Clazz.declarePackage("JSV.common");
Clazz.load(["JSV.common.MeasurementData"], "JSV.common.PeakData", ["JU.DF", "JSV.common.Coordinate", "$.PeakPick"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.thresh = 0;
this.minY = 0;
this.maxY = 0;
Clazz.instantialize(this, arguments);}, JSV.common, "PeakData", JSV.common.MeasurementData);
Clazz.defineMethod(c$, "getThresh", 
function(){
return this.thresh;
});
Clazz.overrideMethod(c$, "getDataHeader", 
function(){
return (this.spec.isHNMR() ? JSV.common.PeakData.HNMR_HEADER :  Clazz.newArray(-1, ["peak", this.spec.getXUnits(), this.spec.getYUnits()]));
});
Clazz.overrideMethod(c$, "getMeasurementListArray", 
function(units){
var data =  new Array(this.size());
var last =  Clazz.newDoubleArray(-1, [-1.0E100, 1e100, 1e100]);
var ddata;
for (var pt = 0, i = this.size(); --i >= 0; pt++) {
ddata = this.spec.getPeakListArray(this.get(i), last, this.maxY);
if (ddata.length == 2) data[pt] =  Clazz.newArray(-1, ["" + (pt + 1), JU.DF.formatDecimalDbl(ddata[0], 2), JU.DF.formatDecimalDbl(ddata[1], 4)]);
 else data[pt] =  Clazz.newArray(-1, ["" + (pt + 1), JU.DF.formatDecimalDbl(ddata[0], 4), JU.DF.formatDecimalDbl(ddata[1], 4), JU.DF.formatDecimalDbl(ddata[2], 2), (ddata[3] == 0 ? "" : JU.DF.formatDecimalDbl(ddata[3], 2)), (ddata[4] == 0 ? "" : JU.DF.formatDecimalDbl(ddata[4], 2)), (ddata[5] == 0 ? "" : JU.DF.formatDecimalDbl(ddata[5], 2))]);
}
return data;
}, "~S");
Clazz.overrideMethod(c$, "getMeasurementListArrayReal", 
function(units){
var data =  Clazz.newDoubleArray (this.size(), 0);
var last =  Clazz.newDoubleArray(-1, [-1.0E100, 1e100, 1e100]);
for (var pt = 0, i = this.size(); --i >= 0; pt++) data[pt] = this.spec.getPeakListArray(this.get(i), last, this.maxY);

return data;
}, "~S");
Clazz.defineMethod(c$, "getInfo", 
function(info){
info.put("interpolation", this.myParams.peakListInterpolation);
info.put("threshold", Double.$valueOf(this.myParams.peakListThreshold));
Clazz.superCall(this, JSV.common.PeakData, "getInfo", [info]);
}, "java.util.Map");
Clazz.defineMethod(c$, "setPeakList", 
function(p, precision, view){
this.precision = (precision == -2147483648 ? this.spec.getDefaultUnitPrecision() : precision);
var xyCoords = this.spec.getXYCoords();
if (xyCoords.length < 3) return;
this.clear();
if (p != null) {
this.myParams.peakListInterpolation = p.peakListInterpolation;
this.myParams.peakListThreshold = p.peakListThreshold;
}var doInterpolate = (this.myParams.peakListInterpolation.equals("parabolic"));
var isInverted = this.spec.isInverted();
this.minY = view.minYOnScale;
this.maxY = view.maxYOnScale;
var minX = view.minXOnScale;
var maxX = view.maxXOnScale;
this.thresh = this.myParams.peakListThreshold;
if (Double.isNaN(this.thresh)) this.thresh = this.myParams.peakListThreshold = (this.minY + this.maxY) / 2;
var yLast = 0;
var y3 =  Clazz.newDoubleArray(-1, [xyCoords[0].getYVal(), yLast = xyCoords[1].getYVal(), 0]);
var n = 0;
if (isInverted) for (var i = 2; i < xyCoords.length; i++) {
var y = y3[i % 3] = xyCoords[i].getYVal();
if (yLast < this.thresh && y3[(i - 2) % 3] > yLast && yLast < y) {
var x = (doInterpolate ? JSV.common.Coordinate.parabolicInterpolation(xyCoords, i - 1) : xyCoords[i - 1].getXVal());
if (x >= minX || x <= maxX) {
var m =  new JSV.common.PeakPick().setValue(x, y, this.spec, null, 0);
this.addLast(m);
if (++n == 100) break;
}}yLast = y;
}
 else for (var i = 2; i < xyCoords.length; i++) {
var y = y3[i % 3] = xyCoords[i].getYVal();
if (yLast > this.thresh && y3[(i - 2) % 3] < yLast && yLast > y) {
var x = (doInterpolate ? JSV.common.Coordinate.parabolicInterpolation(xyCoords, i - 1) : xyCoords[i - 1].getXVal());
if (x >= minX && x <= maxX) {
var m =  new JSV.common.PeakPick().setValue(x, y, this.spec, JU.DF.formatDecimalDbl(x, precision), x);
this.addLast(m);
if (++n == 100) break;
}}yLast = y;
}
}, "JSV.common.Parameters,~N,JSV.common.ScaleData");
c$.HNMR_HEADER =  Clazz.newArray(-1, ["peak", "shift/ppm", "intens", "shift/hz", "diff/hz", "2-diff", "3-diff"]);
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
