Clazz.declarePackage("JSV.common");
Clazz.load(["javajs.api.BytePoster", "J.api.PlatformViewer", "JSV.common.Spectrum"], "JSV.common.JSViewer", ["java.io.File", "java.net.URL", "java.util.Arrays", "$.Hashtable", "JU.CU", "$.Lst", "$.OC", "$.PT", "$.SB", "JSV.common.Annotation", "$.ExportType", "$.JSVFileManager", "$.PanelData", "$.PanelNode", "$.Parameters", "$.PeakInfo", "$.PrintLayout", "$.RepaintManager", "$.ScriptToken", "$.ScriptTokenizer", "JSV.source.JDXReader", "$.JDXSource", "JSV.tree.SimpleTree", "JU.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.si = null;
this.g2d = null;
this.spectraTree = null;
this.currentSource = null;
this.panelNodes = null;
this.parameters = null;
this.repaintManager = null;
this.selectedPanel = null;
this.mainPanel = null;
this.properties = null;
this.scriptQueue = null;
this.fileHelper = null;
this.jsvpPopupMenu = null;
this.dialogManager = null;
this.viewDialog = null;
this.overlayLegendDialog = null;
this.irMode = null;
this.loadImaginary = false;
this.interfaceOverlaid = false;
this.autoIntegrate = false;
this.autoShowLegend = false;
this.obscureTitleFromUser = null;
this.allowMenu = true;
this.initialStartIndex = -1;
this.initialEndIndex = -1;
this.isSingleThreaded = false;
this.isApplet = false;
this.isSigned = false;
this.recentScript = "";
this.appletName = null;
this.fullName = null;
this.syncID = null;
this.html5Applet = null;
this.display = null;
this.maximumSize = 2147483647;
this.screenHeight = 0;
this.screenWidth = 0;
this.fileCount = 0;
this.nViews = 0;
this.scriptLevelCount = 0;
this.returnFromJmolModel = null;
this.integrationRatios = null;
this.apiPlatform = null;
this.popupAllowMenu = true;
this.popupZoomEnabled = true;
this.defaultLoadScript = null;
this.nmrMaxY = NaN;
this.overlayLegendVisible = false;
this.recentStackPercent = 5;
this.lastPrintLayout = null;
this.offWindowFrame = null;
this.recentOpenURL = "http://";
this.recentURL = null;
this.recentSimulation = "tylenol";
Clazz.instantialize(this, arguments);}, JSV.common, "JSViewer", null, [J.api.PlatformViewer, javajs.api.BytePoster]);
Clazz.prepareFields (c$, function(){
this.irMode = JSV.common.Spectrum.IRMode.NO_CONVERT;
});
Clazz.makeConstructor(c$, 
function(si, isApplet, isJSApplet){
this.si = si;
this.isApplet = isApplet;
JSV.common.JSViewer.isJS = isApplet && isJSApplet;
var jmol = null;
{
self.Jmol && (jmol = Jmol);
}JSV.common.JSViewer.jmolObject = jmol;
this.isSigned = si.isSigned();
this.apiPlatform = this.getPlatformInterface("Platform");
this.apiPlatform.setViewer(this, this.display);
this.g2d = this.getPlatformInterface("G2D");
this.spectraTree =  new JSV.tree.SimpleTree(this);
this.parameters = this.getPlatformInterface("Parameters");
this.parameters.setName("applet");
this.fileHelper = (this.getPlatformInterface("FileHelper")).set(this);
this.isSingleThreaded = this.apiPlatform.isSingleThreaded();
this.panelNodes =  new JU.Lst();
this.repaintManager =  new JSV.common.RepaintManager(this);
if (!isApplet) this.setPopupMenu(true, true);
}, "JSV.api.ScriptInterface,~B,~B");
Clazz.defineMethod(c$, "setProperty", 
function(key, value){
if (this.properties != null) this.properties.setProperty(key, value);
}, "~S,~S");
Clazz.defineMethod(c$, "setNode", 
function(node){
if (node.jsvp !== this.selectedPanel) this.si.siSetSelectedPanel(node.jsvp);
this.si.siSendPanelChange();
this.si.siNodeSet(node);
}, "JSV.common.PanelNode");
Clazz.defineMethod(c$, "setPopupMenu", 
function(allowMenu, zoomEnabled){
this.popupAllowMenu = allowMenu;
this.popupZoomEnabled = zoomEnabled;
}, "~B,~B");
Clazz.defineMethod(c$, "showMenu", 
function(x, y){
if (!this.popupAllowMenu) return;
if (this.jsvpPopupMenu == null) {
try {
this.jsvpPopupMenu = this.getPlatformInterface("Popup");
this.jsvpPopupMenu.jpiInitialize(this, this.isApplet ? "appletMenu" : "appMenu");
this.jsvpPopupMenu.setEnabled(this.popupAllowMenu, this.popupZoomEnabled);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
JU.Logger.error(e + " initializing popup menu");
return;
} else {
throw e;
}
}
}this.jsvpPopupMenu.jpiShow(x, y);
}, "~N,~N");
Clazz.defineMethod(c$, "runScriptNow", 
function(script){
System.out.println(this.checkScript(script));
this.scriptLevelCount++;
if (script == null) script = "";
script = script.trim();
if (script.startsWith("!")) script = script.substring(1).trim();
 else if (script.startsWith(">")) {
JU.Logger.error(script);
return true;
}if (script.indexOf("<PeakData") >= 0) {
this.syncScript(script);
return true;
}JU.Logger.info("RUNSCRIPT " + script);
var isOK = true;
var nErrorsLeft = 10;
var commandTokens =  new JSV.common.ScriptTokenizer(script, true);
var msg = null;
while (commandTokens != null && commandTokens.hasMoreTokens() && nErrorsLeft > 0 && isOK) {
var token = commandTokens.nextToken();
var eachParam =  new JSV.common.ScriptTokenizer(token, false);
var key = JSV.common.ScriptToken.getKey(eachParam);
if (key == null) continue;
var st = JSV.common.ScriptToken.getScriptToken(key);
var value = JSV.common.ScriptToken.getValue(st, eachParam, token);
try {
switch (st) {
case JSV.common.ScriptToken.UNKNOWN:
JU.Logger.info("Unrecognized parameter: " + key);
--nErrorsLeft;
break;
default:
if (this.selectedPanel == null) break;
this.parameters.set(this.pd(), st, value);
this.si.siUpdateBoolean(st, JSV.common.Parameters.isTrue(value));
break;
case JSV.common.ScriptToken.PEAKCALLBACKFUNCTIONNAME:
case JSV.common.ScriptToken.SYNCCALLBACKFUNCTIONNAME:
case JSV.common.ScriptToken.COORDCALLBACKFUNCTIONNAME:
case JSV.common.ScriptToken.LOADFILECALLBACKFUNCTIONNAME:
this.si.siExecSetCallback(st, value);
break;
case JSV.common.ScriptToken.DEFAULTLOADSCRIPT:
value = JU.PT.rep(value, "''", "\"");
this.defaultLoadScript = (value.length > 0 ? value : null);
break;
case JSV.common.ScriptToken.DEFAULTNMRNORMALIZATION:
this.nmrMaxY = JU.PT.parseFloat(value);
break;
case JSV.common.ScriptToken.AUTOINTEGRATE:
this.autoIntegrate = JSV.common.Parameters.isTrue(value);
break;
case JSV.common.ScriptToken.CLOSE:
this.execClose(value);
break;
case JSV.common.ScriptToken.DEBUG:
JU.Logger.setLogLevel(value.toLowerCase().equals("high") ? 6 : JSV.common.Parameters.isTrue(value) ? 5 : 4);
break;
case JSV.common.ScriptToken.GETPROPERTY:
var info = (this.selectedPanel == null ? null : this.getPropertyAsJavaObject(value));
if (info != null) this.selectedPanel.showMessage(JU.PT.toJSON(null, info), value);
break;
case JSV.common.ScriptToken.HELP:
this.execHelp(value);
break;
case JSV.common.ScriptToken.HIDDEN:
this.si.siExecHidden(JSV.common.Parameters.isTrue(value));
break;
case JSV.common.ScriptToken.INTEGRATIONRATIOS:
this.integrationRatios = value;
this.execIntegrate(null);
break;
case JSV.common.ScriptToken.INTERFACE:
this.interfaceOverlaid = this.checkOvelayInterface(value);
break;
case JSV.common.ScriptToken.INTEGRALOFFSET:
case JSV.common.ScriptToken.INTEGRALRANGE:
this.execSetIntegralParameter(st, Double.parseDouble(value));
break;
case JSV.common.ScriptToken.INVERTY:
this.execZoom("invertY");
break;
case JSV.common.ScriptToken.JMOL:
this.si.syncToJmol(value);
break;
case JSV.common.ScriptToken.JSV:
this.syncScript(JU.PT.trimQuotes(value));
break;
case JSV.common.ScriptToken.LOAD:
if (value.length == 0) {
if (this.defaultLoadScript != null) this.runScriptNow(this.defaultLoadScript);
break;
}this.execLoad(value, (this.defaultLoadScript == null ? "" : this.defaultLoadScript + ";") + commandTokens.getRemainingScript());
