Clazz.declarePackage("JSV.source");
Clazz.load(["JSV.source.XMLReader"], "JSV.source.AnIMLReader", ["JU.BC", "$.Base64", "JSV.source.JDXSource"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.inResult = false;
Clazz.instantialize(this, arguments);}, JSV.source, "AnIMLReader", JSV.source.XMLReader);
Clazz.makeConstructor(c$, 
function(){
Clazz.superConstructor (this, JSV.source.AnIMLReader, []);
});
Clazz.overrideMethod(c$, "getXML", 
function(br){
try {
this.source =  new JSV.source.JDXSource(0, this.filePath);
this.getSimpleXmlReader(br);
this.parser.nextEvent();
this.processXML(0, 3);
if (!this.checkPointCount()) return null;
this.xFactor = 1;
this.yFactor = 1;
this.populateVariables();
} catch (pe) {
if (Clazz.exceptionOf(pe, Exception)){
System.err.println("That file may be empty...");
this.errorLog.append("That file may be empty... \n");
} else {
throw pe;
}
}
this.processErrors("anIML");
try {
br.close();
} catch (e1) {
if (Clazz.exceptionOf(e1,"java.io.IOException")){
} else {
throw e1;
}
}
return this.source;
}, "java.io.BufferedReader");
Clazz.overrideMethod(c$, "processTag", 
function(tagId){
switch (tagId) {
case 0:
this.processAuditTrail();
return true;
case 1:
this.processExperimentStepSet();
return true;
case 2:
this.processSampleSet();
return true;
case 11:
this.processAuthor();
return true;
case 3:
this.inResult = true;
return true;
default:
System.out.println("AnIMLReader not processing tag " + JSV.source.XMLReader.tagNames[tagId]);
return false;
}
}, "~N");
Clazz.overrideMethod(c$, "processEndTag", 
function(tagId){
switch (tagId) {
case 3:
case 1:
this.inResult = false;
break;
}
}, "~N");
Clazz.defineMethod(c$, "processAuditTrail", 
function(){
if (this.tagName.equals("user")) {
this.parser.qualifiedValue();
} else if (this.tagName.equals("timestamp")) {
this.parser.qualifiedValue();
}});
Clazz.defineMethod(c$, "processSampleSet", 
function(){
if (this.tagName.equals("sample")) this.samplenum++;
 else if (this.tagName.equals("parameter")) {
this.attrList = this.parser.getAttrValueLC("name");
if (this.attrList.equals("name")) {
this.parser.qualifiedValue();
} else if (this.attrList.equals("owner")) {
this.parser.qualifiedValue();
} else if (this.attrList.equals("molecular formula")) {
this.molForm = this.parser.qualifiedValue();
} else if (this.attrList.equals("cas registry number")) {
this.casRN = this.parser.qualifiedValue();
}}});
Clazz.defineMethod(c$, "processExperimentStepSet", 
function(){
if (this.tagName.equals("result")) {
this.inResult = true;
} else if (this.tagName.equals("sampleref")) {
if (this.parser.getAttrValueLC("role").contains("samplemeasurement")) this.sampleID = this.parser.getAttrValue("sampleID");
} else if (this.tagName.equals("author")) {
this.process(11, true);
} else if (this.tagName.equals("timestamp")) {
this.LongDate = this.parser.thisValue();
} else if (this.tagName.equals("technique")) {
this.techname = this.parser.getAttrValue("name").toUpperCase() + " SPECTRUM";
} else if (this.tagName.equals("vectorset") || this.tagName.equals("seriesset") && this.inResult) {
this.npoints = Integer.parseInt(this.parser.getAttrValue("length"));
this.xaxisData =  Clazz.newDoubleArray (this.npoints, 0);
this.yaxisData =  Clazz.newDoubleArray (this.npoints, 0);
} else if (this.tagName.equals("vector") || this.tagName.equals("series") && this.inResult) {
var axisLabel = this.parser.getAttrValue("name");
var dependency = this.parser.getAttrValueLC("dependency");
if (dependency.equals("independent")) {
this.xUnits = axisLabel;
this.getXValues();
} else if (dependency.equals("dependent")) {
this.yUnits = axisLabel;
this.getYValues();
}} else if (this.tagName.equals("parameter")) {
if ((this.attrList = this.parser.getAttrValueLC("name")).equals("identifier")) {
this.title = this.parser.qualifiedValue();
} else if (this.attrList.equals("nucleus")) {
this.obNucleus = this.parser.qualifiedValue();
} else if (this.attrList.equals("observefrequency")) {
this.StrObFreq = this.parser.qualifiedValue();
this.obFreq = Double.parseDouble(this.StrObFreq);
} else if (this.attrList.equals("referencepoint")) {
this.refPoint = Double.parseDouble(this.parser.qualifiedValue());
} else if (this.attrList.equals("sample path length")) {
this.pathlength = this.parser.qualifiedValue();
} else if (this.attrList.equals("scanmode")) {
this.parser.thisValue();
} else if (this.attrList.equals("manufacturer")) {
this.vendor = this.parser.thisValue();
} else if (this.attrList.equals("model name")) {
this.modelType = this.parser.thisValue();
} else if (this.attrList.equals("resolution")) {
this.resolution = this.parser.qualifiedValue();
}}});
Clazz.defineMethod(c$, "getXValues", 
function(){
this.parser.nextTag();
if (this.parser.getTagName().equals("autoincrementedvalueset")) {
this.parser.nextTag();
if (this.parser.getTagName().equals("startvalue")) this.firstX = Double.parseDouble(this.parser.qualifiedValue());
this.nextStartTag();
if (this.parser.getTagName().equals("increment")) this.deltaX = Double.parseDouble(this.parser.qualifiedValue());
}if (!this.inResult) {
this.nextStartTag();
this.xUnits = this.parser.getAttrValue("label");
}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);

this.lastX = this.xaxisData[this.npoints - 1];
});
Clazz.defineMethod(c$, "nextStartTag", 
function(){
this.parser.nextStartTag();
while (this.parser.getTagType() == 6) {
this.parser.nextStartTag();
}
});
Clazz.defineMethod(c$, "getYValues", 
function(){
var vectorType = this.parser.getAttrValueLC("type");
if (vectorType.length == 0) vectorType = this.parser.getAttrValueLC("vectorType");
this.parser.nextTag();
this.tagName = this.parser.getTagName();
if (this.tagName.equals("individualvalueset")) {
for (var ii = 0; ii < this.npoints; ii++) this.yaxisData[ii] = Double.parseDouble(this.parser.qualifiedValue());

} else if (this.tagName.equals("encodedvalueset")) {
this.attrList = this.parser.getCharacters();
var dataArray = JU.Base64.decodeBase64(this.attrList);
if (dataArray.length != 0) {
if (vectorType.equals("float64")) {
for (var i = 0, pt = 0; i < this.npoints; i++, pt += 8) this.yaxisData[i] = JU.BC.bytesToDoubleToFloat(dataArray, pt, false);

} else {
for (var i = 0, pt = 0; i < this.npoints; i++, pt += 4) this.yaxisData[i] = JU.BC.bytesToFloat(dataArray, pt, false);

}}}this.parser.nextStartTag();
this.tagName = this.parser.getTagName();
this.yUnits = this.parser.getAttrValue("label");
this.firstY = this.yaxisData[0];
});
Clazz.defineMethod(c$, "processAuthor", 
function(){
if (this.tagName.equals("name")) this.owner = this.parser.thisValue();
 else if (this.tagName.contains("location")) this.origin = this.parser.thisValue();
});
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
