bs){
var bsNew = JU.BSUtil.copy(bs);
if (this.bsDeleted == null) {
this.bsDeleted = bsNew;
} else {
bsNew.andNot(this.bsDeleted);
this.bsDeleted.or(bs);
}this.bsHidden.andNot(this.bsDeleted);
this.bsSelection.andNot(this.bsDeleted);
return bsNew.cardinality();
}, "JU.BS");
Clazz.defineMethod(c$, "getSelectedAtoms", 
function(){
if (this.bsSubset == null) return this.bsSelection;
var bs = JU.BSUtil.copy(this.bsSelection);
bs.and(this.bsSubset);
return bs;
});
Clazz.defineMethod(c$, "getSelectedAtomsNoSubset", 
function(){
return JU.BSUtil.copy(this.bsSelection);
});
Clazz.defineMethod(c$, "excludeAtoms", 
function(bs, ignoreSubset){
if (this.bsDeleted != null) bs.andNot(this.bsDeleted);
if (!ignoreSubset && this.bsSubset != null) (bs = JU.BSUtil.copy(bs)).and(this.bsSubset);
return bs;
}, "JU.BS,~B");
Clazz.defineMethod(c$, "setMotionFixedAtoms", 
function(bs){
this.bsFixed.clearAll();
if (bs != null) this.bsFixed.or(bs);
}, "JU.BS");
Clazz.defineMethod(c$, "getMotionFixedAtoms", 
function(){
return this.bsFixed;
});
});
;//5.0.1-v7 Tue Jul 22 18:14:29 CDT 2025
