Clazz.declarePackage("J.popup");
Clazz.load(["J.popup.JmolGenericPopup", "JU.Lst"], "J.popup.JmolPopup", ["java.util.Arrays", "$.Hashtable", "JU.PT", "J.i18n.GT", "JM.Group", "J.popup.MainPopupResourceBundle", "JU.Elements", "JV.JC"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.updateMode = 0;
this.titleWidthMax = 20;
this.nullModelSetName = null;
this.modelSetName = null;
this.modelSetFileName = null;
this.modelSetRoot = null;
this.currentFrankId = null;
this.configurationSelected = "";
this.altlocs = null;
this.frankList = null;
this.modelSetInfo = null;
this.modelInfo = null;
this.NotPDB = null;
this.PDBOnly = null;
this.FileUnitOnly = null;
this.FileMolOnly = null;
this.UnitcellOnly = null;
this.SingleModelOnly = null;
this.FramesOnly = null;
this.VibrationOnly = null;
this.Special = null;
this.SymmetryOnly = null;
this.ChargesOnly = null;
this.TemperatureOnly = null;
this.fileHasUnitCell = false;
this.haveBFactors = false;
this.haveCharges = false;
this.isLastFrame = false;
this.isMultiConfiguration = false;
this.isMultiFrame = false;
this.isPDB = false;
this.hasSymmetry = false;
this.isUnitCell = false;
this.isVibration = false;
this.isZapped = false;
this.modelIndex = 0;
this.modelCount = 0;
this.ac = 0;
this.group3List = null;
this.group3Counts = null;
this.cnmrPeaks = null;
this.hnmrPeaks = null;
this.noZapped = null;
Clazz.instantialize(this, arguments);}, J.popup, "JmolPopup", J.popup.JmolGenericPopup);
Clazz.prepareFields (c$, function(){
this.frankList =  new Array(10);
this.NotPDB =  new JU.Lst();
this.PDBOnly =  new JU.Lst();
this.FileUnitOnly =  new JU.Lst();
this.FileMolOnly =  new JU.Lst();
this.UnitcellOnly =  new JU.Lst();
this.SingleModelOnly =  new JU.Lst();
this.FramesOnly =  new JU.Lst();
this.VibrationOnly =  new JU.Lst();
this.Special =  new JU.Lst();
this.SymmetryOnly =  new JU.Lst();
this.ChargesOnly =  new JU.Lst();
this.TemperatureOnly =  new JU.Lst();
this.noZapped =  Clazz.newArray(-1, ["surfaceMenu", "measureMenu", "pickingMenu", "computationMenu", "SIGNEDJAVAcaptureMenuSPECIAL"]);
});
Clazz.defineMethod(c$, "jpiDispose", 
function(){
this.helper.menuClearListeners(this.frankPopup);
this.frankPopup = null;
Clazz.superCall(this, J.popup.JmolPopup, "jpiDispose", []);
});
Clazz.overrideMethod(c$, "getBundle", 
function(menu){
return  new J.popup.MainPopupResourceBundle(this.strMenuStructure = menu, this.menuText);
}, "~S");
Clazz.overrideMethod(c$, "showFrankMenu", 
function(){
this.getViewerData();
this.setFrankMenu(this.currentMenuItemId);
this.thisx = -this.thisx - 50;
if (this.nFrankList > 1) {
this.thisy -= this.nFrankList * 20;
this.menuShowPopup(this.frankPopup, this.thisx, this.thisy);
return true;
}return false;
});
Clazz.overrideMethod(c$, "jpiUpdateComputedMenus", 
function(){
if (this.updateMode == -1) return;
this.isTainted = true;
this.getViewerData();
this.updateMode = 0;
this.updateMenus();
});
Clazz.defineMethod(c$, "updateMenus", 
function(){
this.updateSelectMenu();
this.updateModelSetComputedMenu();
this.updateAboutSubmenu();
if (this.updateMode == 0) {
this.updateFileMenu();
this.updateElementsComputedMenu(this.vwr.getElementsPresentBitSet(this.modelIndex));
this.updateHeteroComputedMenu(this.vwr.ms.getHeteroList(this.modelIndex));
this.updateSurfMoComputedMenu(this.modelInfo.get("moData"));
this.updateFileTypeDependentMenus();
this.updatePDBResidueComputedMenus();
this.updateMode = 1;
this.updateConfigurationComputedMenu();
this.updateSYMMETRYComputedMenus();
this.updateFRAMESbyModelComputedMenu();
this.updateLanguageSubmenu();
} else {
this.updateSpectraMenu();
this.updateFRAMESbyModelComputedMenu();
this.updateSceneComputedMenu();
for (var i = this.Special.size(); --i >= 0; ) this.updateSpecialMenuItem(this.Special.get(i));