msg = (this.selectedPanel == null ? null : this.si.siLoaded(value));
commandTokens = null;
break;
case JSV.common.ScriptToken.LOADIMAGINARY:
this.loadImaginary = JSV.common.Parameters.isTrue(value);
break;
case JSV.common.ScriptToken.PEAK:
this.execPeak(value);
break;
case JSV.common.ScriptToken.PEAKLIST:
this.execPeakList(value);
break;
case JSV.common.ScriptToken.SCALEBY:
this.scaleSelectedBy(this.panelNodes, value);
break;
case JSV.common.ScriptToken.SCRIPT:
if (value.equals("") || value.toLowerCase().startsWith("inline")) {
this.execScriptInline(value);
} else {
var s = JSV.common.JSVFileManager.getFileAsString(value);
if (s != null && this.scriptLevelCount < 100) this.runScriptNow(s);
}break;
case JSV.common.ScriptToken.SELECT:
this.execSelect(value);
break;
case JSV.common.ScriptToken.SPECTRUM:
case JSV.common.ScriptToken.SPECTRUMNUMBER:
if (!this.setSpectrum(value)) isOK = false;
break;
case JSV.common.ScriptToken.STACKOFFSETY:
this.execOverlayOffsetY(JU.PT.parseInt("" + JU.PT.parseFloat(value)));
break;
case JSV.common.ScriptToken.TEST:
this.si.siExecTest(value);
break;
case JSV.common.ScriptToken.OVERLAY:
case JSV.common.ScriptToken.VIEW:
this.execView(value, true);
break;
case JSV.common.ScriptToken.HIGHLIGHT:
isOK = this.highlight(token);
break;
case JSV.common.ScriptToken.FINDX:
case JSV.common.ScriptToken.GETSOLUTIONCOLOR:
case JSV.common.ScriptToken.INTEGRATION:
case JSV.common.ScriptToken.INTEGRATE:
case JSV.common.ScriptToken.IRMODE:
case JSV.common.ScriptToken.LABEL:
case JSV.common.ScriptToken.LINK:
case JSV.common.ScriptToken.OVERLAYSTACKED:
case JSV.common.ScriptToken.PRINT:
case JSV.common.ScriptToken.SETPEAK:
case JSV.common.ScriptToken.SETX:
case JSV.common.ScriptToken.SHIFTX:
case JSV.common.ScriptToken.SHOWERRORS:
case JSV.common.ScriptToken.SHOWMEASUREMENTS:
case JSV.common.ScriptToken.SHOWMENU:
case JSV.common.ScriptToken.SHOWKEY:
case JSV.common.ScriptToken.SHOWPEAKLIST:
case JSV.common.ScriptToken.SHOWINTEGRATION:
case JSV.common.ScriptToken.SHOWPROPERTIES:
case JSV.common.ScriptToken.SHOWSOURCE:
case JSV.common.ScriptToken.YSCALE:
case JSV.common.ScriptToken.WRITE:
case JSV.common.ScriptToken.ZOOM:
if (this.isClosed()) {
isOK = false;
break;
}switch (st) {
default:
break;
case JSV.common.ScriptToken.FINDX:
this.pd().findX(null, Double.parseDouble(value));
break;
case JSV.common.ScriptToken.GETSOLUTIONCOLOR:
this.show("solutioncolor" + value.toLowerCase());
break;
case JSV.common.ScriptToken.INTEGRATION:
case JSV.common.ScriptToken.INTEGRATE:
this.execIntegrate(value);
break;
case JSV.common.ScriptToken.IRMODE:
this.execIRMode(value);
break;
case JSV.common.ScriptToken.LABEL:
this.pd().addAnnotation(JSV.common.ScriptToken.getTokens(value));
break;
case JSV.common.ScriptToken.LINK:
this.pd().linkSpectra(JSV.common.PanelData.LinkMode.getMode(value));
break;
case JSV.common.ScriptToken.OVERLAYSTACKED:
this.pd().splitStack(!JSV.common.Parameters.isTrue(value));
break;
case JSV.common.ScriptToken.PRINT:
msg = this.execWrite(null);
break;
case JSV.common.ScriptToken.SETPEAK:
case JSV.common.ScriptToken.SETX:
case JSV.common.ScriptToken.SHIFTX:
this.execShiftSpectrum(st, token);
break;
case JSV.common.ScriptToken.SHOWERRORS:
this.show("errors");
break;
case JSV.common.ScriptToken.SHOWINTEGRATION:
this.pd().showAnnotation(JSV.common.Annotation.AType.Integration, JSV.common.Parameters.getTFToggle(value));
break;
case JSV.common.ScriptToken.SHOWKEY:
this.setOverlayLegendVisibility(JSV.common.Parameters.getTFToggle(value), true);
break;
case JSV.common.ScriptToken.SHOWMEASUREMENTS:
this.pd().showAnnotation(JSV.common.Annotation.AType.Measurements, JSV.common.Parameters.getTFToggle(value));
break;
case JSV.common.ScriptToken.SHOWMENU:
this.showMenu(-2147483648, 0);
break;
case JSV.common.ScriptToken.SHOWPEAKLIST:
this.pd().showAnnotation(JSV.common.Annotation.AType.PeakList, JSV.common.Parameters.getTFToggle(value));
break;
case JSV.common.ScriptToken.SHOWPROPERTIES:
this.show("properties");
break;
case JSV.common.ScriptToken.SHOWSOURCE:
this.show("source");
break;
case JSV.common.ScriptToken.YSCALE:
this.setYScale(value);
break;
case JSV.common.ScriptToken.WINDOW:
this.si.siNewWindow(JSV.common.Parameters.isTrue(value), false);
break;
case JSV.common.ScriptToken.WRITE:
msg = this.execWrite(value);
break;
case JSV.common.ScriptToken.ZOOM:
isOK = this.execZoom(value);
break;
}
break;
}
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
msg = e.toString();
JU.Logger.error(e.toString());
isOK = false;
--nErrorsLeft;
} else {
throw e;
}
}
}
this.scriptLevelCount--;
this.si.siExecScriptComplete(msg, true);
return isOK;
}, "~S");
Clazz.defineMethod(c$, "execShiftSpectrum", 
function(st, script){
var tokens = JSV.common.ScriptToken.getTokens(script);
var xOld = NaN;
var xNew = NaN;
switch (tokens.size()) {
case 2:
var value = tokens.get(1);
if (value.equals("")) value = "?";
xNew = value.equalsIgnoreCase("NONE") ? 1.7976931348623157E308 : value.equalsIgnoreCase("?") ? NaN : Double.parseDouble(value);
break;
case 3:
xOld = Double.parseDouble(tokens.get(1));
xNew = Double.parseDouble(tokens.get(2));
break;
default:
Double.parseDouble("");
}
var mode = 0;
switch (st) {
case JSV.common.ScriptToken.SETPEAK:
mode = 1;
break;
case JSV.common.ScriptToken.SETX:
mode = 2;
break;
case JSV.common.ScriptToken.SHIFTX:
mode = 3;
if (Double.isNaN(xNew)) Double.parseDouble("");
break;
default:
return;
}
this.pd().shiftSpectrum(mode, xOld, xNew);
}, "JSV.common.ScriptToken,~S");
Clazz.defineMethod(c$, "execClose", 
function(value){
var fromScript = (!value.startsWith("!"));
if (!fromScript) value = value.substring(1);
this.close(JU.PT.trimQuotes(value));
if (!fromScript || this.panelNodes.size() == 0) this.si.siValidateAndRepaint(true);
}, "~S");
Clazz.defineMethod(c$, "checkOvelayInterface", 
function(value){
return (value.equalsIgnoreCase("single") || value.equalsIgnoreCase("overlay"));
}, "~S");
Clazz.defineMethod(c$, "execPeak", 
function(value){
try {
var tokens = JSV.common.ScriptToken.getTokens(JU.PT.rep(value, "#", "INDEX="));
value = " type=\"" + tokens.get(0).toUpperCase() + "\" _match=\"" + JU.PT.trimQuotes(tokens.get(1).toUpperCase()) + "\"";
if (tokens.size() > 2 && tokens.get(2).equalsIgnoreCase("all")) value += " title=\"ALL\"";
this.processPeakPickEvent( new JSV.common.PeakInfo(value), false);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
}, "~S");
Clazz.defineMethod(c$, "execPeakList", 
function(value){
var p = this.parameters;
var b = JSV.common.Parameters.getTFToggle(value);
if (value.indexOf("=") < 0) {
if (!this.isClosed()) this.pd().getPeakListing(null, b);
} else {
var tokens = JSV.common.ScriptToken.getTokens(value);
var threshold = p.peakListThreshold;
var interp = p.peakListInterpolation;
try {
for (var i = tokens.size(); --i >= 0; ) {
var token = tokens.get(i);
var pt = token.indexOf("=");
if (pt <= 0) continue;
var key = token.substring(0, pt);
value = token.substring(pt + 1);
if (key.startsWith("thr")) {
threshold = Double.$valueOf(value).doubleValue();
} else if (key.startsWith("int")) {
interp = (value.equalsIgnoreCase("none") ? "NONE" : "parabolic");
}}
p.peakListThreshold = threshold;
p.peakListInterpolation = interp;
if (!this.isClosed()) this.pd().getPeakListing(p, Boolean.TRUE);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
}}, "~S");
