Clazz.declarePackage("JSV.source");
Clazz.load(["JSV.api.SourceReader", "JU.SB"], "JSV.source.XMLReader", ["JU.Lst", "JSV.common.Coordinate", "$.Spectrum", "JSV.source.JDXReader", "$.XMLParser", "JU.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.source = null;
this.filePath = "";
this.parser = null;
this.tagName = "START";
this.attrList = "";
this.title = "";
this.owner = "UNKNOWN";
this.origin = "UNKNOWN";
this.tmpEnd = "END";
this.molForm = "";
this.techname = "";
this.npoints = -1;
this.samplenum = -1;
this.yaxisData = null;
this.xaxisData = null;
this.xUnits = "";
this.yUnits = "ARBITRARY UNITS";
this.vendor = "na";
this.modelType = "MODEL UNKNOWN";
this.LongDate = "";
this.pathlength = "na";
this.identifier = "";
this.plLabel = "";
this.resolution = "na";
this.resLabel = "";
this.LocName = "";
this.LocContact = "";
this.casName = "";
this.sampleowner = "";
this.obNucleus = "";
this.strObFreq = "";
this.increasing = false;
this.continuous = false;
this.ivspoints = 0;
this.evspoints = 0;
this.sampleRefNum = 0;
this.deltaX = 1.7976931348623157E308;
this.xFactor = 1.7976931348623157E308;
this.yFactor = 1.7976931348623157E308;
this.firstX = 1.7976931348623157E308;
this.lastX = 1.7976931348623157E308;
this.firstY = 1.7976931348623157E308;
this.obFreq = 1.7976931348623157E308;
this.refPoint = 1.7976931348623157E308;
this.casRN = "";
this.sampleID = null;
this.errorLog = null;
Clazz.instantialize(this, arguments);}, JSV.source, "XMLReader", null, JSV.api.SourceReader);
Clazz.prepareFields (c$, function(){
this.errorLog =  new JU.SB();
});
Clazz.makeConstructor(c$, 
function(){
});
Clazz.overrideMethod(c$, "getSource", 
function(filePath, br){
this.filePath = filePath;
return this.getXML(br);
}, "~S,java.io.BufferedReader");
Clazz.defineMethod(c$, "getSimpleXmlReader", 
function(br){
this.parser =  new JSV.source.XMLParser(br);
}, "java.io.BufferedReader");
Clazz.defineMethod(c$, "checkStart", 
function(){
if (this.parser.peek() == 1) return;
var errMsg = "Error: XML <xxx> not found at beginning of file; not an XML document?";
this.errorLog.append(errMsg);
throw  new java.io.IOException(errMsg);
});
Clazz.defineMethod(c$, "populateVariables", 
function(){
var LDRTable =  new JU.Lst();
var spectrum =  new JSV.common.Spectrum();
spectrum.setTitle(this.title);
spectrum.setJcampdx("5.01");
spectrum.setDataClass("XYDATA");
spectrum.setDataType(this.techname);
spectrum.setContinuous(this.continuous);
spectrum.setIncreasing(this.increasing);
spectrum.setXFactor(this.xFactor);
spectrum.setYFactor(this.yFactor);
spectrum.setLongDate(this.LongDate);
spectrum.setOrigin(this.origin);
spectrum.setOwner(this.owner);
spectrum.setNucleusAndFreq(this.obNucleus, true);
JSV.source.JDXReader.addHeader(LDRTable, "##PATHLENGTH", this.pathlength);
JSV.source.JDXReader.addHeader(LDRTable, "##RESOLUTION", this.resolution);
if (!this.strObFreq.equals("")) JSV.source.JDXReader.addHeader(LDRTable, "##.OBSERVEFREQUENCY", this.strObFreq);
if (!this.obNucleus.equals("")) JSV.source.JDXReader.addHeader(LDRTable, "##.OBSERVENUCLEUS", this.obNucleus);
JSV.source.JDXReader.addHeader(LDRTable, "##$MANUFACTURER", this.vendor);
if (!this.casRN.equals("")) JSV.source.JDXReader.addHeader(LDRTable, "##CASREGISTRYNO", this.casRN);
if (!this.molForm.equals("")) JSV.source.JDXReader.addHeader(LDRTable, "##MOLFORM", this.molForm);