}});
Clazz.overrideMethod(c$, "appCheckItem", 
function(item, newMenu){
if (item.indexOf("!PDB") >= 0) {
this.NotPDB.addLast(newMenu);
} else if (item.indexOf("PDB") >= 0) {
this.PDBOnly.addLast(newMenu);
}if (item.indexOf("CHARGE") >= 0) {
this.ChargesOnly.addLast(newMenu);
} else if (item.indexOf("BFACTORS") >= 0) {
this.TemperatureOnly.addLast(newMenu);
} else if (item.indexOf("UNITCELL") >= 0) {
this.UnitcellOnly.addLast(newMenu);
} else if (item.indexOf("FILEUNIT") >= 0) {
this.FileUnitOnly.addLast(newMenu);
} else if (item.indexOf("FILEMOL") >= 0) {
this.FileMolOnly.addLast(newMenu);
}if (item.indexOf("!FRAMES") >= 0) {
this.SingleModelOnly.addLast(newMenu);
} else if (item.indexOf("FRAMES") >= 0) {
this.FramesOnly.addLast(newMenu);
}if (item.indexOf("VIBRATION") >= 0) {
this.VibrationOnly.addLast(newMenu);
} else if (item.indexOf("SYMMETRY") >= 0) {
this.SymmetryOnly.addLast(newMenu);
}if (item.indexOf("SPECIAL") >= 0) this.Special.addLast(newMenu);
}, "~S,J.api.SC");
Clazz.overrideMethod(c$, "appGetMenuAsString", 
function(title){
return ( new J.popup.MainPopupResourceBundle(this.strMenuStructure, null)).getMenuAsText(title);
}, "~S");
Clazz.overrideMethod(c$, "getScriptForCallback", 
function(source, id, script){
var pt;
if (script === "" || id.endsWith("Checkbox")) return script;
if (script.indexOf("SELECT") == 0) {
return "select thisModel and (" + script.substring(6) + ")";
}if ((pt = id.lastIndexOf("[")) >= 0) {
id = id.substring(pt + 1);
if ((pt = id.indexOf("]")) >= 0) id = id.substring(0, pt);
id = id.$replace('_', ' ');
if (script.indexOf("[]") < 0) script = "[] " + script;
script = script.$replace('_', ' ');
return JU.PT.rep(script, "[]", id);
} else if (script.indexOf("?FILEROOT?") >= 0) {
script = JU.PT.rep(script, "FILEROOT?", this.modelSetRoot);
} else if (script.indexOf("?FILE?") >= 0) {
script = JU.PT.rep(script, "FILE?", this.modelSetFileName);
} else if (script.indexOf("?PdbId?") >= 0) {
script = JU.PT.rep(script, "PdbId?", "=xxxx");
}return script;
}, "J.api.SC,~S,~S");
Clazz.overrideMethod(c$, "appRestorePopupMenu", 
function(){
this.thisPopup = this.popupMenu;
if (this.vwr.isJSNoAWT || this.nFrankList < 2) return;
for (var i = this.nFrankList; --i > 0; ) {
var f = this.frankList[i];
this.helper.menuInsertSubMenu(f[0], f[1], (f[2]).intValue());
}
this.nFrankList = 1;
});
Clazz.overrideMethod(c$, "appUpdateSpecialCheckBoxValue", 
function(item, what, TF){
if (!this.updatingForShow && what.indexOf("#CONFIG") >= 0) {
this.configurationSelected = what;
this.updateConfigurationComputedMenu();
this.updateModelSetComputedMenu();
}}, "J.api.SC,~S,~B");
Clazz.defineMethod(c$, "setFrankMenu", 
function(id){
if (this.currentFrankId != null && this.currentFrankId === id && this.nFrankList > 0) return;
if (this.frankPopup == null) this.frankPopup = this.helper.menuCreatePopup("Frank", this.vwr.html5Applet);
this.thisPopup = this.frankPopup;
this.menuRemoveAll(this.frankPopup, 0);
this.menuCreateItem(this.frankPopup, this.getMenuText("mainMenuText"), "MAIN", "");
this.currentFrankId = id;
this.nFrankList = 0;
this.frankList[this.nFrankList++] =  Clazz.newArray(-1, [null, null, null]);
if (id != null) for (var i = id.indexOf(".", 2) + 1; ; ) {
var iNew = id.indexOf(".", i);
if (iNew < 0) break;
var menu = this.htMenus.get(id.substring(i, iNew));
this.frankList[this.nFrankList++] =  Clazz.newArray(-1, [menu.getParent(), menu, Integer.$valueOf(this.vwr.isJSNoAWT ? 0 : this.menuGetListPosition(menu))]);
this.menuAddSubMenu(this.frankPopup, menu);
i = iNew + 1;
}
this.thisPopup = this.popupMenu;
}, "~S");
Clazz.defineMethod(c$, "checkBoolean", 
function(key){
return (this.modelSetInfo != null && this.modelSetInfo.get(key) === Boolean.TRUE);
}, "~S");
Clazz.defineMethod(c$, "getViewerData", 