Clazz.defineMethod(c$, "highlight", 
function(value){
var tokens = JSV.common.ScriptToken.getTokens(value);
var n = tokens.size();
switch (n) {
case 3:
case 5:
case 6:
case 7:
break;
case 2:
case 4:
if (tokens.get(n - 1).equalsIgnoreCase("OFF")) break;
default:
return false;
}
if (!this.isClosed()) {
var x1 = JU.PT.parseFloat(n > 1 ? tokens.get(1) : "");
var x2 = JU.PT.parseFloat(n > 2 ? tokens.get(2) : "");
var r = this.getRGB(n > 3 ? tokens.get(3) : "100");
var g = this.getRGB(n > 4 ? tokens.get(4) : "100");
var b = this.getRGB(n > 5 ? tokens.get(5) : "100");
var a = this.getRGB(n > 6 ? tokens.get(6) : "100");
if (Float.isNaN(x1) || Float.isNaN(x2)) {
this.pd().removeAllHighlights();
} else {
this.pd().removeHighlight(x1, x2);
if (a < 0) a = 150;
if (r >= 0 && g >= 0 && b >= 0) this.pd().addHighlight(null, x1, x2, null, r, g, b, a);
}this.repaint(true);
}return true;
}, "~S");
Clazz.defineMethod(c$, "getRGB", 
function(s){
var f = JU.PT.parseFloat(s);
return Clazz.floatToInt(Float.isNaN(f) ? -1 : f > 1 ? f : f * 255);
}, "~S");
Clazz.defineMethod(c$, "execZoom", 
function(value){
var x1 = 0;
var x2 = 0;
var y1 = 0;
var y2 = 0;
value = JU.PT.rep(value, " - ", " ").$replace(',', ' ');
var tokens = JSV.common.ScriptToken.getTokens(value);
switch (tokens.size()) {
default:
return false;
case 0:
var v = this.pd().getCurrentGraphSet().getCurrentView();
value = Math.round(v.minXOnScale * 100) / 100 + "," + Math.round(v.maxXOnScale * 100) / 100;
value = this.selectedPanel.getInput("Enter zoom range x1 x2", "Zoom", value);
return (value == null || this.execZoom(value));
case 1:
value = tokens.get(0);
if (value.equalsIgnoreCase("next")) {
this.pd().nextView();
} else if (value.toLowerCase().startsWith("prev")) {
this.pd().previousView();
} else if (value.equalsIgnoreCase("out")) {
this.pd().resetView();
} else if (value.equalsIgnoreCase("clear")) {
this.pd().clearAllView();
} else if (value.equalsIgnoreCase("invertY")) {
this.pd().getCurrentGraphSet().invertYAxis();
}return true;
case 2:
x1 = Double.parseDouble(tokens.get(0));
x2 = Double.parseDouble(tokens.get(1));
break;
case 3:
var xy = tokens.get(0);
if (xy.equalsIgnoreCase("X")) {
x1 = Double.parseDouble(tokens.get(1));
x2 = Double.parseDouble(tokens.get(2));
} else if (xy.equalsIgnoreCase("Y")) {
y1 = Double.parseDouble(tokens.get(1));
y2 = Double.parseDouble(tokens.get(2));
}break;
case 4:
x1 = Double.parseDouble(tokens.get(0));
y1 = Double.parseDouble(tokens.get(1));
x2 = Double.parseDouble(tokens.get(2));
y2 = Double.parseDouble(tokens.get(3));
}
this.pd().setZoom(x1, y1, x2, y2);
return true;
}, "~S");
Clazz.defineMethod(c$, "scaleSelectedBy", 
function(nodes, value){
try {
var f = Double.parseDouble(value);
for (var i = nodes.size(); --i >= 0; ) nodes.get(i).pd().scaleSelectedBy(f);

} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
}, "JU.Lst,~S");
Clazz.defineMethod(c$, "pd", 
function(){
return (this.selectedPanel == null ? null : this.selectedPanel.getPanelData());
});
Clazz.defineMethod(c$, "isClosed", 
function(){
return (this.pd() == null);
});
Clazz.defineMethod(c$, "execSelect", 
function(value){
if (value.startsWith("ID ")) {
if (!this.isClosed()) try {
this.pd().selectSpectrum(null, "ID", JU.PT.trimQuotes(value.substring(3)), true);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
return;
}var nodes = this.panelNodes;
for (var i = nodes.size(); --i >= 0; ) nodes.get(i).pd().selectFromEntireSet(-2147483648);

var speclist =  new JU.Lst();
this.fillSpecList(value, speclist, false);
}, "~S");
Clazz.defineMethod(c$, "execView", 
function(value, fromScript){
if (value.equals("")) {
this.checkOverlay();
return;
}var speclist =  new JU.Lst();
var strlist = this.fillSpecList(value, speclist, true);
if (speclist.size() > 0) this.si.siOpenDataOrFile(null, strlist, speclist, strlist, -1, -1, false, null, null);
if (!fromScript) {
this.si.siValidateAndRepaint(false);
}}, "~S,~B");
Clazz.defineMethod(c$, "execIRMode", 
function(value){
var mode = JSV.common.Spectrum.IRMode.getMode(value);
var type = this.pd().getSpectrum().dataType;
for (var i = this.panelNodes.size(); --i >= 0; ) this.panelNodes.get(i).pd().setIRMode(mode, type);

this.setIRmode(value);
}, "~S");
Clazz.defineMethod(c$, "execIntegrate", 
function(value){
if (this.isClosed()) return;
this.pd().checkIntegral(this.parameters, value);
if (this.integrationRatios != null) this.pd().setIntegrationRatios(this.integrationRatios);
this.integrationRatios = null;
this.repaint(true);
}, "~S");
Clazz.defineMethod(c$, "repaint", 
function(andTaintAll){
this.selectedPanel.doRepaint(andTaintAll);
}, "~B");
Clazz.defineMethod(c$, "execSetIntegralParameter", 
function(st, value){
var p = this.parameters;
switch (st) {
case JSV.common.ScriptToken.INTEGRALRANGE:
p.integralRange = value;
break;
case JSV.common.ScriptToken.INTEGRALOFFSET:
p.integralOffset = value;
break;
}
if (!this.isClosed()) this.pd().checkIntegral(this.parameters, "update");
}, "JSV.common.ScriptToken,~N");
Clazz.defineMethod(c$, "setYScale", 
function(value){
var tokens = JSV.common.ScriptToken.getTokens(value);
var pt = 0;
var isAll = false;
if (tokens.size() > 1 && tokens.get(0).equalsIgnoreCase("ALL")) {
isAll = true;
pt++;
}var y1 = Double.parseDouble(tokens.get(pt++));
var y2 = Double.parseDouble(tokens.get(pt));
if (isAll) {
var spec = this.pd().getSpectrum();
for (var i = this.panelNodes.size(); --i >= 0; ) {
var node = this.panelNodes.get(i);
if (node.source !== this.currentSource) continue;
if (JSV.common.Spectrum.areXScalesCompatible(spec, node.getSpectrum(), false, false)) node.pd().setZoom(0, y1, 0, y2);
}
} else {
this.pd().setZoom(0, y1, 0, y2);
}}, "~S");
Clazz.defineMethod(c$, "setOverlayLegendVisibility", 
function(tftoggle, doSet){
if (doSet) this.overlayLegendVisible = (tftoggle == null ? !this.overlayLegendVisible : tftoggle === Boolean.TRUE);
var node = JSV.common.PanelNode.findNode(this.selectedPanel, this.panelNodes);
for (var i = this.panelNodes.size(); --i >= 0; ) this.showOverlayLegend(this.panelNodes.get(i), this.panelNodes.get(i) === node && this.overlayLegendVisible);

}, "Boolean,~B");
Clazz.defineMethod(c$, "showOverlayLegend", 
function(node, visible){
var legend = node.legend;
if (legend == null && visible) {
legend = node.setLegend(node.pd().getNumberOfSpectraInCurrentSet() > 1 && node.pd().getNumberOfGraphSets() == 1 ? this.getDialog(JSV.common.Annotation.AType.OverlayLegend, null) : null);
}if (legend != null) legend.setVisible(visible);
}, "JSV.common.PanelNode,~B");
Clazz.defineMethod(c$, "syncScript", 
function(peakScript){
if (peakScript.equals("TEST")) peakScript = JSV.common.JSViewer.testScript;
JU.Logger.info("JSViewer.syncScript Jmol>JSV " + peakScript);
if (peakScript.indexOf("<PeakData") < 0) {
if (peakScript.startsWith("JSVSTR:")) {
this.si.syncToJmol(peakScript);
return;
}this.runScriptNow(peakScript);
if (peakScript.indexOf("#SYNC_PEAKS") >= 0) this.syncPeaksAfterSyncScript();
return;
}JU.Logger.info(">>toJSV>> " + peakScript);
var sourceID = JU.PT.getQuotedAttribute(peakScript, "sourceID");
var type;
var model;
var file;
var jmolSource;
var index;
var atomKey;
if (sourceID == null) {
file = JU.PT.getQuotedAttribute(peakScript, "file");
index = JU.PT.getQuotedAttribute(peakScript, "index");
if (file == null || index == null) return;
file = JU.PT.rep(file, "#molfile", "");
model = JU.PT.getQuotedAttribute(peakScript, "model");
