protected override void Extract(DataReader uimf, FileInfo originFile, int frameNumber)
{
var heatmapData = GetFullHeatmapData(uimf, frameNumber);
var heatmapOutputFile = DataExporter.GetOutputLocation(originFile, "HeatMap", frameNumber);
DataExporter.OutputHeatMap(heatmapData, heatmapOutputFile, this.Options.Verbose);
}
protected override void Extract(DataReader uimf, FileInfo originFile, int frameNumber)
{
var ticData = GetFullScanInfo(uimf, frameNumber);
var ticOutputFile = DataExporter.GetOutputLocation(originFile, "TiC", frameNumber);
DataExporter.OutputTiCbyTime(ticData, ticOutputFile, this.Options.Verbose);
}
protected override void Extract(DataReader uimf, FileInfo originFile, int frameNumber)
{
var mzData = GetFullMzInfo(uimf, frameNumber);
if (mzData == null)
{
Console.Error.WriteLine(
"ERROR: We had a problem getting the data for the MZ of" + Environment.NewLine + " frame "
+ frameNumber + " in " + originFile.FullName);
}
var mzOutputFile = DataExporter.GetOutputLocation(originFile, "Mz", frameNumber);
DataExporter.OutputMz(mzData, mzOutputFile, this.Options.Verbose);
}
protected override void Extract(DataReader uimf, FileInfo originFile, int frameNumber)
{
foreach (var xicTarget in Options.XicTargetList)
{
var xicData = GetXicInfo(uimf, frameNumber, xicTarget.TargetMz, xicTarget.Tolerance, this.Options.Getmsms);
var xicOutputFile = DataExporter.GetOutputLocation(
originFile,
"XiC_mz_" + xicTarget.TargetMz + "_tolerance_" + xicTarget.Tolerance + "_Frame",
frameNumber);
if (xicData == null)
{
return;
}
DataExporter.OutputXiCbyTime(xicData, xicOutputFile, this.Options.Verbose);
}
}
protected override IEnumerable<PeakSet> BulkPeakFind(DataReader uimf, FileInfo originFile, int frameNumber)
{
var mzData = GetFullMzInfo(uimf, frameNumber);
var doubleMzData =
mzData.Select(
keyValuePair => new KeyValuePair<double, double>(keyValuePair.Key, keyValuePair.Value))
.ToList();
var mzpeaks = PeakFinder.FindPeaks(doubleMzData);
var mzPeakOutputLocation = DataExporter.GetOutputLocation(
originFile,
"Mz_Peaks",
frameNumber,
"xml");
DataExporter.OutputPeaks(mzpeaks, mzPeakOutputLocation);
var peakSet = new List<PeakSet>();
peakSet.Add(mzpeaks);
return peakSet;
}
protected override IEnumerable <PeakSet> BulkPeakFind(DataReader uimf, FileInfo originFile, int frameNumber)
{
var peakSets = new List <PeakSet>();
foreach (var xicTarget in Options.XicTargetList)
{
var xicData = GetXicInfo(uimf, frameNumber, xicTarget.TargetMz, xicTarget.Tolerance, this.Options.Getmsms);
var xicPeaks = PeakFinder.FindPeaks(xicData);
var xicPeakOutputLocation = DataExporter.GetOutputLocation(
originFile,
"XiC_Peaks_mz_" + xicTarget.TargetMz + "_tolerance_" + xicTarget.Tolerance + "_Frame",
frameNumber,
"xml");
DataExporter.OutputPeaks(xicPeaks, xicPeakOutputLocation);
peakSets.Add(xicPeaks);
}
return(peakSets);
}
protected override IEnumerable <PeakSet> BulkPeakFind(DataReader uimf, FileInfo originFile, int frameNumber)
{
var ticData = GetFullScanInfo(uimf, frameNumber);
var doubleTicData =
ticData.Select(scanInfo => new KeyValuePair <double, double>(scanInfo.DriftTime, scanInfo.TIC))
.ToList();
var ticPeaks = PeakFinder.FindPeaks(doubleTicData);
var mzPeakOutputLocation = DataExporter.GetOutputLocation(
originFile,
"TiC_Peaks",
frameNumber,
"xml");
DataExporter.OutputPeaks(ticPeaks, mzPeakOutputLocation);
var peakSets = new List <PeakSet>();
peakSets.Add(ticPeaks);
return(peakSets);
}