function(){
this.modelSetName = this.vwr.ms.modelSetName;
this.modelSetFileName = this.vwr.getModelSetFileName();
var i = this.modelSetFileName.lastIndexOf(".");
this.isZapped = ("zapped".equals(this.modelSetName));
if (this.isZapped || "string".equals(this.modelSetFileName) || "String[]".equals(this.modelSetFileName)) this.modelSetFileName = "";
this.modelSetRoot = this.modelSetFileName.substring(0, i < 0 ? this.modelSetFileName.length : i);
if (this.modelSetRoot.length == 0) this.modelSetRoot = "Jmol";
this.modelIndex = this.vwr.am.cmi;
this.modelCount = this.vwr.ms.mc;
this.ac = this.vwr.ms.getAtomCountInModel(this.modelIndex);
this.modelSetInfo = this.vwr.getModelSetAuxiliaryInfo();
this.modelInfo = this.vwr.ms.getModelAuxiliaryInfo(this.modelIndex);
if (this.modelInfo == null) this.modelInfo =  new java.util.Hashtable();
this.isPDB = this.checkBoolean(JV.JC.getBoolName(4));
this.isMultiFrame = (this.modelCount > 1);
this.hasSymmetry = !this.isPDB && this.modelInfo.containsKey("hasSymmetry");
this.isUnitCell = this.modelInfo.containsKey("unitCellParams");
this.fileHasUnitCell = (this.isPDB && this.isUnitCell || this.checkBoolean("fileHasUnitCell"));
this.isLastFrame = (this.modelIndex == this.modelCount - 1);
this.altlocs = this.vwr.ms.getAltLocListInModel(this.modelIndex);
this.isMultiConfiguration = (this.altlocs.length > 0);
this.isVibration = (this.vwr.modelHasVibrationVectors(this.modelIndex));
this.haveCharges = (this.vwr.ms.getPartialCharges() != null);
this.haveBFactors = (this.vwr.getBooleanProperty("haveBFactors"));
this.cnmrPeaks = this.modelInfo.get("jdxAtomSelect_13CNMR");
this.hnmrPeaks = this.modelInfo.get("jdxAtomSelect_1HNMR");
});
Clazz.overrideMethod(c$, "appCheckSpecialMenu", 
function(item, subMenu, word){
if ("modelSetMenu".equals(item)) {
this.nullModelSetName = word;
this.menuEnable(subMenu, false);
}}, "~S,J.api.SC,~S");
Clazz.overrideMethod(c$, "appUpdateForShow", 
function(){
if (this.updateMode == -1) return;
this.isTainted = true;
this.getViewerData();
this.updateMode = 2;
this.updateMenus();
});
Clazz.defineMethod(c$, "updateFileMenu", 
function(){
var menu = this.htMenus.get("fileMenu");
if (menu == null) return;
var text = this.getMenuText("writeFileTextVARIABLE");
menu = this.htMenus.get("writeFileTextVARIABLE");
if (menu == null) return;
var ignore = (this.modelSetFileName.equals("zapped") || this.modelSetFileName.equals(""));
if (ignore) {
this.menuSetLabel(menu, "");
this.menuEnable(menu, false);
} else {
this.menuSetLabel(menu, J.i18n.GT.o(J.i18n.GT.$(text), this.modelSetFileName));
this.menuEnable(menu, true);
}});
Clazz.defineMethod(c$, "getMenuText", 
function(key){
var str = this.menuText.getProperty(key);
return (str == null ? key : str);
}, "~S");
Clazz.defineMethod(c$, "updateSelectMenu", 
function(){
var menu = this.htMenus.get("selectMenuText");
if (menu == null) return;
this.menuEnable(menu, this.ac != 0);
this.menuSetLabel(menu, this.gti("selectMenuText", this.vwr.slm.getSelectionCount()));
});
Clazz.defineMethod(c$, "updateElementsComputedMenu", 
function(elementsPresentBitSet){
var menu = this.htMenus.get("elementsComputedMenu");
if (menu == null) return;
this.menuRemoveAll(menu, 0);
this.menuEnable(menu, false);
if (elementsPresentBitSet == null) return;
for (var i = elementsPresentBitSet.nextSetBit(0); i >= 0; i = elementsPresentBitSet.nextSetBit(i + 1)) {
var elementName = JU.Elements.elementNameFromNumber(i);
var elementSymbol = JU.Elements.elementSymbolFromNumber(i);
var entryName = elementSymbol + " - " + elementName;
this.menuCreateItem(menu, entryName, "SELECT " + elementName, null);
}
for (var i = 4; i < JU.Elements.altElementMax; ++i) {
var n = JU.Elements.elementNumberMax + i;
if (elementsPresentBitSet.get(n)) {