jmolSource = JU.PT.getQuotedAttribute(peakScript, "src");
var modelSent = (jmolSource != null && jmolSource.startsWith("Jmol") ? null : this.returnFromJmolModel);
if (model != null && modelSent != null && !model.equals(modelSent)) {
JU.Logger.info("JSV ignoring model " + model + "; should be " + modelSent);
return;
}this.returnFromJmolModel = null;
if (this.panelNodes.size() == 0 || !this.checkFileAlreadyLoaded(file)) {
JU.Logger.info("file " + file + " not found -- JSViewer closing all and reopening");
this.si.siSyncLoad(file);
}type = JU.PT.getQuotedAttribute(peakScript, "type");
atomKey = null;
} else {
file = null;
index = model = sourceID;
atomKey = "," + JU.PT.getQuotedAttribute(peakScript, "atom") + ",";
type = "ID";
jmolSource = sourceID;
}var pi = this.selectPanelByPeak(file, index, atomKey);
var pd = this.pd();
pd.selectSpectrum(file, type, model, true);
this.si.siSendPanelChange();
pd.addPeakHighlight(pi);
this.repaint(true);
if (jmolSource == null || (pi != null && pi.getAtoms() != null)) this.si.syncToJmol(this.jmolSelect(pi));
}, "~S");
Clazz.defineMethod(c$, "syncPeaksAfterSyncScript", 
function(){
var source = this.currentSource;
if (source == null) return;
try {
var file = "file=" + JU.PT.esc(source.getFilePath());
var peaks = source.getSpectra().get(0).getPeakList();
var sb =  new JU.SB();
sb.append("[");
var n = peaks.size();
for (var i = 0; i < n; i++) {
var s = peaks.get(i).toString();
s = s + " " + file;
sb.append(JU.PT.esc(s));
if (i > 0) sb.append(",");
}
sb.append("]");
this.si.syncToJmol("Peaks: " + sb);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
});
Clazz.defineMethod(c$, "checkFileAlreadyLoaded", 
function(fileName){
if (this.isClosed()) return false;
if (this.pd().hasFileLoaded(fileName)) return true;
for (var i = this.panelNodes.size(); --i >= 0; ) if (this.panelNodes.get(i).pd().hasFileLoaded(fileName)) {
this.si.siSetSelectedPanel(this.panelNodes.get(i).jsvp);
return true;
}
return false;
}, "~S");
Clazz.defineMethod(c$, "selectPanelByPeak", 
function(file, index, atomKey){
if (this.panelNodes == null) return null;
var pi = null;
for (var i = this.panelNodes.size(); --i >= 0; ) this.panelNodes.get(i).pd().addPeakHighlight(null);

pi = this.pd().selectPeakByFileIndex(file, index, atomKey);
if (pi != null) {
this.setNode(JSV.common.PanelNode.findNode(this.selectedPanel, this.panelNodes));
} else {
for (var i = this.panelNodes.size(); --i >= 0; ) {
var node = this.panelNodes.get(i);
if ((pi = node.pd().selectPeakByFileIndex(file, index, atomKey)) != null) {
this.setNode(node);
break;
}}
}return pi;
}, "~S,~S,~S");
Clazz.defineMethod(c$, "processPeakPickEvent", 
function(eventObj, isApp){
var pi;
if (Clazz.instanceOf(eventObj,"JSV.common.PeakInfo")) {
pi = eventObj;
var pi2 = this.pd().findMatchingPeakInfo(pi);
if (pi2 == null) {
if (!"ALL".equals(pi.getTitle())) return;
var node = null;
for (var i = 0; i < this.panelNodes.size(); i++) if ((pi2 = this.panelNodes.get(i).pd().findMatchingPeakInfo(pi)) != null) {
node = this.panelNodes.get(i);
break;
}
if (node == null) return;
this.setNode(node);
}pi = pi2;
} else {
var e = (eventObj);
this.si.siSetSelectedPanel(e.getSource());
pi = e.getPeakInfo();
}this.pd().addPeakHighlight(pi);
this.syncToJmol(pi);
if (pi.isClearAll()) this.repaint(false);
 else this.pd().selectSpectrum(pi.getFilePath(), pi.getType(), pi.getModel(), true);
this.si.siCheckCallbacks(pi.getTitle());
}, "~O,~B");
Clazz.defineMethod(c$, "newStructToJmol", 
function(data){
JU.Logger.info("sending new structure to Jmol:\n" + data);
this.si.syncToJmol("struct:" + data);
}, "~S");
Clazz.defineMethod(c$, "syncToJmol", 
function(pi){
this.repaint(true);
this.returnFromJmolModel = pi.getModel();
this.si.syncToJmol(this.jmolSelect(pi));
}, "JSV.common.PeakInfo");
Clazz.defineMethod(c$, "sendPanelChange", 
function(){
var pd = this.pd();
var spec = pd.getSpectrum();
var pi = spec.getSelectedPeak();
if (pi == null) pi = spec.getModelPeakInfoForAutoSelectOnLoad();
if (pi == null) pi = spec.getBasePeakInfo();
pd.addPeakHighlight(pi);
JU.Logger.info(Thread.currentThread() + "JSViewer sendFrameChange " + this.selectedPanel);
this.syncToJmol(pi);
});
Clazz.defineMethod(c$, "jmolSelect", 
function(pi){
var script = ("IR".equals(pi.getType()) || "RAMAN".equals(pi.getType()) ? "vibration ON; selectionHalos OFF;" : "vibration OFF; selectionhalos " + (pi.getAtoms() == null ? "OFF" : "ON"));
return "Select: " + pi + " script=\"" + script + " \" sourceID=\"" + this.pd().getSpectrum().sourceID + "\"";
}, "JSV.common.PeakInfo");
Clazz.defineMethod(c$, "getPropertyAsJavaObject", 
function(key){
var map =  new java.util.Hashtable();
if ("SOURCEID".equalsIgnoreCase(key)) {
map.put(key, (this.pd() == null ? "" : this.pd().getSpectrum().sourceID));
return map;
}if (key != null && key.startsWith("DATA_")) {
map.put(key, "" + JSV.common.JSVFileManager.cacheGet(key.substring(5)));
return map;
}var isAll = false;
if (key != null && key.toUpperCase().startsWith("ALL ") || "all".equalsIgnoreCase(key)) {
key = key.substring(3).trim();
isAll = true;
}if ("".equals(key)) key = null;
if ("NAMES".equalsIgnoreCase(key) || "KEYS".equalsIgnoreCase(key)) key = "";
var map0 = this.pd().getInfo(true, key);
if (!isAll && map0 != null) return map0;
if (map0 != null) map.put("current", map0);
var info =  new JU.Lst();
for (var i = 0; i < this.panelNodes.size(); i++) {
var jsvp = this.panelNodes.get(i).jsvp;
if (jsvp == null) continue;
info.addLast(this.panelNodes.get(i).getInfo(key));
}
map.put("items", info);
return map;
}, "~S");
Clazz.defineMethod(c$, "getCoordinate", 
function(){
if (!this.isClosed()) {
var coord = this.pd().getClickedCoordinate();
if (coord != null) return coord.getXVal() + " " + coord.getYVal();
}return "";
});
Clazz.defineMethod(c$, "fillSpecList", 
function(value, speclist, isView){
var prefix = "1.";
var list;
var list0 = null;
var isNone = (value.equalsIgnoreCase("NONE"));
if (isNone || value.equalsIgnoreCase("all")) value = "*";
if (value.indexOf("*") < 0) {
var tokens = value.$plit(" ");
var sb =  new JU.SB();
for (var i = 0; i < tokens.length; i++) {
var pt = tokens[i].indexOf('.');
if (pt != tokens[i].lastIndexOf('.')) tokens[i] = tokens[i].substring(0, pt + 1) + tokens[i].substring(pt + 1).$replace('.', '_');
sb.append(tokens[i]).append(" ");
}
value = sb.toString().trim();
}if (value.equals("*")) {
list = JSV.common.ScriptToken.getTokens(JSV.common.PanelNode.getSpectrumListAsString(this.panelNodes));
} else if (value.startsWith("\"") || value.startsWith("'")) {
list = JSV.common.ScriptToken.getTokens(value);
} else {
value = JU.PT.rep(value, "_", " _ ");
value = JU.PT.rep(value, "-", " - ");
list = JSV.common.ScriptToken.getTokens(value);
list0 = JSV.common.ScriptToken.getTokens(JSV.common.PanelNode.getSpectrumListAsString(this.panelNodes));
if (list0.size() == 0) return null;
}var id0 = (this.isClosed() ? prefix : JSV.common.PanelNode.findNode(this.selectedPanel, this.panelNodes).id);
id0 = id0.substring(0, id0.indexOf(".") + 1);
var sb =  new JU.SB();
var n = list.size();
var idLast = null;
for (var i = 0; i < n; i++) {
var id = list.get(i);
var userYFactor = NaN;
var isubspec = -1;
if (i + 1 < n && list.get(i + 1).equals("*")) {
i += 2;
userYFactor = Double.parseDouble(list.get(i));
} else if (i + 1 < n && list.get(i + 1).equals("_")) {
i += 2;
isubspec = Integer.parseInt(list.get(i));
