public XicUnit(XicUnit copy)
{
Meta = new XicMeta(copy.Meta);
if (copy.RetentionTimes != null)
{
if (copy.RetentionTimes is string)
{
RetentionTimes = (string)copy.RetentionTimes;
}
else
{
ArrayList x = new ArrayList();
foreach (double d in (ArrayList)copy.RetentionTimes)
{
x.Add(d);
}
RetentionTimes = x;
}
}
else
{
RetentionTimes = null;
}
if (copy.Intensities != null)
{
if (copy.Intensities is string)
{
Intensities = (string)copy.Intensities;
}
else
{
ArrayList y = new ArrayList();
foreach (double d in (ArrayList)copy.Intensities)
{
y.Add(d);
}
Intensities = y;
}
}
else
{
Intensities = null;
}
}
public static XicData ParseJSON(string jsonString)
{
List <JSONInputUnit> jsonIn;
XicData data = new XicData();
jsonIn = JsonConvert.DeserializeObject <List <JSONInputUnit> >(jsonString);
foreach (JSONInputUnit xic in jsonIn)
{
XicUnit xicUnit = null;
if (xic.HasSequence())
{
Peptide p = new Peptide(xic.Sequence);
xic.Mz = p.GetMz(xic.Charge);
}
if (xic.HasMz())
{
double delta;
switch (xic.ToleranceUnit.ToLower())
{
case "ppm":
delta = xic.Mz.Value * xic.Tolerance.Value * 1e-6;
break;
case "amu":
delta = xic.Tolerance.Value;
break;
case "mmu":
delta = xic.Tolerance.Value * 1e-3;
break;
case "da":
delta = xic.Tolerance.Value;
break;
case "":
delta = xic.Mz.Value * xic.Tolerance.Value * 1e-6;
break;
default:
delta = 10;
break;
}
xicUnit = new XicUnit(xic.Mz.Value - delta, xic.Mz.Value + delta, xic.RtStart,
xic.RtEnd, xic.Filter);
}
else if (xic.HasMzRange())
{
xicUnit = new XicUnit(xic.MzStart.Value, xic.MzEnd.Value, xic.RtStart, xic.RtEnd, xic.Filter);
}
if (xicUnit == null || !xicUnit.HasValidRanges())
{
throw new RawFileParserException(
$"Invalid M/Z and/or retention time range:\n{JsonConvert.SerializeObject(xic, Formatting.Indented)}");
}
data.Content.Add(xicUnit);
}
return(data);
}
