Clazz.declarePackage("JSV.common");
Clazz.load(["java.lang.Enum", "JSV.source.JDXDataObject", "JU.Lst"], "JSV.common.Spectrum", ["java.util.Hashtable", "JU.PT", "JSV.common.Coordinate", "$.Parameters", "$.PeakInfo", "JSV.source.JDXSourceStreamTokenizer", "JU.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.id = "";
this.fillColor = null;
this.subSpectra = null;
this.peakList = null;
this.peakXLabel = null;
this.peakYLabel = null;
this.selectedPeak = null;
this.highlightedPeak = null;
this.convertedSpectrum = null;
this.specShift = 0;
this.userYFactor = 1;
this.currentSubSpectrumIndex = 0;
this.$isForcedSubset = false;
this.exportXAxisLeftToRight = false;
this.titleLabel = null;
Clazz.instantialize(this, arguments);}, JSV.common, "Spectrum", JSV.source.JDXDataObject);
Clazz.prepareFields (c$, function(){
this.peakList =  new JU.Lst();
});
Clazz.makeConstructor(c$, 
function(){
Clazz.superConstructor (this, JSV.common.Spectrum, []);
this.headerTable =  new JU.Lst();
this.xyCoords =  new Array(0);
this.parent = this;
});
Clazz.defineMethod(c$, "dispose", 
function(){
});
Clazz.defineMethod(c$, "isForcedSubset", 
function(){
return this.$isForcedSubset;
});
Clazz.defineMethod(c$, "setId", 
function(id){
this.id = id;
}, "~S");
Clazz.defineMethod(c$, "copy", 
function(){
var newSpectrum =  new JSV.common.Spectrum();
this.copyTo(newSpectrum);
newSpectrum.setPeakList(this.peakList, this.peakXLabel, null);
newSpectrum.fillColor = this.fillColor;
return newSpectrum;
});
Clazz.defineMethod(c$, "getXYCoords", 
function(){
return this.getCurrentSubSpectrum().xyCoords;
});
Clazz.defineMethod(c$, "getPeakList", 
function(){
return this.peakList;
});
Clazz.defineMethod(c$, "setPeakList", 
function(list, peakXLabel, peakYLabel){
this.peakList = list;
this.peakXLabel = peakXLabel;
this.peakYLabel = peakYLabel;
for (var i = list.size(); --i >= 0; ) this.peakList.get(i).spectrum = this;

if (JU.Logger.debugging) JU.Logger.info("Spectrum " + this.getTitle() + " peaks: " + list.size());
return list.size();
}, "JU.Lst,~S,~S");
Clazz.defineMethod(c$, "selectPeakByFileIndex", 
function(filePath, index, atomKey){
if (this.peakList != null && this.peakList.size() > 0 && (atomKey == null || this.sourceID.equals(index))) for (var i = 0; i < this.peakList.size(); i++) if (this.peakList.get(i).checkFileIndex(filePath, index, atomKey)) {
System.out.println("JSV.Spectrum selecting peak by FileIndex " + this + " " + this.peakList.get(i));
return (this.selectedPeak = this.peakList.get(i));
}
return null;
}, "~S,~S,~S");
Clazz.defineMethod(c$, "selectPeakByFilePathTypeModel", 
function(filePath, type, model){
if (this.peakList != null && this.peakList.size() > 0) for (var i = 0; i < this.peakList.size(); i++) if (this.peakList.get(i).checkFileTypeModel(filePath, type, model)) {
System.out.println("JSV.Spectrum selecting peak byFilePathTypeModel " + this + " " + this.peakList.get(i));
return (this.selectedPeak = this.peakList.get(i));
}
return null;
}, "~S,~S,~S");
Clazz.defineMethod(c$, "matchesPeakTypeModel", 
function(type, model){
if (type.equals("ID")) return (this.sourceID.equalsIgnoreCase(model));
if (this.peakList != null && this.peakList.size() > 0) for (var i = 0; i < this.peakList.size(); i++) if (this.peakList.get(i).checkTypeModel(type, model)) return true;

return false;
}, "~S,~S");
Clazz.defineMethod(c$, "setSelectedPeak", 
function(peak){
this.selectedPeak = peak;
}, "JSV.common.PeakInfo");
Clazz.defineMethod(c$, "setHighlightedPeak", 
function(peak){
