Clazz.declarePackage("JV");
Clazz.load(["java.util.Hashtable"], ["JV.Connection", "$.Scene", "$.StateManager", "$.Connections"], ["java.util.Arrays", "JU.BS", "$.Lst", "$.SB", "JM.Orientation", "JU.BSUtil", "$.Escape"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.maxUndo = 20;
this.vwr = null;
this.saved = null;
this.lastOrientation = "";
this.lastContext = "";
this.lastConnections = "";
this.lastScene = "";
this.lastSelected = "";
this.lastState = "";
this.lastShape = "";
this.lastCoordinates = "";
this.lastUnitcell = "";
this.undoStateStack = null;
this.redoStateStack = null;
Clazz.instantialize(this, arguments);}, JV, "StateManager", null);
Clazz.prepareFields (c$, function(){
this.saved =  new java.util.Hashtable();
});
Clazz.makeConstructor(c$, 
function(vwr){
this.vwr = vwr;
}, "JV.Viewer");
c$.getVariableList = Clazz.defineMethod(c$, "getVariableList", 
function(htVariables, nMax, withSites, definedOnly){
var sb =  new JU.SB();
var n = 0;
var list =  new Array(htVariables.size());
for (var entry, $entry = htVariables.entrySet().iterator (); $entry.hasNext()&& ((entry = $entry.next ()) || true);) {
var key = entry.getKey();
var $var = entry.getValue();
if ((withSites || !key.startsWith("site_")) && (!definedOnly || key.charAt(0) == '@')) list[n++] = key + (key.charAt(0) == '@' ? " " + $var.asString() : " = " + JV.StateManager.varClip(key, $var.escape(), nMax));
}
java.util.Arrays.sort(list, 0, n);
for (var i = 0; i < n; i++) if (list[i] != null) sb.append("  ").append(list[i]).append(";\n");

if (n == 0 && !definedOnly) sb.append("# --no global user variables defined--;\n");
return sb.toString();
}, "java.util.Map,~N,~B,~B");
c$.getObjectIdFromName = Clazz.defineMethod(c$, "getObjectIdFromName", 
function(name){
if (name == null) return -1;
var objID = "background axis1      axis2      axis3      boundbox   unitcell   frank      ".indexOf(name.toLowerCase());
return (objID < 0 ? objID : Clazz.doubleToInt(objID / 11));
}, "~S");
c$.getObjectNameFromId = Clazz.defineMethod(c$, "getObjectNameFromId", 
function(objId){
if (objId < 0 || objId >= 7) return null;
return "background axis1      axis2      axis3      boundbox   unitcell   frank      ".substring(objId * 11, objId * 11 + 11).trim();
}, "~N");
Clazz.defineMethod(c$, "clear", 
function(global){
this.vwr.setShowAxes(false);
this.vwr.setShowBbcage(false);
this.vwr.setShowUnitCell(false);
global.clear();
}, "JV.GlobalSettings");
Clazz.defineMethod(c$, "resetLighting", 
function(){
this.vwr.setIntProperty("ambientPercent", 45);
this.vwr.setIntProperty("celShadingPower", 10);
this.vwr.setIntProperty("diffusePercent", 84);
this.vwr.setIntProperty("phongExponent", 64);
this.vwr.setIntProperty("specularExponent", 6);
this.vwr.setIntProperty("specularPercent", 22);
this.vwr.setIntProperty("specularPower", 40);
this.vwr.setIntProperty("zDepth", 0);
this.vwr.setIntProperty("zShadePower", 3);
this.vwr.setIntProperty("zSlab", 50);
this.vwr.setBooleanProperty("specular", true);
this.vwr.setBooleanProperty("celShading", false);
this.vwr.setBooleanProperty("zshade", false);
});
Clazz.defineMethod(c$, "setCrystallographicDefaults", 
function(){
this.vwr.setAxesMode(603979808);
this.vwr.setShowAxes(true);
this.vwr.setShowUnitCell(true);