n = JU.Elements.altElementNumberFromIndex(i);
var elementName = JU.Elements.elementNameFromNumber(n);
var elementSymbol = JU.Elements.elementSymbolFromNumber(n);
var entryName = elementSymbol + " - " + elementName;
this.menuCreateItem(menu, entryName, "SELECT " + elementName, null);
}}
this.menuEnable(menu, true);
}, "JU.BS");
Clazz.defineMethod(c$, "updateSpectraMenu", 
function(){
var menu = this.htMenus.get("spectraMenu");
if (menu == null) return;
var menuh = this.htMenus.get("hnmrMenu");
if (menuh != null) this.menuRemoveAll(menuh, 0);
var menuc = this.htMenus.get("cnmrMenu");
if (menuc != null) this.menuRemoveAll(menuc, 0);
this.menuRemoveAll(menu, 0);
var isOK =  new Boolean (this.setSpectraMenu(menuh, this.hnmrPeaks) | this.setSpectraMenu(menuc, this.cnmrPeaks)).valueOf();
if (isOK) {
if (menuh != null) this.menuAddSubMenu(menu, menuh);
if (menuc != null) this.menuAddSubMenu(menu, menuc);
}this.menuEnable(menu, isOK);
});
Clazz.defineMethod(c$, "setSpectraMenu", 
function(menu, peaks){
var n = (peaks == null ? 0 : peaks.size());
if (n == 0) return false;
if (menu == null) return false;
this.menuEnable(menu, false);
for (var i = 0; i < n; i++) {
var peak = peaks.get(i);
var title = JU.PT.getQuotedAttribute(peak, "title");
var atoms = JU.PT.getQuotedAttribute(peak, "atoms");
if (atoms != null) this.menuCreateItem(menu, title, "select visible & (@" + JU.PT.rep(atoms, ",", " or @") + ")", "Focus" + i);
}
this.menuEnable(menu, true);
return true;
}, "J.api.SC,JU.Lst");
Clazz.defineMethod(c$, "updateHeteroComputedMenu", 
function(htHetero){
var menu = this.htMenus.get("PDBheteroComputedMenu");
if (menu == null) return;
this.menuRemoveAll(menu, 0);
this.menuEnable(menu, false);
if (htHetero == null) return;
var n = 0;
for (var hetero, $hetero = htHetero.entrySet().iterator (); $hetero.hasNext()&& ((hetero = $hetero.next ()) || true);) {
var heteroCode = hetero.getKey();
var heteroName = hetero.getValue();
if (heteroName.length > 20) heteroName = heteroName.substring(0, 20) + "...";
var entryName = heteroCode + " - " + heteroName;
this.menuCreateItem(menu, entryName, "SELECT [" + heteroCode + "]", null);
n++;
}
this.menuEnable(menu, (n > 0));
}, "java.util.Map");
Clazz.defineMethod(c$, "updateSurfMoComputedMenu", 
function(moData){
var menu = this.htMenus.get("surfMoComputedMenuText");
if (menu == null) return;
this.menuRemoveAll(menu, 0);
var mos = (moData == null ? null : (moData.get("mos")));
var nOrb = (mos == null ? 0 : mos.size());
var text = this.getMenuText("surfMoComputedMenuText");
if (nOrb == 0) {
this.menuSetLabel(menu, J.i18n.GT.o(J.i18n.GT.$(text), ""));
this.menuEnable(menu, false);
return;
}this.menuSetLabel(menu, J.i18n.GT.i(J.i18n.GT.$(text), nOrb));
this.menuEnable(menu, true);
var subMenu = menu;
var nmod = (nOrb % 25);
if (nmod == 0) nmod = 25;
var pt = (nOrb > 25 ? 0 : -2147483648);
for (var i = nOrb; --i >= 0; ) {
if (pt >= 0 && (pt++ % nmod) == 0) {
if (pt == nmod + 1) nmod = 25;
var id = "mo" + pt + "Menu";
subMenu = this.menuNewSubMenu(Math.max(i + 2 - nmod, 1) + "..." + (i + 1), this.menuGetId(menu) + "." + id);
this.menuAddSubMenu(menu, subMenu);
this.htMenus.put(id, subMenu);
pt = 1;
}var mo = mos.get(i);
var entryName = "#" + (i + 1) + " " + (mo.containsKey("type") ? mo.get("type") + " " : "") + (mo.containsKey("symmetry") ? mo.get("symmetry") + " " : "") + (mo.containsKey("occupancy") ? "(" + mo.get("occupancy") + ") " : "") + (mo.containsKey("energy") ? mo.get("energy") : "");
var script = "mo " + (i + 1);
this.menuCreateItem(subMenu, entryName, script, null);
}
}, "java.util.Map");
Clazz.defineMethod(c$, "updateFileTypeDependentMenus", 
function(){
for (var i = this.NotPDB.size(); --i >= 0; ) this.menuEnable(this.NotPDB.get(i), !this.isPDB);

