Clazz.declarePackage("JSV.source");
Clazz.load(["JSV.source.XMLReader"], "JSV.source.CMLReader", ["java.util.Vector", "JU.PT", "JSV.source.JDXSource"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.specfound = false;
this.Ydelim = "";
this.peakData = null;
Clazz.instantialize(this, arguments);}, JSV.source, "CMLReader", JSV.source.XMLReader);
Clazz.makeConstructor(c$, 
function(){
Clazz.superConstructor (this, JSV.source.CMLReader, []);
});
Clazz.overrideMethod(c$, "getXML", 
function(br){
try {
this.source =  new JSV.source.JDXSource(0, this.filePath);
this.getSimpleXmlReader(br);
this.processXML(4, 10);
if (!this.checkPointCount()) return null;
this.populateVariables();
} catch (pe) {
if (Clazz.exceptionOf(pe, Exception)){
System.err.println("Error: " + pe);
} else {
throw pe;
}
}
this.processErrors("CML");
try {
br.close();
} catch (e1) {
if (Clazz.exceptionOf(e1,"java.io.IOException")){
} else {
throw e1;
}
}
return this.source;
}, "java.io.BufferedReader");
Clazz.overrideMethod(c$, "processTag", 
function(tagId){
switch (tagId) {
case 4:
this.processSpectrum();
return false;
case 9:
this.processSpectrumData();
return true;
case 10:
this.processPeaks();
return false;
case 8:
this.processSample();
return true;
case 5:
this.processMetadataList();
return true;
case 6:
this.processConditionList();
return true;
case 7:
this.processParameterList();
return true;
case 12:
this.processPeakList();
return true;
default:
System.out.println("CMLSource not processing tag " + JSV.source.XMLReader.tagNames[tagId]);
return false;
}
}, "~N");
Clazz.overrideMethod(c$, "processEndTag", 
function(tagId){
}, "~N");
Clazz.defineMethod(c$, "processSpectrum", 
function(){
if (this.attrList.contains("title")) this.title = this.parser.getAttrValue("title");
 else if (this.attrList.contains("id")) this.title = this.parser.getAttrValue("id");
if (this.attrList.contains("type")) this.techname = this.parser.getAttrValue("type").toUpperCase() + " SPECTRUM";
});
Clazz.defineMethod(c$, "processMetadataList", 
function(){
if (this.tagName.equals("metadata")) {
this.tagName = this.parser.getAttrValueLC("name");
if (this.tagName.contains(":origin")) {
if (this.attrList.contains("content")) this.origin = this.parser.getAttrValue("content");
 else this.origin = this.parser.thisValue();
} else if (this.tagName.contains(":owner")) {
if (this.attrList.contains("content")) this.owner = this.parser.getAttrValue("content");
 else this.owner = this.parser.thisValue();
} else if (this.tagName.contains("observenucleus")) {
if (this.attrList.contains("content")) this.obNucleus = this.parser.getAttrValue("content");
 else this.obNucleus = this.parser.thisValue();
}}});
Clazz.defineMethod(c$, "processParameterList", 
function(){
if (this.tagName.equals("parameter")) {
var title = this.parser.getAttrValueLC("title");
if (title.equals("nmr.observe frequency")) {
this.StrObFreq = this.parser.qualifiedValue();
this.obFreq = Double.parseDouble(this.StrObFreq);
} else if (title.equals("nmr.observe nucleus")) {
this.obNucleus = this.parser.getAttrValue("value");
} else if (title.equals("spectrometer/data system")) {
this.modelType = this.parser.getAttrValue("value");
} else if (title.equals("resolution")) {
this.resolution = this.parser.qualifiedValue();
}}});
Clazz.defineMethod(c$, "processConditionList", 
function(){
if (this.tagName.equals("scalar")) {
var dictRef = this.parser.getAttrValueLC("dictRef");
if (dictRef.contains(":field")) {
this.StrObFreq = this.parser.thisValue();
if ((this.StrObFreq.charAt(0)).charCodeAt(0) > 47 && (this.StrObFreq.charAt(0)).charCodeAt(0) < 58) this.obFreq = Double.parseDouble(this.StrObFreq);
}}});
Clazz.defineMethod(c$, "processSample", 
function(){
if (this.tagName.equals("formula")) {
if (this.attrList.contains("concise")) this.molForm = this.parser.getAttrValue("concise");
 else if (this.attrList.contains("inline")) this.molForm = this.parser.getAttrValue("inline");
} else if (this.tagName.equals("name")) {
this.casName = this.parser.thisValue();
}});
Clazz.defineMethod(c$, "processSpectrumData", 
function(){
if (this.tagName.equals("xaxis")) {
if (this.attrList.contains("multipliertodata")) this.xFactor = Double.parseDouble(this.parser.getAttrValue("multiplierToData"));
this.parser.nextTag();
this.tagName = this.parser.getTagName();
this.attrList = this.parser.getAttributeList();
if (this.tagName.equals("array")) {
this.xUnits = JSV.source.CMLReader.checkUnits(this.parser.getAttrValue("units"));
this.npoints = Integer.parseInt(this.parser.getAttrValue("size"));
this.xaxisData =  Clazz.newDoubleArray (this.npoints, 0);
if (this.attrList.contains("start")) {
this.firstX = Double.parseDouble(this.parser.getAttrValue("start"));