}if (id.equals("-")) {
if (idLast == null) idLast = list0.get(0);
id = (i + 1 == n ? list0.get(list0.size() - 1) : list.get(++i));
if (!id.contains(".")) id = id0 + id;
var pt = 0;
while (pt < list0.size() && !list0.get(pt).equals(idLast)) pt++;

pt++;
while (pt < list0.size() && !idLast.equals(id)) {
var node = JSV.common.PanelNode.findNodeById((idLast = list0.get(pt++)), this.panelNodes);
speclist.addLast(node.pd().getSpectrumAt(0));
sb.append(",").append(idLast);
}
continue;
}var node;
if (id.startsWith("'") && id.endsWith("'")) id = "\"" + JU.PT.trim(id, "'") + "\"";
if (id.startsWith("\"")) {
id = JU.PT.trim(id, "\"");
var pn = this.panelNodes.size();
for (var j = 0; j < pn; j++) {
node = this.panelNodes.get(j);
if (node.fileName != null && node.fileName.startsWith(id) || node.frameTitle != null && node.frameTitle.startsWith(id)) {
this.addSpecToList(node.pd(), userYFactor, -1, speclist, isView);
sb.append(",").append(node.id);
}}
continue;
}if (!id.contains(".")) id = id0 + id;
node = JSV.common.PanelNode.findNodeById(id, this.panelNodes);
if (node == null) continue;
idLast = id;
this.addSpecToList(node.pd(), userYFactor, isubspec, speclist, isView);
sb.append(",").append(id);
if (isubspec > 0) sb.append(".").appendI(isubspec);
}
if (isView && speclist.size() > 0) {
var node = JSV.common.PanelNode.findNodeById(sb.substring(1), this.panelNodes);
if (node != null) {
this.setNode(node);
speclist.clear();
}}return (isNone ? "NONE" : sb.length() > 0 ? sb.toString().substring(1) : null);
}, "~S,JU.Lst,~B");
Clazz.defineMethod(c$, "addSpecToList", 
function(pd, userYFactor, isubspec, list, isView){
if (isView) {
var spec = pd.getSpectrumAt(0);
spec.setUserYFactor(Double.isNaN(userYFactor) ? 1 : userYFactor);
pd.addToList(isubspec - 1, list);
} else {
pd.selectFromEntireSet(isubspec - 1);
}}, "JSV.common.PanelData,~N,~N,JU.Lst,~B");
Clazz.defineMethod(c$, "getSolutionColor", 
function(asFitted){
var spectrum = this.pd().getSpectrum();
var vi = (spectrum.canShowSolutionColor() ? JSV.common.JSViewer.getInterface("JSV.common.Visible") : null);
return (vi == null ? -1 : vi.getColour(spectrum, asFitted));
}, "~B");
Clazz.defineMethod(c$, "openDataOrFile", 
function(data, name, specs, strUrl, firstSpec, lastSpec, isAppend, id){
if ("NONE".equals(name)) {
this.close("View*");
return 0;
}this.si.writeStatus("");
var filePath = null;
var newPath = null;
var fileName = null;
var isView = false;
if (strUrl != null && strUrl.startsWith("cache://")) {
{
data = Jmol.Cache.get(name = strUrl);
}}var file = null;
if (data != null) {
try {
fileName = name;
newPath = filePath = JSV.common.JSVFileManager.getFullPathName(name);
} catch (e) {
if (Clazz.exceptionOf(e,"JSV.exception.JSVException")){
} else {
throw e;
}
}
} else if (specs != null) {
isView = true;
newPath = fileName = filePath = "View" + (++this.nViews);
} else if (strUrl != null) {
try {
file = this.apiPlatform.newFile(strUrl);
var u =  new java.net.URL(JSV.common.JSVFileManager.appletDocumentBase, strUrl, null);
filePath = u.toString();
this.recentURL = filePath;
fileName = JSV.common.JSVFileManager.getTagName(filePath);
} catch (e) {
if (Clazz.exceptionOf(e,"java.net.MalformedURLException")){
fileName = file.getName();
newPath = filePath = file.getFullPath();
this.recentURL = null;
} else {
throw e;
}
}
}var pt = -1;
if ((pt = JSV.common.PanelNode.isOpen(this.panelNodes, filePath)) >= 0 || (pt = JSV.common.PanelNode.isOpen(this.panelNodes, strUrl)) >= 0) {
if (isView) {
--this.nViews;
this.setNode(this.panelNodes.get(pt));
} else {
this.si.writeStatus(filePath + " is already open");
}return -1;
}if (!isAppend && !isView) this.close("all");
this.si.setCursor(3);
try {
this.si.siSetCurrentSource(isView ? JSV.source.JDXSource.createView(specs) : JSV.source.JDXReader.createJDXSource(file, data, filePath, this.obscureTitleFromUser === Boolean.TRUE, this.loadImaginary, firstSpec, lastSpec, this.nmrMaxY));
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
{
alert(e.toString())
}this.si.setCursor(0);
if (this.isApplet) {
this.selectedPanel.showMessage(e.toString(), "Error Opening File");
}return -3;
} else {
throw e;
}
}
this.si.setCursor(0);
System.gc();
if (newPath == null) {
newPath = this.currentSource.getFilePath();
if (newPath != null) fileName = newPath.substring(newPath.lastIndexOf("/") + 1);
} else {
this.currentSource.setFilePath(newPath);
}if (id == null && !isView) id = newPath;
if (id != null) this.currentSource.setID(id);
this.si.siSetLoaded(fileName, newPath);
var spec = this.currentSource.getJDXSpectrum(0);
if (spec == null) {
return -4;
}specs = this.currentSource.getSpectra();
JSV.common.Spectrum.process(specs, this.irMode);
var autoOverlay = this.interfaceOverlaid || spec.isAutoOverlayFromJmolClick();
var combine = isView || autoOverlay && this.currentSource.isCompoundSource;
if (combine) {
this.combineSpectra((isView ? strUrl : null));
} else {
this.splitSpectra();
}this.pd().setTaintedAll();
if (!isView) this.si.siUpdateRecentMenus(filePath);
return 0;
}, "~O,~S,JU.Lst,~S,~N,~N,~B,~S");
Clazz.defineMethod(c$, "close", 
function(value){
var n0 = 0;
var pt = (value == null ? -2 : value.indexOf(">"));
if (pt > 0) {
n0 = JU.PT.parseInt(value.substring(pt + 1).trim());
value = value.substring(0, pt).trim();
}if ("*".equals(value)) value = "all";
var isAll = (value === "all");
if (value == null || n0 == 0 && value.equalsIgnoreCase("all")) {
this.closeSource(null);
return;
}var isViews = value.equalsIgnoreCase("views");
var list =  new JU.Lst();
var source;
value = value.$replace('\\', '/');
var n = this.panelNodes.size();
var nMax = n - n0;
if (value.endsWith("*")) {
value = value.substring(0, value.length - 1);
for (var i = n; --i >= 0; ) if (this.panelNodes.get(i).fileName.startsWith(value)) list.addLast(this.panelNodes.get(i).source);

} else if (value.equalsIgnoreCase("selected")) {
var lastSource = null;
for (var i = n; --i >= 0; ) {
source = this.panelNodes.get(i).source;
if (this.panelNodes.get(i).isSelected && (lastSource == null || lastSource !== source)) list.addLast(source);
lastSource = source;
}
} else if (isAll || isViews || value.equalsIgnoreCase("simulations")) {
for (var n1 = 0, i = n; --i >= 0 && n1 < nMax; ) if (isAll ? true : isViews ? this.panelNodes.get(i).isView : this.panelNodes.get(i).isSimulation) {
list.addLast(this.panelNodes.get(i).source);
n1++;
}
} else {
source = (value.length == 0 ? this.currentSource : JSV.common.PanelNode.findSourceByNameOrId(value, this.panelNodes));
if (source != null) list.addLast(source);
}for (var i = list.size(); --i >= 0; ) this.closeSource(list.get(i));

if (this.selectedPanel == null && this.panelNodes.size() > 0) this.si.siSetSelectedPanel(JSV.common.PanelNode.getLastFileFirstNode(this.panelNodes));
}, "~S");
Clazz.defineMethod(c$, "execLoad", 
function(value, script){
var applet = this.html5Applet;
var isID = false;
if (isID) {
applet._search(value);
return;
}var tokens = JSV.common.ScriptToken.getTokens(value);
var filename = tokens.get(0);
var id = null;
var pt = 0;
if (filename.equalsIgnoreCase("ID")) {
id = JU.PT.trimQuotes(tokens.get(1));
filename = tokens.get(2);
pt = 2;
}var isAppend = filename.equalsIgnoreCase("APPEND");
var isCheck = filename.equalsIgnoreCase("CHECK");
if (isAppend || isCheck) pt++;
if (pt > 0) filename = tokens.get(pt);
if (script == null) script = this.defaultLoadScript;
if (filename.equals("?")) {