for (var i = this.PDBOnly.size(); --i >= 0; ) this.menuEnable(this.PDBOnly.get(i), this.isPDB);

for (var i = this.UnitcellOnly.size(); --i >= 0; ) this.menuEnable(this.UnitcellOnly.get(i), this.isUnitCell);

for (var i = this.FileUnitOnly.size(); --i >= 0; ) this.menuEnable(this.FileUnitOnly.get(i), this.isUnitCell || this.fileHasUnitCell);

for (var i = this.FileMolOnly.size(); --i >= 0; ) this.menuEnable(this.FileMolOnly.get(i), this.isUnitCell || this.fileHasUnitCell);

for (var i = this.SingleModelOnly.size(); --i >= 0; ) this.menuEnable(this.SingleModelOnly.get(i), this.isLastFrame);

for (var i = this.FramesOnly.size(); --i >= 0; ) this.menuEnable(this.FramesOnly.get(i), this.isMultiFrame);

for (var i = this.VibrationOnly.size(); --i >= 0; ) this.menuEnable(this.VibrationOnly.get(i), this.isVibration);

for (var i = this.SymmetryOnly.size(); --i >= 0; ) this.menuEnable(this.SymmetryOnly.get(i), this.hasSymmetry && this.isUnitCell);

for (var i = this.ChargesOnly.size(); --i >= 0; ) this.menuEnable(this.ChargesOnly.get(i), this.haveCharges);

for (var i = this.TemperatureOnly.size(); --i >= 0; ) this.menuEnable(this.TemperatureOnly.get(i), this.haveBFactors);

this.updateSignedAppletItems();
});
Clazz.defineMethod(c$, "updateSceneComputedMenu", 
function(){
var menu = this.htMenus.get("sceneComputedMenu");
if (menu == null) return;
this.menuRemoveAll(menu, 0);
this.menuEnable(menu, false);
var scenes = this.vwr.ms.getInfoM("scenes");
if (scenes == null) return;
for (var i = 0; i < scenes.length; i++) this.menuCreateItem(menu, scenes[i], "restore scene " + JU.PT.esc(scenes[i]) + " 1.0", null);

this.menuEnable(menu, true);
});
Clazz.defineMethod(c$, "updatePDBResidueComputedMenus", 
function(){
var haveMenu = false;
var menu3 = this.htMenus.get("PDBaaResiduesComputedMenu");
if (menu3 != null) {
this.menuRemoveAll(menu3, 0);
this.menuEnable(menu3, false);
haveMenu = true;
}var menu1 = this.htMenus.get("PDBnucleicResiduesComputedMenu");
if (menu1 != null) {
this.menuRemoveAll(menu1, 0);
this.menuEnable(menu1, false);
haveMenu = true;
}var menu2 = this.htMenus.get("PDBcarboResiduesComputedMenu");
if (menu2 != null) {
this.menuRemoveAll(menu2, 0);
this.menuEnable(menu2, false);
haveMenu = true;
}if (this.modelSetInfo == null || !haveMenu) return;
var n = (this.modelIndex < 0 ? 0 : this.modelIndex + 1);
var lists = (this.modelSetInfo.get("group3Lists"));
this.group3List = (lists == null ? null : lists[n]);
this.group3Counts = (lists == null ? null : (this.modelSetInfo.get("group3Counts"))[n]);
if (this.group3List == null) return;
var nItems = 0;
var groupList = JM.Group.standardGroupList;
if (menu3 != null) {
for (var i = 1; i < 24; ++i) nItems += this.updateGroup3List(menu3, groupList.substring(i * 6 - 4, i * 6 - 1).trim());

nItems += this.augmentGroup3List(menu3, "p>", true);
this.menuEnable(menu3, (nItems > 0));
this.menuEnable(this.htMenus.get("PDBproteinMenu"), (nItems > 0));
}if (menu1 != null) {
nItems = this.augmentGroup3List(menu1, "n>", false);
this.menuEnable(menu1, nItems > 0);
this.menuEnable(this.htMenus.get("PDBnucleicMenu"), (nItems > 0));
var dssr = (nItems > 0 && this.modelIndex >= 0 ? this.vwr.ms.getInfo(this.modelIndex, "dssr") : null);
if (dssr != null) this.setSecStrucMenu(this.htMenus.get("aaStructureMenu"), dssr);
}if (menu2 != null) {
nItems = this.augmentGroup3List(menu2, "c>", false);
this.menuEnable(menu2, nItems > 0);
this.menuEnable(this.htMenus.get("PDBcarboMenu"), (nItems > 0));
}});
Clazz.defineMethod(c$, "setSecStrucMenu", 
function(menu, dssr){
var counts = dssr.get("counts");
if (counts == null) return false;
var keys =  new Array(counts.size());
counts.keySet().toArray(keys);
java.util.Arrays.sort(keys);
if (keys.length == 0) return false;
menu.removeAll();
for (var i = 0; i < keys.length; i++) this.menuCreateItem(menu, keys[i] + " (" + counts.get(keys[i]) + ")", "select modelIndex=" + this.modelIndex + " && within('dssr', '" + keys[i] + "');", null);