this.vwr.setBooleanProperty("perspectiveDepth", false);
});
Clazz.defineMethod(c$, "setCommonDefaults", 
function(){
this.vwr.setBooleanProperty("perspectiveDepth", true);
this.vwr.setFloatProperty("bondTolerance", 0.45);
this.vwr.setFloatProperty("minBondDistance", 0.4);
this.vwr.setIntProperty("bondingVersion", 0);
this.vwr.setBooleanProperty("translucent", true);
});
Clazz.defineMethod(c$, "setJmolDefaults", 
function(){
this.setCommonDefaults();
this.vwr.setStringProperty("defaultColorScheme", "Jmol");
this.vwr.setBooleanProperty("axesOrientationRasmol", false);
this.vwr.setBooleanProperty("zeroBasedXyzRasmol", false);
this.vwr.setIntProperty("percentVdwAtom", 23);
this.vwr.setIntProperty("bondRadiusMilliAngstroms", 150);
this.vwr.setVdwStr("auto");
});
Clazz.defineMethod(c$, "setRasMolDefaults", 
function(){
this.setCommonDefaults();
this.vwr.setStringProperty("defaultColorScheme", "RasMol");
this.vwr.setBooleanProperty("axesOrientationRasmol", true);
this.vwr.setBooleanProperty("zeroBasedXyzRasmol", true);
this.vwr.setIntProperty("percentVdwAtom", 0);
this.vwr.setIntProperty("bondRadiusMilliAngstroms", 1);
this.vwr.setVdwStr("Rasmol");
});
Clazz.defineMethod(c$, "setPyMOLDefaults", 
function(){
this.setCommonDefaults();
this.vwr.setStringProperty("measurementUnits", "ANGSTROMS");
this.vwr.setBooleanProperty("zoomHeight", true);
});
c$.getNoCase = Clazz.defineMethod(c$, "getNoCase", 
function(saved, name){
for (var e, $e = saved.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) if (e.getKey().equalsIgnoreCase(name)) return e.getValue();

return null;
}, "java.util.Map,~S");
Clazz.defineMethod(c$, "listSavedStates", 
function(){
var names = "";
for (var name, $name = this.saved.keySet().iterator (); $name.hasNext()&& ((name = $name.next ()) || true);) names += "\n" + name;

return names;
});
Clazz.defineMethod(c$, "deleteSavedType", 
function(type){
var e = this.saved.keySet().iterator();
while (e.hasNext()) if (e.next().startsWith(type)) e.remove();

}, "~S");
Clazz.defineMethod(c$, "deleteSaved", 
function(namelike){
var e = this.saved.keySet().iterator();
while (e.hasNext()) {
var name = e.next();
if (name.startsWith(namelike) || name.endsWith("_" + namelike) && name.indexOf("_") == name.lastIndexOf("_" + namelike)) e.remove();
}
}, "~S");
Clazz.defineMethod(c$, "saveSelection", 
function(saveName, bsSelected){
if (saveName.equalsIgnoreCase("DELETE")) {
this.deleteSavedType("Selected_");
return;
}saveName = this.lastSelected = "Selected_" + saveName;
this.saved.put(saveName, JU.BSUtil.copy(bsSelected));
}, "~S,JU.BS");
Clazz.defineMethod(c$, "restoreSelection", 
function(saveName){
var name = (saveName.length > 0 ? "Selected_" + saveName : this.lastSelected);
var bsSelected = JV.StateManager.getNoCase(this.saved, name);
if (bsSelected == null) {
this.vwr.selectStatus( new JU.BS(), false, 0, false, false);
return false;
}this.vwr.selectStatus(bsSelected, false, 0, false, false);
return true;
}, "~S");
Clazz.defineMethod(c$, "saveUnitCell", 
function(saveName){
if (saveName.equalsIgnoreCase("DELETE")) {
this.deleteSavedType("unitcell_");
return;
}saveName = this.lastUnitcell = "unitcell_" + saveName;
var uc = this.vwr.getCurrentUnitCell();
if (uc != null) {
var state = "UNITCELL " + JU.Escape.e(uc.getUnitCellVectors());
