/// <summary>
/// Temporary Data Dumping Point
/// Will be removed when GUI is developed
/// </summary>
/// <param name="input"></param>
public static void DataDump(IqTarget input, Run Run)
{
//Temporary Data Dumping Point
//Data Dump also in TopDownIqTesting and ChromCorrelationData
var target = input as ChromPeakIqTarget;
var status = "UNK";
var result = target.GetResult();
var parent = result.Target.ParentTarget as IqChargeStateTarget;
if (parent.ObservedScan != -1)
{
if (((target.ChromPeak.XValue - target.ChromPeak.Width / 2) <= parent.ObservedScan) &&
((target.ChromPeak.XValue + target.ChromPeak.Width / 2) >= parent.ObservedScan))
{
status = "T-POS";
}
else
{
status = "T-NEG";
}
}
using (var sipper = File.AppendText(Outfile))
{
sipper.WriteLine(target.ID + "\t" + parent.AlternateID + "\t" + target.ChargeState + "\t" + target.Code + "\t" + target.EmpiricalFormula + "\t" +
target.MZTheor.ToString("0.0000") + "\t" + target.MonoMassTheor + "\t" +
Run.NetAlignmentInfo.GetScanForNet(target.ElutionTimeTheor) +
"\t" + parent.ObservedScan + "\t" + target.ChromPeak.XValue.ToString("0.00") + "\t" +
result.NETError.ToString("0.0000") + "\t" + result.MassErrorBefore.ToString("0.0000") + "\t" +
result.FitScore.ToString("0.0000") + "\t" + result.CorrelationData.RSquaredValsMedian + "\t" +
result.CorrelationData.RSquaredValsAverage + "\t" + result.CorrelationData.RSquaredValsStDev + "\t" +
result.CorrelationData.ToStringWithDetails() + "\t" + target.GetResult().Abundance + "\t" + result.IsIsotopicProfileFlagged + "\t" +
status);
}
}
public List <ChromPeakQualityData> GetChromPeakQualityData(Run run, IqTarget target, List <Peak> chromPeakList)
{
var peakQualityList = new List <ChromPeakQualityData>();
if (MSGenerator == null)
{
MSGenerator = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
MSGenerator.IsTICRequested = false;
}
//iterate over peaks within tolerance and score each peak according to MSFeature quality
#if DEBUG
var tempMinScanWithinTol = (int)run.NetAlignmentInfo.GetScanForNet(target.ElutionTimeTheor - Parameters.ChromNETTolerance);
var tempMaxScanWithinTol = (int)run.NetAlignmentInfo.GetScanForNet(target.ElutionTimeTheor + Parameters.ChromNETTolerance);
var tempCenterTol = (int)run.NetAlignmentInfo.GetScanForNet(target.ElutionTimeTheor);
Console.WriteLine("SmartPeakSelector --> NETTolerance= " + Parameters.ChromNETTolerance + "; chromMinCenterMax= " +
tempMinScanWithinTol + "\t" + tempCenterTol + "" +
"\t" + tempMaxScanWithinTol);
Console.WriteLine("MT= " + target.ID + ";z= " + target.ChargeState + "; mz= " + target.MZTheor.ToString("0.000") +
"; ------------------------- PeaksWithinTol = " + chromPeakList.Count);
#endif
//target.NumChromPeaksWithinTolerance = peaksWithinTol.Count;
foreach (ChromPeak chromPeak in chromPeakList)
{
// TODO: Currently hard-coded to sum only 1 scan
var lcscanset = _chromPeakUtilities.GetLCScanSetForChromPeak(chromPeak, run, 1);
//generate a mass spectrum
var massSpectrumXYData = MSGenerator.GenerateMS(run, lcscanset);
//find isotopic profile
var mspeakList = new List <Peak>();
var observedIso = TargetedMSFeatureFinder.IterativelyFindMSFeature(massSpectrumXYData, target.TheorIsotopicProfile, out mspeakList);
double fitScore = 1;
double iscore = 1;
//get fit score
fitScore = FitScoreCalc.CalculateFitScore(target.TheorIsotopicProfile, observedIso, massSpectrumXYData);
//get i_score
iscore = InterferenceScorer.GetInterferenceScore(target.TheorIsotopicProfile, mspeakList);
var leftOfMonoPeakLooker = new LeftOfMonoPeakLooker();
var peakToTheLeft = leftOfMonoPeakLooker.LookforPeakToTheLeftOfMonoPeak(target.TheorIsotopicProfile.getMonoPeak(), target.ChargeState,
mspeakList);
var hasPeakTotheLeft = peakToTheLeft != null;
//collect the results together
var pq = new ChromPeakQualityData(chromPeak);
if (observedIso == null)
{
pq.IsotopicProfileFound = false;
}
else
{
pq.IsotopicProfileFound = true;
pq.Abundance = observedIso.IntensityMostAbundant;
pq.FitScore = fitScore;
pq.InterferenceScore = iscore;
pq.IsotopicProfile = observedIso;
pq.IsIsotopicProfileFlagged = hasPeakTotheLeft;
pq.ScanLc = lcscanset.PrimaryScanNumber;
}
peakQualityList.Add(pq);
#if DEBUG
pq.Display();
#endif
}
return(peakQualityList);
}
public override List <IqTarget> Import()
{
var allTargets = new List <IqTarget>();
StreamReader reader;
if (!File.Exists(Filename))
{
throw new IOException("Cannot import. File does not exist.");
}
try
{
reader = new StreamReader(this.Filename);
}
catch (Exception)
{
throw new IOException("There was a problem importing from the file.");
}
//Sequence is the key and processed line is the value
var parentTargetGroup = new Dictionary <string, List <List <string> > >();
using (var sr = reader)
{
if (sr.Peek() == -1)
{
sr.Close();
throw new InvalidDataException("There is no data in the file we are trying to read.");
}
var headerLine = sr.ReadLine();
CreateHeaderLookupTable(headerLine);
string line;
var lineCounter = 1; //used for tracking which line is being processed.
//read and process each line of the file
while (sr.Peek() > -1)
{
line = sr.ReadLine();
var processedData = ProcessLine(line);
//ensure that processed line is the same size as the header line
if (processedData.Count != m_columnHeaders.Count)
{
throw new InvalidDataException("In File: " + Path.GetFileName(Filename) + "; Data in row # " + lineCounter.ToString() + " is NOT valid - \nThe number of columns does not match that of the header line");
}
//Implement EValueCutoff
var EValueCutoff = 1.0E-3;
if (ParseDoubleField(processedData, EValueHeader) < EValueCutoff)
{
if (!parentTargetGroup.ContainsKey(ParseStringField(processedData, PeptideHeader)))
{
parentTargetGroup.Add(ParseStringField(processedData, PeptideHeader), new List <List <string> >());
}
parentTargetGroup[ParseStringField(processedData, PeptideHeader)].Add(processedData);
}
lineCounter++;
}
sr.Close();
}
var target_id = 1;
foreach (var keyValuePair in parentTargetGroup)
{
IqTarget target = CreateParentTarget(keyValuePair.Value);
target.ID = target_id;
allTargets.Add(target);
target_id++;
}
return(allTargets);
}
/// <summary>
/// Copies the target parameter to a new IqTarget.
/// </summary>
/// <param name="target">target parameter</param>
/// <param name="includeRecursion">whether or not to include the root, parent, and children in the clone</param>
public IqTargetBasic(IqTarget target)
: base(target)
{
}