return true;
}, "J.api.SC,java.util.Map");
Clazz.defineMethod(c$, "updateGroup3List", 
function(menu, name){
var nItems = 0;
var n = this.group3Counts[Clazz.doubleToInt(this.group3List.indexOf(name) / 6)];
name = name.trim();
var script = null;
if (n > 0) {
script = "SELECT " + name;
name += "  (" + n + ")";
nItems++;
}var item = this.menuCreateItem(menu, name, script, this.menuGetId(menu) + "." + name);
if (n == 0) this.menuEnable(item, false);
return nItems;
}, "J.api.SC,~S");
Clazz.defineMethod(c$, "augmentGroup3List", 
function(menu, type, addSeparator){
var pt = 138;
var nItems = 0;
while (true) {
pt = this.group3List.indexOf(type, pt);
if (pt < 0) break;
if (nItems++ == 0 && addSeparator) this.menuAddSeparator(menu);
var n = this.group3Counts[Clazz.doubleToInt(pt / 6)];
var heteroCode = this.group3List.substring(pt + 2, pt + 5);
var name = heteroCode + "  (" + n + ")";
this.menuCreateItem(menu, name, "SELECT [" + heteroCode + "]", this.menuGetId(menu) + "." + name);
pt++;
}
return nItems;
}, "J.api.SC,~S,~B");
Clazz.defineMethod(c$, "updateSYMMETRYComputedMenus", 
function(){
this.updateSYMMETRYSelectComputedMenu();
this.updateSYMMETRYShowComputedMenu();
});
Clazz.defineMethod(c$, "updateSYMMETRYShowComputedMenu", 
function(){
var menu = this.htMenus.get("SYMMETRYShowComputedMenu");
if (menu == null) return;
this.menuRemoveAll(menu, 0);
this.menuEnable(menu, false);
if (!this.hasSymmetry || this.modelIndex < 0) return;
var info = this.vwr.getProperty("DATA_API", "spaceGroupInfo", null);
if (info == null) return;
var infolist = info.get("operations");
if (infolist == null) return;
var name = info.get("spaceGroupName");
this.menuSetLabel(menu, name == null ? J.i18n.GT.$("Space Group") : name);
var subMenu = menu;
var pt = (infolist.length > 25 ? 0 : -2147483648);
for (var i = 0; i < infolist.length; i++) {
if (pt >= 0 && (pt++ % 25) == 0) {
var id = "drawsymop" + pt + "Menu";
subMenu = this.menuNewSubMenu((i + 1) + "..." + Math.min(i + 25, infolist.length), this.menuGetId(menu) + "." + id);
this.menuAddSubMenu(menu, subMenu);
this.htMenus.put(id, subMenu);
pt = 1;
}if (i == 0) this.menuEnable(this.menuCreateItem(subMenu, J.i18n.GT.$("none"), "draw sym_* delete", null), true);
var sym = infolist[i][1];
if (sym.indexOf("x1") < 0) sym = infolist[i][0];
var entryName = (i + 1) + " " + infolist[i][2] + " (" + sym + ")";
this.menuEnable(this.menuCreateItem(subMenu, entryName, "draw SYMOP " + (i + 1), null), true);
}
this.menuEnable(menu, true);
});
Clazz.defineMethod(c$, "updateSYMMETRYSelectComputedMenu", 
function(){
var menu = this.htMenus.get("SYMMETRYSelectComputedMenu");
if (menu == null) return;
this.menuRemoveAll(menu, 0);
this.menuEnable(menu, false);
if (!this.hasSymmetry || this.modelIndex < 0) return;
var list = this.modelInfo.get("symmetryOperations");
if (list == null) return;
var enableSymop = (this.vwr.getOperativeSymmetry() != null);
var subMenu = menu;
var nmod = 25;
var pt = (list.length > 25 ? 0 : -2147483648);
for (var i = 0; i < list.length; i++) {
if (pt >= 0 && (pt++ % nmod) == 0) {
var id = "symop" + pt + "Menu";
subMenu = this.menuNewSubMenu((i + 1) + "..." + Math.min(i + 25, list.length), this.menuGetId(menu) + "." + id);
this.menuAddSubMenu(menu, subMenu);