this.openFileFromDialog(isAppend, false, null, script);
return;
}if (filename.equals("http://?")) {
this.openFileFromDialog(isAppend, true, null, null);
return;
}if (filename.equals("$?") || filename.equals("$H1?")) {
this.openFileFromDialog(isAppend, true, "H1", null);
return;
}if (filename.equals("$C13?")) {
this.openFileFromDialog(isAppend, true, "C13", null);
return;
}var isH1 = filename.equalsIgnoreCase("MOL") || filename.equalsIgnoreCase("H1");
var isC13 = filename.equalsIgnoreCase("C13");
if (isH1 || isC13) filename = "http://SIMULATION/" + (isH1 ? "H1/" : "C13/") + "MOL=" + JU.PT.trimQuotes(tokens.get(++pt));
if (!isCheck && !isAppend) {
if (filename.equals("\"\"") && this.currentSource != null) filename = this.currentSource.getFilePath();
this.close("all");
}filename = JU.PT.trimQuotes(filename);
var isSimulation = filename.startsWith("$");
if (isSimulation) {
if (!filename.startsWith("$H1") && !filename.startsWith("$C13")) filename = "$H1/" + filename.substring(1);
filename = "http://SIMULATION/" + filename.substring(1);
}var firstSpec = (pt + 1 < tokens.size() ? Integer.$valueOf(tokens.get(++pt)).intValue() : -1);
var lastSpec = (pt + 1 < tokens.size() ? Integer.$valueOf(tokens.get(++pt)).intValue() : firstSpec);
this.si.siOpenDataOrFile(null, null, null, filename, firstSpec, lastSpec, isAppend, script, id);
if (isSimulation) {
this.close("views");
this.execView("*", true);
}}, "~S,~S");
Clazz.defineMethod(c$, "combineSpectra", 
function(name){
var source = this.currentSource;
var specs = source.getSpectra();
var haveSimulation = false;
for (var i = specs.size(); --i >= 0; ) if (specs.get(i).isSimulation) {
haveSimulation = true;
break;
}
var jsvp = this.si.siGetNewJSVPanel2(specs);
jsvp.setTitle(source.getTitle());
if (jsvp.getTitle().equals("")) {
jsvp.getPanelData().setViewTitle(source.getFilePath());
jsvp.setTitle(name);
}this.si.siSetPropertiesFromPreferences(jsvp, true);
this.spectraTree.createTree(++this.fileCount, source,  Clazz.newArray(-1, [jsvp])).getPanelNode().isView = true;
var node = JSV.common.PanelNode.findNode(this.selectedPanel, this.panelNodes);
node.setFrameTitle(name);
node.isView = true;
if (this.autoShowLegend && this.pd().getNumberOfGraphSets() == 1) node.setLegend(this.getDialog(JSV.common.Annotation.AType.OverlayLegend, null));
this.si.siSetMenuEnables(node, false);
if (haveSimulation) this.pd().splitStack(true);
}, "~S");
Clazz.defineMethod(c$, "closeSource", 
function(source){
var rootNode = this.spectraTree.getRootNode();
var fileName = (source == null ? null : source.getFilePath());
var toDelete =  new JU.Lst();
var enume = rootNode.children();
while (enume.hasMoreElements()) {
var node = enume.nextElement();
if (fileName == null || node.getPanelNode().source.matchesFilePath(fileName)) {
JU.Logger.info("Closing " + node.getPanelNode().source.getFilePath());
for (var e = node.children(); e.hasMoreElements(); ) {
var childNode = e.nextElement();
toDelete.addLast(childNode);
this.panelNodes.removeObj(childNode.getPanelNode());
}
toDelete.addLast(node);
if (fileName != null) break;
}}
this.spectraTree.deleteNodes(toDelete);
if (source == null) {
if (this.currentSource != null) this.currentSource.dispose();
this.currentSource = null;
if (this.selectedPanel != null) this.selectedPanel.dispose();
} else {
}if (this.currentSource === source) {
this.si.siSetSelectedPanel(null);
this.si.siSetCurrentSource(null);
}var max = 0;
for (var i = 0; i < this.panelNodes.size(); i++) {
var f = JU.PT.parseFloat(this.panelNodes.get(i).id);
if (f >= max + 1) max = Clazz.doubleToInt(Math.floor(f));
}
this.fileCount = max;
System.gc();
if (JU.Logger.debugging) JU.Logger.checkMemory();
this.si.siSourceClosed(source);
}, "JSV.source.JDXSource");
Clazz.defineMethod(c$, "setFrameAndTreeNode", 
function(i){
if (this.panelNodes == null || i < 0 || i >= this.panelNodes.size()) return;
this.setNode(this.panelNodes.get(i));
}, "~N");
Clazz.defineMethod(c$, "selectFrameNode", 
function(jsvp){
var node = JSV.common.PanelNode.findNode(jsvp, this.panelNodes);
if (node == null) return null;
this.spectraTree.setPath(this.spectraTree.newTreePath(node.treeNode.getPath()));
this.setOverlayLegendVisibility(null, false);
return node;
}, "JSV.api.JSVPanel");
Clazz.defineMethod(c$, "setSpectrum", 
function(value){
if (value.indexOf('.') >= 0) {
var node = JSV.common.PanelNode.findNodeById(value, this.panelNodes);
if (node == null) return false;
this.setNode(node);
} else {
var n = JU.PT.parseInt(value);
if (n <= 0) {
this.checkOverlay();
return false;
}this.setFrameAndTreeNode(n - 1);
}return true;
}, "~S");
Clazz.defineMethod(c$, "splitSpectra", 
function(){
var source = this.currentSource;
var specs = source.getSpectra();
var panels =  new Array(specs.size());
var jsvp = null;
for (var i = 0; i < specs.size(); i++) {
var spec = specs.get(i);
jsvp = this.si.siGetNewJSVPanel(spec);
this.si.siSetPropertiesFromPreferences(jsvp, true);
panels[i] = jsvp;
}
this.spectraTree.createTree(++this.fileCount, source, panels);
this.si.siGetNewJSVPanel(null);
var node = JSV.common.PanelNode.findNode(this.selectedPanel, this.panelNodes);
this.si.siSetMenuEnables(node, true);
});
Clazz.defineMethod(c$, "selectedTreeNode", 
function(node){
if (node == null) {
return;
}if (node.isLeaf()) {
this.setNode(node.getPanelNode());
} else {
System.out.println("not a leaf");
}this.si.siSetCurrentSource(node.getPanelNode().source);
}, "JSV.api.JSVTreeNode");
Clazz.defineMethod(c$, "dispose", 
function(){
this.fileHelper = null;
if (this.viewDialog != null) this.viewDialog.dispose();
this.viewDialog = null;
if (this.overlayLegendDialog != null) this.overlayLegendDialog.dispose();
this.overlayLegendDialog = null;
if (this.jsvpPopupMenu != null) {
this.jsvpPopupMenu.jpiDispose();
this.jsvpPopupMenu = null;
}if (this.panelNodes != null) for (var i = this.panelNodes.size(); --i >= 0; ) {
this.panelNodes.get(i).dispose();
this.panelNodes.removeItemAt(i);
}
});
Clazz.defineMethod(c$, "runScript", 
function(script){
if (this.scriptQueue == null) this.si.siProcessCommand(script);
 else this.scriptQueue.addLast(script);
}, "~S");
Clazz.defineMethod(c$, "requestRepaint", 
function(){
if (this.selectedPanel != null) this.repaintManager.refresh();
});
Clazz.defineMethod(c$, "repaintDone", 
function(){
this.repaintManager.repaintDone();
});
Clazz.defineMethod(c$, "checkOverlay", 
function(){
if (this.mainPanel != null) this.markSelectedPanels(this.panelNodes, this.mainPanel.getCurrentPanelIndex());
this.viewDialog = this.getDialog(JSV.common.Annotation.AType.Views, null);
});
Clazz.defineMethod(c$, "markSelectedPanels", 
function(panelNodes, ip){
for (var i = panelNodes.size(); --i >= 0; ) panelNodes.get(i).isSelected = (ip == i);

}, "JU.Lst,~N");
Clazz.defineMethod(c$, "execOverlayOffsetY", 
function(offset){
if (offset == -2147483648) {
if (this.selectedPanel == null) return;
var soffset = this.selectedPanel.getInput("Enter a vertical offset in percent for stacked plots", "Overlay", "" + this.recentStackPercent);
var f = JU.PT.parseFloat(soffset);
if (Float.isNaN(f)) return;
offset = Clazz.floatToInt(f);
}this.recentStackPercent = offset;
this.parameters.viewOffset = offset;
if (this.isClosed()) this.pd().setYStackOffsetPercent(offset);
}, "~N");
Clazz.defineMethod(c$, "execScriptInline", 
function(script){
if (script.length > 0) script = script.substring(6).trim();
