Clazz.declarePackage("JM");
Clazz.load(null, "JM.Trajectory", ["JU.BS", "$.P3", "$.V3"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.vwr = null;
this.ms = null;
this.steps = null;
this.isFractional = true;
Clazz.instantialize(this, arguments);}, JM, "Trajectory", null);
/*LV!1824 unnec constructor*/Clazz.defineMethod(c$, "set", 
function(vwr, ms, steps){
this.vwr = vwr;
this.ms = ms;
this.steps = steps;
return this;
}, "JV.Viewer,JM.ModelSet,JU.Lst");
Clazz.defineMethod(c$, "setUnitCell", 
function(imodel){
var c = this.ms.getUnitCell(imodel);
if (c != null && c.getCoordinatesAreFractional() && c.isSupercell()) {
var list = this.ms.trajectory.steps.get(imodel);
for (var i = list.length; --i >= 0; ) if (list[i] != null) c.toSupercell(list[i]);

}}, "~N");
Clazz.defineMethod(c$, "setModel", 
function(modelIndex){
var am = this.ms.am;
var baseModelIndex = am[modelIndex].trajectoryBaseIndex;
am[baseModelIndex].selectedTrajectory = modelIndex;
this.isFractional = !this.ms.getMSInfoB("ignoreUnitCell");
this.setAtomPositions(baseModelIndex, modelIndex, this.steps.get(modelIndex), null, 0, (this.ms.vibrationSteps == null ? null : this.ms.vibrationSteps.get(modelIndex)), this.isFractional);
var currentModelIndex = this.vwr.am.cmi;
if (currentModelIndex >= 0 && currentModelIndex != modelIndex && am[currentModelIndex].fileIndex == am[modelIndex].fileIndex) this.vwr.setCurrentModelIndexClear(modelIndex, false);
}, "~N");
Clazz.defineMethod(c$, "setAtomPositions", 
function(baseModelIndex, modelIndex, t1, t2, f, vibs, isFractional){
var bs =  new JU.BS();
var vib =  new JU.V3();
var am = this.ms.am;
var at = this.ms.at;
var iFirst = am[baseModelIndex].firstAtomIndex;
var iMax = iFirst + this.ms.getAtomCountInModel(baseModelIndex);
if (f == 0) {
for (var pt = 0, i = iFirst; i < iMax && pt < t1.length; i++, pt++) {
var a = at[i];
if (a == null) continue;
a.mi = modelIndex;
if (t1[pt] == null) continue;
if (isFractional) a.setFractionalCoordTo(t1[pt], true);
 else a.setT(t1[pt]);
if (this.ms.vibrationSteps != null) {
if (vibs != null && vibs[pt] != null) vib = vibs[pt];
this.ms.setVibrationVector(i, vib);
}bs.set(i);
}
} else {
var p =  new JU.P3();
var n = Math.min(t1.length, t2.length);
for (var pt = 0, i = iFirst; i < iMax && pt < n; i++, pt++) {
var a = at[i];
if (a == null) continue;
a.mi = modelIndex;
if (t1[pt] == null || t2[pt] == null) continue;
p.sub2(t2[pt], t1[pt]);
p.scaleAdd2(f, p, t1[pt]);
if (isFractional) a.setFractionalCoordTo(p, true);
 else a.setT(p);
bs.set(i);
}
}this.ms.initializeBspf();
this.ms.validateBspfForModel(baseModelIndex, false);
this.ms.recalculateLeadMidpointsAndWingVectors(baseModelIndex);
this.ms.sm.notifyAtomPositionsChanged(baseModelIndex, bs, null);
if (am[baseModelIndex].hasRasmolHBonds) (am[baseModelIndex]).resetRasmolBonds(bs, 2);
}, "~N,~N,~A,~A,~N,~A,~B");
Clazz.defineMethod(c$, "getModelsSelected", 
function(){
var bsModels =  new JU.BS();
for (var i = this.ms.mc; --i >= 0; ) {
var t = this.ms.am[i].selectedTrajectory;
if (t >= 0) {
bsModels.set(t);
i = this.ms.am[i].trajectoryBaseIndex;
}}
return bsModels;
});
Clazz.defineMethod(c$, "morph", 
function(m1, m2, f){
if (f == 0) {
this.ms.setTrajectory(m1);
return;
}if (f == 1) {
this.ms.setTrajectory(m2);
return;
}var baseModelIndex = this.ms.am[m1].trajectoryBaseIndex;
this.ms.am[baseModelIndex].selectedTrajectory = m1;
this.setAtomPositions(baseModelIndex, m1, this.steps.get(m1), this.steps.get(m2), f, (this.ms.vibrationSteps == null ? null : this.ms.vibrationSteps.get(m1)), true);
var m = this.vwr.am.cmi;
if (m >= 0 && m != m1 && this.ms.am[m].fileIndex == this.ms.am[m1].fileIndex) this.vwr.setCurrentModelIndexClear(m1, false);
}, "~N,~N,~N");
Clazz.defineMethod(c$, "fixAtom", 
function(a){
var m = a.mi;
var isFrac = (this.ms.unitCells != null && this.ms.unitCells[m].getCoordinatesAreFractional());
var pt = this.steps.get(m)[a.i - this.ms.am[m].firstAtomIndex];
pt.set(a.x, a.y, a.z);
if (isFrac) this.ms.unitCells[m].toFractional(pt, true);
}, "JM.Atom");
Clazz.defineMethod(c$, "getFractional", 
function(a, ptTemp){
a.setFractionalCoordPt(ptTemp, this.steps.get(a.mi)[a.i - this.ms.am[a.mi].firstAtomIndex], true);
}, "JM.Atom,JU.P3");
Clazz.defineMethod(c$, "getState", 
function(){
var s = "";
for (var i = this.ms.mc; --i >= 0; ) {
var t = this.ms.am[i].selectedTrajectory;
if (t >= 0) {
s = " or " + this.ms.getModelNumberDotted(t) + s;
i = this.ms.am[i].trajectoryBaseIndex;
}}
return (s.length > 0 ? s = "set trajectory {" + s.substring(4) + "}" : "");
});
Clazz.defineMethod(c$, "hasMeasure", 
function(measure){
if (measure != null) {
var atomIndex;
for (var i = 1, count = measure[0]; i <= count; i++) if ((atomIndex = measure[i]) >= 0 && this.ms.am[this.ms.at[atomIndex].mi].isTrajectory) return true;

}return false;
}, "~A");
Clazz.defineMethod(c$, "selectDisplayed", 
function(bs){
var a;
for (var i = this.ms.mc; --i >= 0; ) {
if (this.ms.am[i].isTrajectory && ((a = this.ms.at[this.ms.am[i].firstAtomIndex]) == null || a.mi != i)) bs.clear(i);
}
}, "JU.BS");
Clazz.defineMethod(c$, "getModelBS", 
function(modelIndex, bs){
var iBase = this.ms.am[modelIndex].trajectoryBaseIndex;
for (var i = this.ms.mc; --i >= iBase; ) if (this.ms.am[i].trajectoryBaseIndex == iBase) bs.set(i);

}, "~N,JU.BS");
Clazz.defineMethod(c$, "setBaseModels", 
function(bsModels){
for (var i = this.ms.mc; --i >= 0; ) if (bsModels.get(i) && this.ms.am[i].isTrajectory) bsModels.set(this.ms.am[i].trajectoryBaseIndex);

}, "JU.BS");
});
;//5.0.1-v7 Mon Aug 24 10:01:38 CDT 2026