this.htMenus.put(id, subMenu);
pt = 1;
}var entryName = "symop=" + (i + 1) + " # " + list[i];
this.menuEnable(this.menuCreateItem(subMenu, entryName, "SELECT symop=" + (i + 1), null), enableSymop);
}
this.menuEnable(menu, true);
});
Clazz.defineMethod(c$, "updateFRAMESbyModelComputedMenu", 
function(){
var menu = this.htMenus.get("FRAMESbyModelComputedMenu");
if (menu == null) return;
this.menuEnable(menu, (this.modelCount > 0));
this.menuSetLabel(menu, (this.modelIndex < 0 ? this.gti("allModelsText", this.modelCount) : this.gto("modelMenuText", (this.modelIndex + 1) + "/" + this.modelCount)));
this.menuRemoveAll(menu, 0);
if (this.modelCount < 1) return;
if (this.modelCount > 1) this.menuCreateCheckboxItem(menu, J.i18n.GT.$("All"), "frame 0 ##", null, (this.modelIndex < 0), false);
var subMenu = menu;
var pt = (this.modelCount > 25 ? 0 : -2147483648);
for (var i = 0; i < this.modelCount; i++) {
if (pt >= 0 && (pt++ % 25) == 0) {
var id = "model" + pt + "Menu";
subMenu = this.menuNewSubMenu((i + 1) + "..." + Math.min(i + 25, this.modelCount), this.menuGetId(menu) + "." + id);
this.menuAddSubMenu(menu, subMenu);
this.htMenus.put(id, subMenu);
pt = 1;
}var script = "" + this.vwr.getModelNumberDotted(i);
var entryName = this.vwr.getModelName(i);
var spectrumTypes = this.vwr.ms.getInfo(i, "spectrumTypes");
if (spectrumTypes != null && entryName.startsWith(spectrumTypes)) spectrumTypes = null;
if (!entryName.equals(script)) {
var ipt = entryName.indexOf(";PATH");
if (ipt >= 0) entryName = entryName.substring(0, ipt);
if (entryName.indexOf("Model[") == 0 && (ipt = entryName.indexOf("]:")) >= 0) entryName = entryName.substring(ipt + 2);
entryName = script + ": " + entryName;
}if (entryName.length > 60) entryName = entryName.substring(0, 55) + "...";
if (spectrumTypes != null) entryName += " (" + spectrumTypes + ")";
this.menuCreateCheckboxItem(subMenu, entryName, "model " + script + " ##", null, (this.modelIndex == i), false);
}
});
Clazz.defineMethod(c$, "updateConfigurationComputedMenu", 
function(){
var menu = this.htMenus.get("configurationComputedMenu");
if (menu == null) return;
this.menuEnable(menu, this.isMultiConfiguration);
if (!this.isMultiConfiguration) return;
var nAltLocs = this.altlocs.length;
this.menuSetLabel(menu, this.gti("configurationMenuText", nAltLocs));
this.menuRemoveAll(menu, 0);
var script = "hide none ##CONFIG";
this.menuCreateCheckboxItem(menu, J.i18n.GT.$("All"), script, null, (this.updateMode == 1 && this.configurationSelected.equals(script)), false);
for (var i = 0; i < nAltLocs; i++) {
script = "configuration " + (i + 1) + "; hide thisModel and not selected ##CONFIG";
var entryName = "" + (i + 1) + " -- \"" + this.altlocs.charAt(i) + "\"";
this.menuCreateCheckboxItem(menu, entryName, script, null, (this.updateMode == 1 && this.configurationSelected.equals(script)), false);
}
});
Clazz.defineMethod(c$, "updateModelSetComputedMenu", 
function(){
var menu = this.htMenus.get("modelSetMenu");
if (menu == null) return;
this.menuRemoveAll(menu, 0);
this.menuSetLabel(menu, this.nullModelSetName);
this.menuEnable(menu, false);
for (var i = this.noZapped.length; --i >= 0; ) this.menuEnable(this.htMenus.get(this.noZapped[i]), !this.isZapped);