if (!this.modelType.equals("")) JSV.source.JDXReader.addHeader(LDRTable, "##SPECTROMETER/DATA SYSTEM", this.modelType);
spectrum.setHeaderTable(LDRTable);
var xScale = 1;
if (this.obFreq != 1.7976931348623157E308) {
spectrum.setObservedFreq(this.obFreq);
if (this.xUnits.toUpperCase().equals("HZ")) {
this.xUnits = "PPM";
spectrum.setHZtoPPM(true);
xScale = this.obFreq;
}}var xyCoords =  new Array(this.npoints);
for (var x = 0; x < this.npoints; x++) xyCoords[x] =  new JSV.common.Coordinate().set(this.xaxisData[x] / xScale, this.yaxisData[x]);

if (!this.increasing) xyCoords = JSV.common.Coordinate.reverse(xyCoords);
spectrum.setXUnits(this.xUnits);
spectrum.setYUnits(this.yUnits);
spectrum.setXYCoords(xyCoords);
this.source.addJDXSpectrum(this.filePath, spectrum, false);
});
Clazz.defineMethod(c$, "checkPointCount", 
function(){
if (this.continuous && this.npoints < 5) {
System.err.println("Insufficient points to plot");
this.errorLog.append("Insufficient points to plot \n");
this.source.setErrorLog(this.errorLog.toString());
return false;
}return true;
});
Clazz.defineMethod(c$, "processErrors", 
function(type){
this.parser = null;
if (this.errorLog.length() > 0) {
this.errorLog.append("these errors were found in " + type + " \n");
this.errorLog.append("=====================\n");
}this.source.setErrorLog(this.errorLog.toString());
}, "~S");
Clazz.defineMethod(c$, "processXML", 
function(i0, i1){
while (this.parser.hasNext()) {
if (this.parser.nextEvent() != 1) continue;
var theTag = this.parser.getTagName();
var requiresEndTag = this.parser.requiresEndTag();
if (JU.Logger.debugging) JU.Logger.info(this.tagName);
for (var i = i0; i <= i1; i++) if (theTag.equals(JSV.source.XMLReader.tagNames[i])) {
this.process(i, requiresEndTag);
break;
}
}
}, "~N,~N");
Clazz.defineMethod(c$, "process", 
function(tagId, requiresEndTag){
var thisTagName = JSV.source.XMLReader.tagNames[tagId];
try {
this.tagName = this.parser.getTagName();
this.attrList = this.parser.getAttributeList();
if (!this.processTag(tagId) || !requiresEndTag) return;
while (this.parser.hasNext()) {
switch (this.parser.nextEvent()) {
default:
continue;
case 2:
if (this.parser.getEndTag().equals(thisTagName)) {
this.processEndTag(tagId);
return;
}continue;
case 1:
break;
}
this.tagName = this.parser.getTagName();
if (this.tagName.startsWith("!--")) continue;
this.attrList = this.parser.getAttributeList();
if (!this.processTag(tagId)) return;
}
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
var msg = "error reading " + this.tagName + " section: " + e + "\n" + e.getStackTrace();
JU.Logger.error(msg);
this.errorLog.append(msg + "\n");
} else {
throw e;
}
}
}, "~N,~B");
c$.tagNames =  Clazz.newArray(-1, ["audittrail", "experimentstepset", "sampleset", "xx result", "spectrum", "metadatalist", "conditionlist", "parameterlist", "sample", "spectrumdata", "peaklist", "author", "peaklist", "acquisitionnucleus", "effectiveexcitationfield", "spectrum1d", "spectrumAnnotationList", "chemicalcompound", "identifier", "npmrd_id", "structure", "atomlist", "atom", "bondlist", "bond", "atomassignmentlist", "multiplet", "atoms", "multiplicity", "peakList", "peak", "acquisition", "spectrumdataarray", "spectrumlist"]);
});
;//5.0.1-v7 Thu May 08 14:17:10 CDT 2025