this.highlightedPeak = peak;
}, "JSV.common.PeakInfo");
Clazz.defineMethod(c$, "getSelectedPeak", 
function(){
return this.selectedPeak;
});
Clazz.defineMethod(c$, "getModelPeakInfoForAutoSelectOnLoad", 
function(){
if (this.peakList != null) for (var i = 0; i < this.peakList.size(); i++) if (this.peakList.get(i).autoSelectOnLoad()) return this.peakList.get(i);

return null;
});
Clazz.defineMethod(c$, "getAssociatedPeakInfo", 
function(xPixel, coord){
this.selectedPeak = this.findPeakByCoord(xPixel, coord);
return (this.selectedPeak == null ? this.getBasePeakInfo() : this.selectedPeak);
}, "~N,JSV.common.Coordinate");
Clazz.defineMethod(c$, "findPeakByCoord", 
function(xPixel, coord){
if (coord != null && this.peakList != null && this.peakList.size() > 0) {
var xVal = coord.getXVal();
var iBest = -1;
var dBest = 1e100;
for (var i = 0; i < this.peakList.size(); i++) {
var d = this.peakList.get(i).checkRange(xPixel, xVal);
if (d < dBest) {
dBest = d;
iBest = i;
}}
if (iBest >= 0) return this.peakList.get(iBest);
}return null;
}, "~N,JSV.common.Coordinate");
Clazz.defineMethod(c$, "getPeakTitle", 
function(){
var s = null;
if (this.highlightedPeak != null) s = this.highlightedPeak.getTitle();
if ((s == null || s.length == 0) && this.selectedPeak != null) s = this.selectedPeak.getTitle();
if (s == null || s.length == 0) s = this.getTitleLabel();
return s;
});
Clazz.defineMethod(c$, "getTitleLabel", 
function(){
if (this.titleLabel != null) return this.titleLabel;
var type = (this.peakList == null || this.peakList.size() == 0 ? this.getQualifiedDataType() : this.peakList.get(0).getType());
if (type != null && type.startsWith("NMR")) {
if (this.nucleusY != null && !this.nucleusY.equals("?")) {
type = "2D" + type;
} else {
type = JSV.source.JDXDataObject.getNominalSpecFreq(this.nucleusX, this.getObservedFreq()) + " MHz " + this.nucleusX + " " + type;
}}return this.titleLabel = (type != null && type.length > 0 ? type + " " : "") + this.getTitle();
});
Clazz.defineMethod(c$, "setNextPeak", 
function(coord, istep){
if (this.peakList == null || this.peakList.size() == 0) return -1;
var x0 = coord.getXVal() + istep * 0.000001;
var ipt1 = -1;
var ipt2 = -1;
var dmin1 = 1.7976931348623157E308 * istep;
var dmin2 = 0;
for (var i = this.peakList.size(); --i >= 0; ) {
var x = this.peakList.get(i).getX();
if (istep > 0) {
if (x > x0 && x < dmin1) {
ipt1 = i;
dmin1 = x;
} else if (x < x0 && x - x0 < dmin2) {
ipt2 = i;
dmin2 = x - x0;
}} else {
if (x < x0 && x > dmin1) {
ipt1 = i;
dmin1 = x;
} else if (x > x0 && x - x0 > dmin2) {
ipt2 = i;
dmin2 = x - x0;
}}}
if (ipt1 < 0) {
if (ipt2 < 0) return -1;
ipt1 = ipt2;
}return ipt1;
}, "JSV.common.Coordinate,~N");
Clazz.defineMethod(c$, "getPercentYValueAt", 
function(x){
if (!this.isContinuous()) return NaN;
return this.getYValueAt(x);
}, "~N");
Clazz.defineMethod(c$, "getYValueAt", 
function(x){
return JSV.common.Coordinate.getYValueAt(this.xyCoords, x);
}, "~N");
Clazz.defineMethod(c$, "setUserYFactor", 
function(userYFactor){
this.userYFactor = userYFactor;
}, "~N");
Clazz.defineMethod(c$, "getUserYFactor", 
function(){
return this.userYFactor;
});
Clazz.defineMethod(c$, "getConvertedSpectrum", 
function(){
return this.convertedSpectrum;
});
Clazz.defineMethod(c$, "setConvertedSpectrum", 
function(spectrum){
this.convertedSpectrum = spectrum;
}, "JSV.common.Spectrum");
c$.taConvert = Clazz.defineMethod(c$, "taConvert", 
function(spectrum, mode){
if (!spectrum.isContinuous()) return spectrum;
switch (mode) {
case JSV.common.Spectrum.IRMode.NO_CONVERT:
return spectrum;
case JSV.common.Spectrum.IRMode.TO_ABS:
if (!spectrum.isTransmittance()) return spectrum;
break;
case JSV.common.Spectrum.IRMode.TO_TRANS:
if (!spectrum.isAbsorbance()) return spectrum;
break;
case JSV.common.Spectrum.IRMode.TOGGLE:
break;
}
var spec = spectrum.getConvertedSpectrum();
return (spec != null ? spec : spectrum.isAbsorbance() ? JSV.common.Spectrum.toT(spectrum) : JSV.common.Spectrum.toA(spectrum));
}, "JSV.common.Spectrum,JSV.common.Spectrum.IRMode");
c$.toT = Clazz.defineMethod(c$, "toT", 
function(spectrum){
if (!spectrum.isAbsorbance()) return null;
var xyCoords = spectrum.getXYCoords();
var newXYCoords =  new Array(xyCoords.length);
if (!JSV.common.Coordinate.isYInRange(xyCoords, 0, 4.0)) xyCoords = JSV.common.Coordinate.normalise(xyCoords, 0, 4.0);
for (var i = 0; i < xyCoords.length; i++) newXYCoords[i] =  new JSV.common.Coordinate().set(xyCoords[i].getXVal(), JSV.common.Spectrum.toTransmittance(xyCoords[i].getYVal()));

return JSV.common.Spectrum.newSpectrum(spectrum, newXYCoords, "TRANSMITTANCE");
}, "JSV.common.Spectrum");
c$.toA = Clazz.defineMethod(c$, "toA", 
function(spectrum){
if (!spectrum.isTransmittance()) return null;
var xyCoords = spectrum.getXYCoords();
var newXYCoords =  new Array(xyCoords.length);
var isPercent = JSV.common.Coordinate.isYInRange(xyCoords, -2, 2);
for (var i = 0; i < xyCoords.length; i++) newXYCoords[i] =  new JSV.common.Coordinate().set(xyCoords[i].getXVal(), JSV.common.Spectrum.toAbsorbance(xyCoords[i].getYVal(), isPercent));

return JSV.common.Spectrum.newSpectrum(spectrum, newXYCoords, "ABSORBANCE");
}, "JSV.common.Spectrum");
c$.newSpectrum = Clazz.defineMethod(c$, "newSpectrum", 
function(spectrum, newXYCoords, units){
var specNew = spectrum.copy();
specNew.setOrigin("JSpecView Converted");
specNew.setOwner("JSpecView Generated");
specNew.setXYCoords(newXYCoords);
specNew.setYUnits(units);
spectrum.setConvertedSpectrum(specNew);
specNew.setConvertedSpectrum(spectrum);
return specNew;
}, "JSV.common.Spectrum,~A,~S");
c$.toAbsorbance = Clazz.defineMethod(c$, "toAbsorbance", 
function(x, isPercent){
return (Math.min(4.0, isPercent ? 2 - JSV.common.Spectrum.log10(x) : -JSV.common.Spectrum.log10(x)));
}, "~N,~B");
c$.toTransmittance = Clazz.defineMethod(c$, "toTransmittance", 
function(x){
return (x <= 0 ? 1 : Math.pow(10, -x));
}, "~N");
c$.log10 = Clazz.defineMethod(c$, "log10", 
function(value){
return Math.log(value) / Math.log(10);
}, "~N");
c$.process = Clazz.defineMethod(c$, "process", 
function(specs, irMode){
if (irMode === JSV.common.Spectrum.IRMode.TO_ABS || irMode === JSV.common.Spectrum.IRMode.TO_TRANS) for (var i = 0; i < specs.size(); i++) specs.set(i, JSV.common.Spectrum.taConvert(specs.get(i), irMode));

return true;
}, "JU.Lst,JSV.common.Spectrum.IRMode");
Clazz.defineMethod(c$, "getSubSpectra", 
function(){
return this.subSpectra;
});
Clazz.defineMethod(c$, "getCurrentSubSpectrum", 
function(){
return (this.subSpectra == null ? this : this.subSpectra.get(this.currentSubSpectrumIndex));
});
Clazz.defineMethod(c$, "advanceSubSpectrum", 
function(dir){
return this.setCurrentSubSpectrum(this.currentSubSpectrumIndex + dir);
}, "~N");
Clazz.defineMethod(c$, "setCurrentSubSpectrum", 
function(n){
return (this.currentSubSpectrumIndex = JSV.common.Coordinate.intoRange(n, 0, this.subSpectra.size() - 1));
}, "~N");
Clazz.defineMethod(c$, "addSubSpectrum", 
function(spectrum, forceSub){
if (!forceSub && (this.is1D() || this.blockID != spectrum.blockID) || !JSV.common.Spectrum.allowSubSpec(this, spectrum)) return false;