this.saved.put(saveName, "unitcell reset;" + state);
}}, "~S");
Clazz.defineMethod(c$, "getSavedUnitCell", 
function(saveName){
var name = (saveName.length > 0 ? "unitcell_" + saveName : this.lastUnitcell);
var ucstate = JV.StateManager.getNoCase(this.saved, name);
return ucstate;
}, "~S");
Clazz.defineMethod(c$, "restoreUnitCell", 
function(saveName){
var ucstate = this.getSavedUnitCell(saveName);
if (ucstate == null) {
this.vwr.ms.setModelCagePts(-1, null, null);
return false;
}this.vwr.runScript(ucstate);
return true;
}, "~S");
Clazz.defineMethod(c$, "saveState", 
function(saveName){
if (saveName.equalsIgnoreCase("DELETE")) {
this.deleteSavedType("State_");
this.clearStateStack();
return;
}if (saveName.length == 0) {
this.vwr.setBooleanProperty("undoAuto", false);
this.appendState(this.getStack(603984065));
this.redoStateStack.clear();
return;
}saveName = this.lastState = "State_" + saveName;
this.saved.put(saveName, this.vwr.getStateInfo());
}, "~S");
Clazz.defineMethod(c$, "getSavedState", 
function(saveName){
if (saveName.length == 0) {
var stack = this.getStack(603984065);
return (stack.size() > 0 ? stack.get(stack.size() - 1) : null);
}var name = (saveName.length > 0 ? "State_" + saveName : this.lastState);
var script = JV.StateManager.getNoCase(this.saved, name);
return (script == null ? "" : script);
}, "~S");
Clazz.defineMethod(c$, "popStack", 
function(type){
var stack = this.getStack(type);
var state = (stack.size() > 0 ? stack.removeItemAt(stack.size() - 1) : null);
if (state != null) {
this.appendState(this.getStack(type == 603984065 ? 4139 : 603984065));
}this.checkStack(this.getStack(603984065));
return state;
}, "~N");
Clazz.defineMethod(c$, "appendState", 
function(stack){
this.checkStack(stack);
if (this.maxUndo > 0) stack.addLast(this.vwr.getStateInfo());
}, "JU.Lst");
Clazz.defineMethod(c$, "checkStack", 
function(stack){
while (stack.size() > this.maxUndo) stack.removeItemAt(0);

}, "JU.Lst");
Clazz.defineMethod(c$, "getStack", 
function(type){
if (this.undoStateStack == null) {
this.undoStateStack =  new JU.Lst();
this.redoStateStack =  new JU.Lst();
}return (type == 603984065 ? this.undoStateStack : this.redoStateStack);
}, "~N");
Clazz.defineMethod(c$, "clearStateStack", 
function(){
if (this.undoStateStack == null) return;
this.undoStateStack.clear();
this.redoStateStack.clear();
});
Clazz.defineMethod(c$, "saveStructure", 
function(saveName){
if (saveName.equalsIgnoreCase("DELETE")) {
this.deleteSavedType("Shape_");
return;
}saveName = this.lastShape = "Shape_" + saveName;
this.saved.put(saveName, this.vwr.getStructureState());
}, "~S");
Clazz.defineMethod(c$, "getSavedStructure", 
function(saveName){
var name = (saveName.length > 0 ? "Shape_" + saveName : this.lastShape);
var script = JV.StateManager.getNoCase(this.saved, name);
return (script == null ? "" : script);
}, "~S");
Clazz.defineMethod(c$, "saveCoordinates", 
function(saveName, bsSelected){
if (saveName.equalsIgnoreCase("DELETE")) {
this.deleteSavedType("Coordinates_");
return;
}saveName = this.lastCoordinates = "Coordinates_" + saveName;
this.saved.put(saveName, this.vwr.getCoordinateState(bsSelected));
}, "~S,JU.BS");
Clazz.defineMethod(c$, "getSavedCoordinates", 
function(saveName){
