internal IsosResult CreateIsosResult()
{
IsosResult result;
switch (this.ResultType)
{
case Globals.ResultType.BASIC_TRADITIONAL_RESULT:
result = new StandardIsosResult(this.Run, this.Run.CurrentScanSet);
break;
case Globals.ResultType.UIMF_TRADITIONAL_RESULT:
Check.Require(this.Run is UIMFRun, "Tried to create an IMS_TRADITIONAL_RESULT but the Dataset is not a UIMF file.");
var uimfRun = (UIMFRun)run;
result = new UIMFIsosResult(this.Run, uimfRun.CurrentScanSet, uimfRun.CurrentIMSScanSet);
break;
case Globals.ResultType.O16O18_TRADITIONAL_RESULT:
result = new O16O18IsosResult(this.Run, this.Run.CurrentScanSet);
break;
case Globals.ResultType.IMS_TRADITIONAL_RESULT:
result = new StandardIsosResult(this.Run, this.Run.CurrentScanSet);
break;
case Globals.ResultType.BASIC_TARGETED_RESULT:
throw new ApplicationException("ResultType is a Targeted type but currently we are trying to create a Traditional result");
case Globals.ResultType.O16O18_TARGETED_RESULT:
throw new ApplicationException("ResultType is a Targeted type but currently we are trying to create a Traditional result");
case Globals.ResultType.N14N15_TARGETED_RESULT:
throw new ApplicationException("ResultType is a Targeted type but currently we are trying to create a Traditional result");
case Globals.ResultType.DEUTERATED_TARGETED_RESULT:
throw new ApplicationException("ResultType is a Targeted type but currently we are trying to create a Traditional result");
default:
throw new ApplicationException("ResultType is not of a know type: " + this.ResultType);
}
return(result);
}
private IsosResult convertTextToIsosResult(List <string> processedData, List <string> headers)
{
IsosResult result;
if (fileType == Globals.MSFileType.PNNL_UIMF)
{
result = new UIMFIsosResult();
}
else
{
result = new StandardIsosResult();
}
result.IsotopicProfile = new IsotopicProfile();
//result.Run = getRunFromIsosFilename(this.importFilename, this.fileType); AM commenting this out since this gives me an error
//get ScanSet number from file
if (fileType == Globals.MSFileType.PNNL_UIMF)
{
var imsScanNum = parseIntField(lookup(processedData, headers, "ims_scan_num"));
var frame_num = parseIntField(lookup(processedData, headers, "frame_num"));
((UIMFIsosResult)result).DriftTime = parseDoubleField(lookup(processedData, headers, "drift_time"));
result.ScanSet = new LCScanSetIMS(frame_num);
((UIMFIsosResult)result).IMSScanSet = new IMSScanSet(imsScanNum);
}
else
{
var scan_num = parseIntField(lookup(processedData, headers, "scan_num"));
result.ScanSet = new ScanSet(scan_num);
}
result.IsotopicProfile.ChargeState = parseIntField(lookup(processedData, headers, "charge"));
result.IsotopicProfile.MonoIsotopicMass = parseDoubleField(lookup(processedData, headers, "monoisotopic_mw"));
result.IsotopicProfile.Score = parseDoubleField(lookup(processedData, headers, "fit"));
result.IntensityAggregate = parseFloatField(lookup(processedData, headers, "abundance"));
//result.IsotopicProfile.IntensityMostAbundant = parseFloatField(lookup(processedData, headers, "abundance"));
result.IsotopicProfile.MonoPeakMZ = parseDoubleField(lookup(processedData, headers, "mz"));
result.InterferenceScore = parseDoubleField(lookup(processedData, headers, "interference_score"));
result.IsotopicProfile.OriginalIntensity = parseDoubleField(lookup(processedData, headers, "unsummed_intensity"));
var saturationFlagString = lookup(processedData, headers, "saturation_flag");
result.IsotopicProfile.IsSaturated = saturationFlagString == "1";
var mz = parseFloatField(lookup(processedData, headers, "mz"));
var intensity = parseIntField(lookup(processedData, headers, "mono_abundance"));
var peak = new MSPeak(mz, intensity)
{
Width = parseFloatField(lookup(processedData, headers, "fwhm")),
SignalToNoise = parseFloatField(lookup(processedData, headers, "signal_noise"))
};
//mono mz isn't available from _isos file AM modification, while this is true, we still need this.
var flagString = lookup(processedData, headers, "flag");
if (string.IsNullOrEmpty(flagString))
{
}
else
{
var flagNum = parseIntField(flagString);
if (flagNum == 1)
{
result.Flags.Add(new PeakToTheLeftResultFlag()); // TODO: it'll be good to make a factory class for creating flags.
}
}
result.IsotopicProfile.Peaklist.Add(peak);
return(result);
}