this.lastX = Double.parseDouble(this.parser.getAttrValue("end"));
this.deltaX = (this.lastX - this.firstX) / (this.npoints - 1);
this.increasing = this.deltaX > 0 ? true : false;
this.continuous = true;
for (var j = 0; j < this.npoints; j++) this.xaxisData[j] = this.firstX + (this.deltaX * j);

} else {
var posDelim = 0;
var jj = -1;
var tempX = "";
this.Ydelim = " ";
this.attrList = this.parser.getCharacters().$replace('\n', ' ').$replace('\r', ' ').trim();
do {
jj++;
posDelim = this.attrList.indexOf(this.Ydelim);
tempX = this.attrList.substring(0, posDelim);
this.xaxisData[jj] = Double.parseDouble(tempX) * this.xFactor;
this.attrList = this.attrList.substring(posDelim + 1, this.attrList.length).trim();
posDelim = this.attrList.indexOf(this.Ydelim);
while (posDelim > 0) {
jj++;
tempX = this.attrList.substring(0, posDelim);
this.xaxisData[jj] = Double.parseDouble(tempX) * this.xFactor;
this.attrList = this.attrList.substring(posDelim + 1, this.attrList.length).trim();
posDelim = this.attrList.indexOf(this.Ydelim);
}
if (jj < this.npoints - 1) {
jj++;
this.xaxisData[jj] = Double.parseDouble(this.attrList) * this.xFactor;
}} while (jj < this.npoints - 1);
this.firstX = this.xaxisData[0];
this.lastX = this.xaxisData[this.npoints - 1];
this.continuous = true;
}}} else if (this.tagName.equals("yaxis")) {
if (this.attrList.contains("multipliertodata")) this.yFactor = Double.parseDouble(this.parser.getAttrValue("multiplierToData"));
this.parser.nextTag();
this.tagName = this.parser.getTagName();
this.attrList = this.parser.getAttributeList();
if (this.tagName.equals("array")) {
this.yUnits = JSV.source.CMLReader.checkUnits(this.parser.getAttrValue("units"));
var npointsY = Integer.$valueOf(this.parser.getAttrValue("size"));
if (this.npoints != npointsY.intValue()) System.err.println("npoints variation between X and Y arrays");
this.yaxisData =  Clazz.newDoubleArray (this.npoints, 0);
this.Ydelim = this.parser.getAttrValue("delimeter");
if (this.Ydelim.equals("")) this.Ydelim = " ";
var posDelim = 0;
var jj = -1;
var tempY = "";
this.attrList = this.parser.getCharacters().$replace('\n', ' ').$replace('\r', ' ').trim();
do {
jj++;
posDelim = this.attrList.indexOf(this.Ydelim);
tempY = this.attrList.substring(0, posDelim);
this.yaxisData[jj] = Double.parseDouble(tempY) * this.yFactor;
this.attrList = this.attrList.substring(posDelim + 1, this.attrList.length).trim();
posDelim = this.attrList.indexOf(this.Ydelim);
while (posDelim > 0) {
jj++;
tempY = this.attrList.substring(0, posDelim);
this.yaxisData[jj] = Double.parseDouble(tempY) * this.yFactor;
this.attrList = this.attrList.substring(posDelim + 1, this.attrList.length).trim();
posDelim = this.attrList.indexOf(this.Ydelim);
}
if (jj < this.npoints - 1) {
jj++;
this.yaxisData[jj] = Double.parseDouble(this.attrList) * this.yFactor;
}} while (jj < this.npoints - 1);
}this.firstY = this.yaxisData[0];
this.specfound = true;
}});
Clazz.defineMethod(c$, "processPeaks", 
function(){
if (this.specfound) return;
this.peakData =  new java.util.Vector();
this.process(12, true);
this.npoints = this.peakData.size();
this.xaxisData =  Clazz.newDoubleArray (this.npoints, 0);
this.yaxisData =  Clazz.newDoubleArray (this.npoints, 0);
for (var i = 0; i < this.npoints; i++) {
var xy = this.peakData.get(i);
this.xaxisData[i] = xy[0];
this.yaxisData[i] = xy[1];
}
this.peakData = null;
this.firstX = this.xaxisData[0];
this.lastX = this.xaxisData[this.npoints - 1];
this.firstY = this.yaxisData[0];
this.increasing = (this.lastX > this.firstX);
this.continuous = false;
});
Clazz.defineMethod(c$, "processPeakList", 
function(){
if (this.tagName.equals("peak")) {
if (this.attrList.contains("xvalue")) {
var xy =  Clazz.newDoubleArray (2, 0);
xy[1] = 50;
xy[0] = Double.parseDouble(this.parser.getAttrValue("xValue"));
if (this.attrList.contains("xunits")) this.xUnits = JSV.source.CMLReader.checkUnits(this.parser.getAttrValue("xUnits"));
if (this.attrList.contains("yvalue")) xy[1] = Double.parseDouble(this.parser.getAttrValue("yValue"));
if (this.attrList.contains("yunits")) this.yUnits = JSV.source.CMLReader.checkUnits(this.parser.getAttrValue("yUnits"));
if (this.attrList.contains("atomrefs")) xy[1] = 49 * JU.PT.getTokens(this.parser.getAttrValue("atomRefs")).length;
this.peakData.add(xy);
}}});
c$.checkUnits = Clazz.defineMethod(c$, "checkUnits", 
function(units){
units = units.substring(units.indexOf(":") + 1).toUpperCase();
return (units.equals("RELABUNDANCE") ? "RELATIVE ABUNDANCE" : units.contains("ARBITRARY") ? "ARBITRARY UNITS" : units.equals("MOVERZ") ? "M/Z" : units.equals("CM-1") ? "1/CM" : units.equals("NM") ? "NANOMETERS" : units);
}, "~S");
});
;//5.0.1-v2 Mon Mar 04 12:59:58 CST 2024