if (script.length == 0) script = this.selectedPanel.getInput("Enter a JSpecView script", "Script", this.recentScript);
if (script == null) return;
this.recentScript = script;
this.runScriptNow(script);
}, "~S");
Clazz.defineMethod(c$, "setDisplay", 
function(canvas){
this.apiPlatform.setViewer(this, this.display = canvas);
var wh =  Clazz.newIntArray (2, 0);
this.apiPlatform.getFullScreenDimensions(canvas, wh);
this.setScreenDimension(wh[0], wh[1]);
}, "~O");
Clazz.defineMethod(c$, "setScreenDimension", 
function(width, height){
height = Math.min(height, this.maximumSize);
width = Math.min(width, this.maximumSize);
if (this.screenWidth == width && this.screenHeight == height) return;
this.resizeImage(width, height);
}, "~N,~N");
Clazz.defineMethod(c$, "resizeImage", 
function(width, height){
if (width > 0) {
this.screenWidth = width;
this.screenHeight = height;
} else {
width = (this.screenWidth == 0 ? this.screenWidth = 500 : this.screenWidth);
height = (this.screenHeight == 0 ? this.screenHeight = 500 : this.screenHeight);
}this.g2d.setWindowParameters(width, height);
}, "~N,~N");
Clazz.defineMethod(c$, "updateJS", 
function(){
if (this.selectedPanel != null) this.selectedPanel.paintComponent(this.apiPlatform.getGraphics(null));
});
Clazz.defineMethod(c$, "processMouseEvent", 
function(id, x, y, modifiers, time){
return (this.selectedPanel != null && this.selectedPanel.processMouseEvent(id, x, y, modifiers, time));
}, "~N,~N,~N,~N,~N");
Clazz.defineMethod(c$, "processTwoPointGesture", 
function(touches){
if (!this.isClosed()) this.selectedPanel.processTwoPointGesture(touches);
}, "~A");
Clazz.defineMethod(c$, "getApplet", 
function(){
return this.html5Applet;
});
Clazz.defineMethod(c$, "openFileAsyncSpecial", 
function(fileName, flags){
var ans = (this.currentSource == null ? "NO" : this.getDialogManager().getDialogInput(this, "Do you want to append this file? (Answer NO to replace.)", "Drag/Drop Action", 3, null, null, "YES"));
if (ans == null) return;
var pre = (ans.toLowerCase().startsWith("y") ? "append" : "");
var post = (pre === "" ? "" : "; view *");
this.runScript("load " + pre + " \"" + fileName + "\"" + post);
}, "~S,~N");
Clazz.defineMethod(c$, "getHeight", 
function(){
return this.screenHeight;
});
Clazz.defineMethod(c$, "getWidth", 
function(){
return this.screenWidth;
});
Clazz.defineMethod(c$, "getPlatformInterface", 
function(type){
return JSV.common.JSViewer.getInterface("JSV." + (JSV.common.JSViewer.isJS ? "js2d.Js" : "java.Awt") + type);
}, "~S");
Clazz.defineMethod(c$, "getDialogManager", 
function(){
if (this.dialogManager != null) return this.dialogManager;
this.dialogManager = this.getPlatformInterface("DialogManager");
return this.dialogManager.set(this);
});
Clazz.defineMethod(c$, "getDialog", 
function(type, spec){
var root = "JSV.dialog.";
switch (type) {
case JSV.common.Annotation.AType.Integration:
return (JSV.common.JSViewer.getInterface(root + "IntegrationDialog")).setParams("Integration for " + spec, this, spec);
case JSV.common.Annotation.AType.Measurements:
return (JSV.common.JSViewer.getInterface(root + "MeasurementsDialog")).setParams("Measurements for " + spec, this, spec);
case JSV.common.Annotation.AType.PeakList:
return (JSV.common.JSViewer.getInterface(root + "PeakListDialog")).setParams("Peak List for " + spec, this, spec);
case JSV.common.Annotation.AType.OverlayLegend:
return this.overlayLegendDialog = (JSV.common.JSViewer.getInterface(root + "OverlayLegendDialog")).setParams(this.pd().getViewTitle(), this, null);
case JSV.common.Annotation.AType.Views:
return this.viewDialog = (JSV.common.JSViewer.getInterface(root + "ViewsDialog")).setParams("View/Combine/Close Spectra", this, null);
default:
return null;
}
}, "JSV.common.Annotation.AType,JSV.common.Spectrum");
Clazz.defineMethod(c$, "show", 
function(what){
this.getDialogManager();
if (what.equals("properties")) {
this.dialogManager.showProperties(null, this.pd().getSpectrum());
} else if (what.equals("errors")) {
this.dialogManager.showSourceErrors(null, this.currentSource);
} else if (what.equals("source")) {
if (this.currentSource == null) {
if (this.panelNodes.size() > 0) this.dialogManager.showMessageDialog(null, "Please Select a Spectrum", "Select Spectrum", 0);
return;
}this.dialogManager.showSource(this, this.pd().getSpectrum());
} else if (what.startsWith("solutioncolorfill")) {
if (what.indexOf("all") >= 0) {
for (var i = this.panelNodes.size(); --i >= 0; ) this.panelNodes.get(i).pd().setSolutionColor(what);

} else {
this.pd().setSolutionColor(what);
}} else if (what.startsWith("solutioncolor")) {
var msg = this.getSolutionColorStr(what.indexOf("false") < 0);
msg = "background-color:rgb(" + msg + ")'><br />Predicted Solution Colour- RGB(" + msg + ")<br /><br />";
if (JSV.common.JSViewer.isJS) {
this.dialogManager.showMessage(this, "<div style='width:100%;height:100%;" + msg + "</div>", "Predicted Colour");
} else {
this.selectedPanel.showMessage("<html><body style='" + msg + "</body></html>", "Predicted Colour");
}}}, "~S");
Clazz.defineMethod(c$, "getDialogPrint", 
function(isJob){
if (!JSV.common.JSViewer.isJS) try {
var pl = (this.getPlatformInterface("PrintDialog")).set(this.offWindowFrame, this.lastPrintLayout, isJob).getPrintLayout();
if (pl != null) this.lastPrintLayout = pl;
return pl;
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
return  new JSV.common.PrintLayout(this.pd());
}, "~B");
Clazz.defineMethod(c$, "setIRmode", 
function(mode){
if (mode.equals("AtoT")) {
this.irMode = JSV.common.Spectrum.IRMode.TO_TRANS;
} else if (mode.equals("TtoA")) {
this.irMode = JSV.common.Spectrum.IRMode.TO_ABS;
} else {
this.irMode = JSV.common.Spectrum.IRMode.getMode(mode);
}}, "~S");
Clazz.defineMethod(c$, "getOptionFromDialog", 
function(items, title, label){
return this.getDialogManager().getOptionFromDialog(null, items, this.selectedPanel, title, label);
}, "~A,~S,~S");
Clazz.defineMethod(c$, "print", 
function(fileName){
return this.execWrite("PDF \"" + fileName + "\"");
}, "~S");
Clazz.defineMethod(c$, "execWrite", 
function(value){
if (JSV.common.JSViewer.isJS && value == null) value = "PDF";
var msg = (JSV.common.JSViewer.getInterface("JSV.export.Exporter")).write(this, value == null ? null : JSV.common.ScriptToken.getTokens(value), false);
this.si.writeStatus(msg);
return msg;
}, "~S");
Clazz.defineMethod(c$, "$export", 
function(type, n){
if (type == null) type = "XY";
var pd = this.pd();
var nMax = pd.getNumberOfSpectraInCurrentSet();
if (n < -1 || n >= nMax) return "Maximum spectrum index (0-based) is " + (nMax - 1) + ".";
var spec = (n < 0 ? pd.getSpectrum() : pd.getSpectrumAt(n));
try {
return (JSV.common.JSViewer.getInterface("JSV.export.Exporter")).exportTheSpectrum(this, JSV.common.ExportType.getType(type), null, spec, 0, spec.getXYCoords().length - 1, null, type.equalsIgnoreCase("PDF"));
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
JU.Logger.error(e.toString());
return null;
} else {
throw e;
}
}
}, "~S,~N");
Clazz.overrideMethod(c$, "postByteArray", 
function(fileName, bytes){
return JSV.common.JSVFileManager.postByteArray(fileName, bytes);
}, "~S,~A");
Clazz.defineMethod(c$, "getOutputChannel", 
function(fileName, isBinary){
var os = null;
{
while (fileName.startsWith("/")) fileName =
fileName.substring(1);
}return  new JU.OC().setParams(this, fileName, !isBinary, os);
}, "~S,~B");