this.$isForcedSubset = forceSub;
if (this.subSpectra == null) {
this.subSpectra =  new JU.Lst();
this.addSubSpectrum(this, true);
}this.subSpectra.addLast(spectrum);
spectrum.parent = this;
return true;
}, "JSV.common.Spectrum,~B");
Clazz.defineMethod(c$, "getSubIndex", 
function(){
return (this.subSpectra == null ? -1 : this.currentSubSpectrumIndex);
});
Clazz.defineMethod(c$, "setExportXAxisDirection", 
function(leftToRight){
this.exportXAxisLeftToRight = leftToRight;
}, "~B");
Clazz.defineMethod(c$, "isExportXAxisLeftToRight", 
function(){
return this.exportXAxisLeftToRight;
});
Clazz.defineMethod(c$, "getInfo", 
function(key){
var info =  new java.util.Hashtable();
if ("id".equalsIgnoreCase(key)) {
info.put(key, this.id);
return info;
}var keys = null;
if ("".equals(key)) {
keys = "id specShift header";
}info.put("id", this.id);
JSV.common.Parameters.putInfo(key, info, "specShift", Double.$valueOf(this.specShift));
var justHeader = ("header".equals(key));
if (!justHeader && key != null && keys == null) {
for (var i = this.headerTable.size(); --i >= 0; ) {
var entry = this.headerTable.get(i);
if (entry[0].equalsIgnoreCase(key) || entry[2].equalsIgnoreCase(key)) {
info.put(key, entry[1]);
return info;
}}
}var head =  new java.util.Hashtable();
var list = this.getHeaderRowDataAsArray();
for (var i = 0; i < list.length; i++) {
var label = JSV.source.JDXSourceStreamTokenizer.cleanLabel(list[i][0]);
if (keys != null) {
keys += " " + label;
continue;
}if (key != null && !justHeader && !label.equals(key)) continue;
var val = JSV.common.Spectrum.fixInfoValue(list[i][1]);
if (key == null) {
var data =  new java.util.Hashtable();
data.put("value", val);
data.put("index", Integer.$valueOf(i + 1));
info.put(label, data);
} else {
info.put(label, val);
}}
if (head.size() > 0) info.put("header", head);
if (!justHeader) {
if (keys != null) {
keys += "  titleLabel type isHZToPPM subSpectrumCount";
} else {
JSV.common.Parameters.putInfo(key, info, "titleLabel", this.getTitleLabel());
JSV.common.Parameters.putInfo(key, info, "type", this.getDataType());
JSV.common.Parameters.putInfo(key, info, "isHZToPPM", Boolean.$valueOf(this.isHZtoPPM()));
JSV.common.Parameters.putInfo(key, info, "subSpectrumCount", Integer.$valueOf(this.subSpectra == null ? 0 : this.subSpectra.size()));
}}if (keys != null) info.put("KEYS", keys);
return info;
}, "~S");
c$.fixInfoValue = Clazz.defineMethod(c$, "fixInfoValue", 
function(info){
try {
return (Integer.$valueOf(info));
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
try {
return (Double.$valueOf(info));
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
return info;
}, "~S");
Clazz.defineMethod(c$, "findMatchingPeakInfo", 
function(pi){
for (var i = 0; i < this.peakList.size(); i++) if (this.peakList.get(i).checkTypeMatch(pi)) return this.peakList.get(i);

return null;
}, "JSV.common.PeakInfo");
Clazz.defineMethod(c$, "getBasePeakInfo", 
function(){
return (this.peakList.size() == 0 ?  new JSV.common.PeakInfo() :  new JSV.common.PeakInfo(" baseModel=\"\" " + this.peakList.get(0)));
});
Clazz.defineMethod(c$, "getAxisLabel", 
function(isX){
var label = (isX ? this.peakXLabel : this.peakYLabel);
if (label == null) label = (isX ? this.xLabel : this.yLabel);
if (label == null) label = (isX ? this.xUnits : this.yUnits);
return (label == null ? "" : label.equalsIgnoreCase("WAVENUMBERS") ? "1/cm" : label.equalsIgnoreCase("nanometers") ? "nm" : label);
}, "~B");