var name = (saveName.length > 0 ? "Coordinates_" + saveName : this.lastCoordinates);
var script = JV.StateManager.getNoCase(this.saved, name);
return (script == null ? "" : script);
}, "~S");
Clazz.defineMethod(c$, "getOrientation", 
function(){
return  new JM.Orientation(this.vwr, false, null);
});
Clazz.defineMethod(c$, "getSavedOrientationText", 
function(saveName){
var o;
if (saveName != null) {
o = this.getOrientationFor(saveName);
return (o == null ? "" : o.getMoveToText(true));
}var sb =  new JU.SB();
for (var e, $e = this.saved.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
var name = e.getKey();
if (name.startsWith("Orientation_")) sb.append((e.getValue()).getMoveToText(true));
}
return sb.toString();
}, "~S");
Clazz.defineMethod(c$, "saveScene", 
function(saveName, scene){
if (saveName.equalsIgnoreCase("DELETE")) {
this.deleteSavedType("Scene_");
return;
}var o =  new JV.Scene(scene);
o.saveName = this.lastScene = "Scene_" + saveName;
this.saved.put(o.saveName, o);
}, "~S,java.util.Map");
Clazz.defineMethod(c$, "restoreScene", 
function(saveName, timeSeconds){
var o = JV.StateManager.getNoCase(this.saved, (saveName.length > 0 ? "Scene_" + saveName : this.lastScene));
return (o != null && o.restore(this.vwr, timeSeconds));
}, "~S,~N");
Clazz.defineMethod(c$, "saveOrientation", 
function(saveName, pymolView){
if (saveName.equalsIgnoreCase("DELETE")) {
this.deleteSavedType("Orientation_");
return;
}var o =  new JM.Orientation(this.vwr, saveName.equalsIgnoreCase("default"), pymolView);
o.saveName = this.lastOrientation = "Orientation_" + saveName;
this.saved.put(o.saveName, o);
}, "~S,~A");
Clazz.defineMethod(c$, "restoreOrientation", 
function(saveName, timeSeconds, isAll){
var o = this.getOrientationFor(saveName);
return (o != null && o.restore(timeSeconds, isAll));
}, "~S,~N,~B");
Clazz.defineMethod(c$, "getOrientationFor", 
function(saveName){
var name = (saveName.length > 0 ? "Orientation_" + saveName : this.lastOrientation);
return JV.StateManager.getNoCase(this.saved, name);
}, "~S");
Clazz.defineMethod(c$, "saveContext", 
function(saveName, context){
if (saveName.equalsIgnoreCase("DELETE")) {
this.deleteSavedType("Context_");
return;
}this.saved.put((this.lastContext = "Context_" + saveName), context);
}, "~S,~O");
Clazz.defineMethod(c$, "getContext", 
function(saveName){
return this.saved.get(saveName.length == 0 ? this.lastContext : "Context_" + saveName);
}, "~S");
Clazz.defineMethod(c$, "saveBonds", 
function(saveName){
if (saveName.equalsIgnoreCase("DELETE")) {
this.deleteSavedType("Bonds_");
return;
}var b =  new JV.Connections(this.vwr);
b.saveName = this.lastConnections = "Bonds_" + saveName;
this.saved.put(b.saveName, b);
}, "~S");
Clazz.defineMethod(c$, "restoreBonds", 
function(saveName){
this.vwr.clearModelDependentObjects();
var name = (saveName.length > 0 ? "Bonds_" + saveName : this.lastConnections);
var c = JV.StateManager.getNoCase(this.saved, name);
return (c != null && c.restore());
}, "~S");
c$.varClip = Clazz.defineMethod(c$, "varClip", 
function(name, sv, nMax){
if (nMax > 0 && sv.length > nMax) sv = sv.substring(0, nMax) + " #...more (" + sv.length + " bytes -- use SHOW " + name + " or MESSAGE @" + name + " to view)";
return sv;
}, "~S,~S,~N");