if (this.modelSetName == null || this.isZapped) return;
if (this.isMultiFrame) {
this.modelSetName = this.gti("modelSetCollectionText", this.modelCount);
if (this.modelSetName.length > this.titleWidthMax) this.modelSetName = this.modelSetName.substring(0, this.titleWidthMax) + "...";
} else if (this.vwr.getBooleanProperty("hideNameInPopup")) {
this.modelSetName = this.getMenuText("hiddenModelSetText");
} else if (this.modelSetName.length > this.titleWidthMax) {
this.modelSetName = this.modelSetName.substring(0, this.titleWidthMax) + "...";
}this.menuSetLabel(menu, this.modelSetName);
this.menuEnable(menu, true);
this.menuEnable(this.htMenus.get("computationMenu"), this.ac <= 100);
this.addMenuItem(menu, this.gti("atomsText", this.ac));
this.addMenuItem(menu, this.gti("bondsText", this.vwr.ms.getBondCountInModel(this.modelIndex)));
if (this.isPDB) {
this.menuAddSeparator(menu);
this.addMenuItem(menu, this.gti("groupsText", this.vwr.ms.getGroupCountInModel(this.modelIndex)));
this.addMenuItem(menu, this.gti("chainsText", this.vwr.ms.getChainCountInModelWater(this.modelIndex, false)));
this.addMenuItem(menu, this.gti("polymersText", this.vwr.ms.getBioPolymerCountInModel(this.modelIndex)));
var submenu = this.htMenus.get("BiomoleculesMenu");
if (submenu == null) {
submenu = this.menuNewSubMenu(J.i18n.GT.$(this.getMenuText("biomoleculesMenuText")), this.menuGetId(menu) + ".biomolecules");
this.menuAddSubMenu(menu, submenu);
}this.menuRemoveAll(submenu, 0);
this.menuEnable(submenu, false);
var biomolecules;
if (this.modelIndex >= 0 && (biomolecules = this.vwr.ms.getInfo(this.modelIndex, "biomolecules")) != null) {
this.menuEnable(submenu, true);
var nBiomolecules = biomolecules.size();
for (var i = 0; i < nBiomolecules; i++) {
var script = (this.isMultiFrame ? "" : "save orientation;load \"\" FILTER \"biomolecule " + (i + 1) + "\";restore orientation;");
var nAtoms = (biomolecules.get(i).get("atomCount")).intValue();
var entryName = this.gto(this.isMultiFrame ? "biomoleculeText" : "loadBiomoleculeText",  Clazz.newArray(-1, [Integer.$valueOf(i + 1), Integer.$valueOf(nAtoms)]));
this.menuCreateItem(submenu, entryName, script, null);
}
}}if (this.isApplet && !this.vwr.getBooleanProperty("hideNameInPopup")) {
this.menuAddSeparator(menu);
this.menuCreateItem(menu, this.gto("viewMenuText", this.modelSetFileName), "show url", null);
}});
Clazz.defineMethod(c$, "gti", 
function(s, n){
return J.i18n.GT.i(J.i18n.GT.$(this.getMenuText(s)), n);
}, "~S,~N");
Clazz.defineMethod(c$, "gto", 
function(s, o){
return J.i18n.GT.o(J.i18n.GT.$(this.getMenuText(s)), o);
}, "~S,~O");
Clazz.defineMethod(c$, "updateAboutSubmenu", 
function(){
if (this.isApplet) this.setText("APPLETid", this.vwr.appletName);
{
}});
Clazz.defineMethod(c$, "updateLanguageSubmenu", 
function(){
var menu = this.htMenus.get("languageComputedMenu");
if (menu == null) return;
this.menuRemoveAll(menu, 0);
var language = J.i18n.GT.getLanguage();
var id = this.menuGetId(menu);
var languages = J.i18n.GT.getLanguageList(null);
for (var i = 0, p = 0; i < languages.length; i++) {
if (language.equals(languages[i].code)) languages[i].display = true;
if (languages[i].display) {
var code = languages[i].code;
var name = languages[i].language;
var nativeName = languages[i].nativeLanguage;
var menuLabel = code + " - " + J.i18n.GT.$(name);
if ((nativeName != null) && (!nativeName.equals(J.i18n.GT.$(name)))) {
menuLabel += " - " + nativeName;
}if (p++ > 0 && (p % 4 == 1)) this.menuAddSeparator(menu);
this.menuCreateCheckboxItem(menu, menuLabel, "language = \"" + code + "\" ##" + name, id + "." + code, language.equals(code), false);
}}
});
Clazz.defineMethod(c$, "updateSpecialMenuItem", 
function(m){
m.setText(this.getSpecialLabel(m.getName(), m.getText()));
}, "J.api.SC");
Clazz.defineMethod(c$, "getSpecialLabel", 
function(name, text){
var pt = text.indexOf(" (");
if (pt < 0) pt = text.length;
var info = null;
if (name.indexOf("captureLooping") >= 0) info = (this.vwr.am.animationReplayMode == 1073742070 ? "ONCE" : "LOOP");
 else if (name.indexOf("captureFps") >= 0) info = "" + this.vwr.getInt(553648132);
 else if (name.indexOf("captureMenu") >= 0) info = (this.vwr.captureParams == null ? J.i18n.GT.$("not capturing") : this.vwr.fm.getFilePath(this.vwr.captureParams.get("captureFileName"), false, true) + " " + this.vwr.captureParams.get("captureCount"));
return (info == null ? text : text.substring(0, pt) + " (" + info + ")");
}, "~S,~S");
});
;//5.0.1-v7 Sat Feb 21 18:17:38 CST 2026