c$.getInterface = Clazz.defineMethod(c$, "getInterface", 
function(name){
try {
var x = Clazz._4Name(name);
return (x == null ? null : x.newInstance());
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
JU.Logger.error("Interface.java Error creating instance for " + name + ": \n" + e);
return null;
} else {
throw e;
}
}
}, "~S");
Clazz.defineMethod(c$, "showMessage", 
function(msg){
if (this.selectedPanel != null && msg != null) this.selectedPanel.showMessage(msg, null);
}, "~S");
Clazz.defineMethod(c$, "openFileFromDialog", 
function(isAppend, isURL, simulationType, script){
var url = null;
if (simulationType != null) {
url = this.fileHelper.getUrlFromDialog("Enter the name or identifier of a compound", this.recentSimulation);
if (url == null) return;
this.recentSimulation = url;
url = "$" + simulationType + "/" + url;
} else if (isURL) {
url = this.fileHelper.getUrlFromDialog("Enter the URL of a JCAMP-DX File", this.recentURL == null ? this.recentOpenURL : this.recentURL);
if (url == null) return;
this.recentOpenURL = url;
} else {
var userData =  Clazz.newArray(-1, [Boolean.$valueOf(isAppend), script]);
var file = this.fileHelper.showFileOpenDialog(this.mainPanel, userData);
if (file != null) url = file.getFullPath();
}if (url != null) this.runScriptNow("load " + (isAppend ? "APPEND " : "") + "\"" + url + "\"" + (script == null ? "" : ";" + script));
}, "~B,~B,~S,~S");
Clazz.defineMethod(c$, "openFile", 
function(fileName, closeFirst){
if (closeFirst && this.panelNodes != null) {
var source = JSV.common.PanelNode.findSourceByNameOrId(( new java.io.File(fileName)).getAbsolutePath(), this.panelNodes);
if (source != null) this.closeSource(source);
}this.si.siOpenDataOrFile(null, null, null, fileName, -1, -1, true, this.defaultLoadScript, null);
}, "~S,~B");
Clazz.defineMethod(c$, "selectPanel", 
function(jsvp, panelNodes){
var iPanel = -1;
if (panelNodes != null) {
for (var i = panelNodes.size(); --i >= 0; ) {
var j = panelNodes.get(i).jsvp;
if (j === jsvp) {
iPanel = i;
} else {
j.setEnabled(false);
j.setFocusable(false);
j.getPanelData().closeAllDialogsExcept(JSV.common.Annotation.AType.NONE);
}}
this.markSelectedPanels(panelNodes, iPanel);
}return iPanel;
}, "JSV.api.JSVPanel,JU.Lst");
Clazz.defineMethod(c$, "checkAutoIntegrate", 
function(){
if (this.autoIntegrate) this.pd().integrateAll(this.parameters);
});
Clazz.defineMethod(c$, "parseInitScript", 
function(params){
if (params == null) params = "";
var allParamTokens =  new JSV.common.ScriptTokenizer(params, true);
if (JU.Logger.debugging) {
JU.Logger.info("Running in DEBUG mode");
}while (allParamTokens.hasMoreTokens()) {
var token = allParamTokens.nextToken();
var eachParam =  new JSV.common.ScriptTokenizer(token, false);
var key = eachParam.nextToken();
if (key.equalsIgnoreCase("SET")) key = eachParam.nextToken();
key = key.toUpperCase();
var st = JSV.common.ScriptToken.getScriptToken(key);
var value = JSV.common.ScriptToken.getValue(st, eachParam, token);
JU.Logger.info("KEY-> " + key + " VALUE-> " + value + " : " + st);
try {
switch (st) {
default:
this.parameters.set(null, st, value);
break;
case JSV.common.ScriptToken.UNKNOWN:
break;
case JSV.common.ScriptToken.APPLETID:
this.fullName = this.appletName + "__" + (this.appletName = value) + "__";
var applet = null;
{
self.Jmol && (applet = Jmol._applets[value]);
}this.html5Applet = applet;
break;
case JSV.common.ScriptToken.AUTOINTEGRATE:
this.autoIntegrate = JSV.common.Parameters.isTrue(value);
break;
case JSV.common.ScriptToken.COMPOUNDMENUON:
break;
case JSV.common.ScriptToken.APPLETREADYCALLBACKFUNCTIONNAME:
case JSV.common.ScriptToken.COORDCALLBACKFUNCTIONNAME:
case JSV.common.ScriptToken.LOADFILECALLBACKFUNCTIONNAME:
case JSV.common.ScriptToken.PEAKCALLBACKFUNCTIONNAME:
case JSV.common.ScriptToken.SYNCCALLBACKFUNCTIONNAME:
this.si.siExecSetCallback(st, value);
break;
case JSV.common.ScriptToken.ENDINDEX:
this.initialEndIndex = Integer.parseInt(value);
break;
case JSV.common.ScriptToken.INTERFACE:
this.checkOvelayInterface(value);
break;
case JSV.common.ScriptToken.IRMODE:
this.setIRmode(value);
break;
case JSV.common.ScriptToken.MENUON:
this.allowMenu = Boolean.parseBoolean(value);
break;
case JSV.common.ScriptToken.OBSCURE:
if (this.obscureTitleFromUser == null) this.obscureTitleFromUser = Boolean.$valueOf(value);
break;
case JSV.common.ScriptToken.STARTINDEX:
this.initialStartIndex = Integer.parseInt(value);
break;
case JSV.common.ScriptToken.SYNCID:
this.fullName = this.appletName + "__" + (this.syncID = value) + "__";
break;
}
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
}
}, "~S");
Clazz.defineMethod(c$, "getSolutionColorStr", 
function(asFit){
var pt = JU.CU.colorPtFromInt(this.getSolutionColor(asFit), null);
return Clazz.floatToInt(pt.x) + "," + Clazz.floatToInt(pt.y) + "," + Clazz.floatToInt(pt.z);
}, "~B");
Clazz.defineMethod(c$, "checkCommandLineForTip", 
function(c, cmd, oneLineOnly){
var isHelp = (c == '\1');
if (!isHelp && c != '\0') {
if (c != '\t' && (c == '\n' || c.charCodeAt(0) < 32 || c.charCodeAt(0) > 126)) return null;
cmd += (Character.isISOControl(c) ? "" : "" + c);
}var tip;
if (cmd.indexOf(";") >= 0) cmd = cmd.substring(cmd.lastIndexOf(";") + 1);
var ret = null;
while (cmd.startsWith(" ")) cmd = cmd.substring(1);

if (cmd.length == 0 && !isHelp) {
tip = "";
} else {
var tokens = JSV.common.ScriptToken.getTokens(cmd);
if (tokens.size() == 0 && !isHelp) return "";
var isExact = (cmd.endsWith(" ") || tokens.size() > 1 && oneLineOnly);
var list = JSV.common.ScriptToken.getScriptTokenList(tokens.size() == 0 ? null : tokens.get(0), isExact);
switch (list.size()) {
case 0:
tip = "?";
break;
case 1:
var st = list.get(0);
tip = st.getTip();
try {
if (tip.indexOf("TRUE") >= 0) tip = " (" + this.parameters.getBoolean(st) + ")";
 else if (st.name().indexOf("COLOR") >= 0) tip = " (" + JU.CU.toRGBHexString(this.parameters.getElementColor(st)) + ")";
 else tip = "";
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
return null;
} else {
throw e;
}
}
if (c == '\t' || isExact || !oneLineOnly) {
tip = st.name() + " " + st.getTip() + tip + " " + st.getDescription();
if (c == '\t') ret = st.name() + " ";
break;
}tip = st.name() + " " + tip;
break;
default:
tip = JSV.common.ScriptToken.getNameList(list);
}
}if (oneLineOnly) {
this.si.writeStatus(tip);
} else {
ret = tip;
}return ret;
}, "~S,~S,~B");
Clazz.defineMethod(c$, "checkScript", 
function(script){
return this.checkCommandLineForTip('\0', script, false);
}, "~S");
Clazz.defineMethod(c$, "execHelp", 
function(value){
var s = this.checkCommandLineForTip('\1', value, false);
if (s.indexOf(" ") < 0 && s.indexOf(",") > 0) {
var tokens = JU.PT.split(s, ",");
java.util.Arrays.sort(tokens);
s = "";
for (var i = 0; i < tokens.length; i++) {
var st = JSV.common.ScriptToken.getScriptToken(tokens[i]);
s += tokens[i] + " " + st.getTip() + "\n  " + st.getDescription() + "\n\n";
}
this.getDialogManager().showMessage(null, s, "HELP " + value);
} else {
this.selectedPanel.showMessage(s, "Help " + value);
}System.out.println(s);
}, "~S");
c$.testScript = "<PeakData  index=\"1\" title=\"\" model=\"~1.1\" type=\"1HNMR\" xMin=\"3.2915\" xMax=\"3.2965\" atoms=\"15,16,17,18,19,20\" multiplicity=\"\" integral=\"1\"> src=\"JPECVIEW\" file=\"http://SIMULATION/$caffeine\"";
c$.isJS = false;
c$.isSwingJS = false;
c$.jmolObject = null;
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