Clazz.defineMethod(c$, "getUndoMax", 
function(){
return this.maxUndo;
});
Clazz.defineMethod(c$, "setUndoMax", 
function(n){
this.maxUndo = Math.max(n, 0);
this.checkStack(this.getStack(603984065));
this.checkStack(this.getStack(4139));
}, "~N");
Clazz.defineMethod(c$, "getUndoRedoState", 
function(tok){
return this.popStack(tok);
}, "~N");
Clazz.defineMethod(c$, "canDo", 
function(type){
return (this.maxUndo > 0 && this.vwr.getBoolean(603979898) && !this.getStack(type).isEmpty());
}, "~N");
Clazz.defineMethod(c$, "getUndoInfo", 
function(){
var auto = this.vwr.getBooleanProperty("undoAuto");
return (this.vwr.getBoolean(603979898) ? "undoAuto=" + auto + (!auto ? "; user stack sizes: UNDO=" + this.getStack(603984065).size() + ", REDO=" + this.getStack(4139).size() : "") : "SET preserveState = FALSE -- undo/redo is disabled");
});
var c$ = Clazz.decorateAsClass(function(){
this.saveName = null;
this.scene = null;
Clazz.instantialize(this, arguments);}, JV, "Scene", null);
Clazz.makeConstructor(c$, 
function(scene){
this.scene = scene;
}, "java.util.Map");
Clazz.defineMethod(c$, "restore", 
function(vwr, timeSeconds){
var gen = this.scene.get("generator");
if (gen != null) gen.generateScene(this.scene);
var pv = this.scene.get("pymolView");
return (pv != null && vwr.tm.moveToPyMOL(vwr.eval, timeSeconds, pv));
}, "JV.Viewer,~N");
var c$ = Clazz.decorateAsClass(function(){
this.saveName = null;
this.bondCount = 0;
this.connections = null;
this.vwr = null;
Clazz.instantialize(this, arguments);}, JV, "Connections", null);
Clazz.makeConstructor(c$, 
function(vwr){
var modelSet = vwr.ms;
if (modelSet == null) return;
this.vwr = vwr;
this.bondCount = modelSet.bondCount;
this.connections =  new Array(this.bondCount + 1);
var bonds = modelSet.bo;
for (var i = this.bondCount; --i >= 0; ) {
var b = bonds[i];
if (b != null) this.connections[i] =  new JV.Connection(b.atom1.i, b.atom2.i, b.mad, b.colix, b.order, b.getEnergy(), b.shapeVisibilityFlags);
}
}, "JV.Viewer");
Clazz.defineMethod(c$, "restore", 
function(){
var modelSet = this.vwr.ms;
if (modelSet == null) return false;
modelSet.deleteAllBonds();
for (var i = this.bondCount; --i >= 0; ) {
var c = this.connections[i];
var ac = modelSet.ac;
if (c.atomIndex1 >= ac || c.atomIndex2 >= ac) continue;
var b = modelSet.bondAtoms(modelSet.at[c.atomIndex1], modelSet.at[c.atomIndex2], c.order, c.mad, null, c.energy, false, true);
b.colix = c.colix;
b.shapeVisibilityFlags = c.shapeVisibilityFlags;
}
var bonds = modelSet.bo;
for (var i = modelSet.bondCount; --i >= 0; ) if (bonds[i] != null) bonds[i].index = i;

this.vwr.setShapeProperty(1, "reportAll", null);
return true;
});
var c$ = Clazz.decorateAsClass(function(){
this.atomIndex1 = 0;
this.atomIndex2 = 0;
this.mad = 0;
this.colix = 0;
this.order = 0;
this.energy = 0;
this.shapeVisibilityFlags = 0;
Clazz.instantialize(this, arguments);}, JV, "Connection", null);
Clazz.makeConstructor(c$, 
function(atom1, atom2, mad, colix, order, energy, shapeVisibilityFlags){
this.atomIndex1 = atom1;
this.atomIndex2 = atom2;
this.mad = mad;
this.colix = colix;
this.order = order;
this.energy = energy;
this.shapeVisibilityFlags = shapeVisibilityFlags;
}, "~N,~N,~N,~N,~N,~N,~N");
});
;//5.0.1-v7 Thu Jun 04 11:07:16 CDT 2026