Clazz.defineMethod(c$, "findXForPeakNearest", 
function(x){
return JSV.common.Coordinate.findXForPeakNearest(this.xyCoords, x, this.isInverted());
}, "~N");
Clazz.defineMethod(c$, "addSpecShift", 
function(dx){
if (dx != 0) {
this.specShift += dx;
JSV.common.Coordinate.shiftX(this.xyCoords, dx);
if (this.subSpectra != null) for (var i = this.subSpectra.size(); --i >= 0; ) {
var spec = this.subSpectra.get(i);
if (spec !== this && spec !== this.parent) spec.addSpecShift(dx);
}
}return this.specShift;
}, "~N");
c$.allowSubSpec = Clazz.defineMethod(c$, "allowSubSpec", 
function(s1, s2){
return (s1.is1D() == s2.is1D() && s1.xUnits.equalsIgnoreCase(s2.xUnits) && s1.isHNMR() == s2.isHNMR());
}, "JSV.common.Spectrum,JSV.common.Spectrum");
c$.areXScalesCompatible = Clazz.defineMethod(c$, "areXScalesCompatible", 
function(s1, s2, isSubspecCheck, isLinkCheck){
var isNMR1 = s1.isNMR();
if (isNMR1 != s2.isNMR() || s1.isContinuous() != s2.isContinuous() || !isLinkCheck && !JSV.common.Spectrum.areUnitsCompatible(s1.xUnits, s2.xUnits)) return false;
if (isSubspecCheck) {
if (s1.is1D() != s2.is1D()) return false;
} else if (isLinkCheck) {
if (!isNMR1) return true;
} else if (!s1.is1D() || !s2.is1D()) {
return false;
}return (!isNMR1 || s2.is1D() && s1.parent.nucleusX.equals(s2.parent.nucleusX));
}, "JSV.common.Spectrum,JSV.common.Spectrum,~B,~B");
c$.areUnitsCompatible = Clazz.defineMethod(c$, "areUnitsCompatible", 
function(u1, u2){
if (u1.equalsIgnoreCase(u2)) return true;
u1 = u1.toUpperCase();
u2 = u2.toUpperCase();
return (u1.equals("HZ") && u2.equals("PPM") || u1.equals("PPM") && u2.equals("HZ"));
}, "~S,~S");
c$.areLinkableX = Clazz.defineMethod(c$, "areLinkableX", 
function(s1, s2){
return (s1.isNMR() && s2.isNMR() && s1.nucleusX.equals(s2.nucleusX));
}, "JSV.common.Spectrum,JSV.common.Spectrum");
c$.areLinkableY = Clazz.defineMethod(c$, "areLinkableY", 
function(s1, s2){
return (s1.isNMR() && s2.isNMR() && s1.nucleusX.equals(s2.nucleusY));
}, "JSV.common.Spectrum,JSV.common.Spectrum");
Clazz.defineMethod(c$, "getPeakWidth", 
function(){
var w = this.getLastX() - this.getFirstX();
return (w / 100);
});
Clazz.defineMethod(c$, "setSimulated", 
function(filePath){
this.isSimulation = true;
var s = this.sourceID;
if (s.length == 0) s = JU.PT.rep(filePath, "http://SIMULATION/", "");
if (s.indexOf("MOL=") >= 0) s = "";
this.title = "SIMULATED " + JU.PT.rep(s, "$", "");
}, "~S");
Clazz.defineMethod(c$, "setFillColor", 
function(color){
this.fillColor = color;
if (this.convertedSpectrum != null) this.convertedSpectrum.fillColor = color;
}, "javajs.api.GenericColor");
Clazz.overrideMethod(c$, "toString", 
function(){
return this.getTitleLabel() + (this.xyCoords == null ? "" : " xyCoords.length=" + this.xyCoords.length);
});
/*if2*/;(function(){
var c$ = Clazz.declareType(JSV.common.Spectrum, "IRMode", Enum);
c$.getMode = Clazz.defineMethod(c$, "getMode", 
function(value){
switch ((value == null ? 'I' : value.toUpperCase().charAt(0)).charCodeAt(0)) {
case 65:
return JSV.common.Spectrum.IRMode.TO_ABS;
case 84:
return (value.equalsIgnoreCase("TOGGLE") ? JSV.common.Spectrum.IRMode.TOGGLE : JSV.common.Spectrum.IRMode.TO_TRANS);
case 78:
return JSV.common.Spectrum.IRMode.NO_CONVERT;
default:
return JSV.common.Spectrum.IRMode.TOGGLE;
}
}, "~S");
Clazz.defineEnumConstant(c$, "NO_CONVERT", 0, []);
Clazz.defineEnumConstant(c$, "TO_TRANS", 1, []);
Clazz.defineEnumConstant(c$, "TO_ABS", 2, []);
Clazz.defineEnumConstant(c$, "TOGGLE", 3, []);
/*eoif2*/})();
});
;//5.0.1-v7 Wed Jun 03 09:22:38 CDT 2026
