public void ChromPeakAnalyzerWorkflowTest()
{
//Reference JIRA: https://jira.pnnl.gov/jira/browse/OMCS-884
string testFile = UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
string peaksTestFile = UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
Run run = new RunFactory().CreateRun(testFile);
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
ChromPeakIqTarget testTarget = new ChromPeakIqTarget();
ITheorFeatureGenerator TheorFeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
ChromPeak testPeak = new ChromPeak(5184, 840963, 50, 0);
testTarget.SetWorkflow(new ChromPeakAnalyzerIqWorkflow(run, parameters));
testTarget.Code = "NGIIMMENR";
testTarget.EmpiricalFormula = "C43H76N14O14S2";
testTarget.MonoMassTheor = 1076.510631;
testTarget.ChromPeak = testPeak;
testTarget.ChargeState = 1;
testTarget.TheorIsotopicProfile = TheorFeatureGen.GenerateTheorProfile(testTarget.EmpiricalFormula, testTarget.ChargeState);
testTarget.DoWorkflow();
IqResult result = testTarget.GetResult();
Console.WriteLine("Fit Score: " + result.FitScore + " Flagged: " + result.IsIsotopicProfileFlagged);
}
protected override IqResult CreateIqResult()
{
IqTarget target = new IqChargeStateTarget();
var result = new IqResult(target);
return(result);
}
public override ChromCorrelationData CorrelateData(Run run, IqResult iqResult, int startScan, int stopScan)
{
var correlationData = new ChromCorrelationData();
var o16MzValue = iqResult.Target.TheorIsotopicProfile.Peaklist[0].XValue;
var o18SingleLabelMzValue = iqResult.Target.TheorIsotopicProfile.Peaklist[2].XValue;
var o18DoubleLabelMzValue = iqResult.Target.TheorIsotopicProfile.Peaklist[4].XValue;
var o16ChromXyData = GetBaseChromXYData(run, startScan, stopScan, o16MzValue);
var o18SingleLabelChromXyData = GetBaseChromXYData(run, startScan, stopScan, o18SingleLabelMzValue);
var o18DoubleLabelChromXyData = GetBaseChromXYData(run, startScan, stopScan, o18DoubleLabelMzValue);
double slope, intercept, rsquaredVal;
GetElutionCorrelationData(o16ChromXyData, o18SingleLabelChromXyData, out slope, out intercept, out rsquaredVal);
correlationData.AddCorrelationData(slope, intercept, rsquaredVal);
GetElutionCorrelationData(o16ChromXyData, o18DoubleLabelChromXyData, out slope, out intercept, out rsquaredVal);
correlationData.AddCorrelationData(slope, intercept, rsquaredVal);
GetElutionCorrelationData(o18SingleLabelChromXyData, o18DoubleLabelChromXyData, out slope, out intercept, out rsquaredVal);
correlationData.AddCorrelationData(slope, intercept, rsquaredVal);
return(correlationData);
}
public override ChromCorrelationData CorrelateData(Run run, IqResult iqResult, int startScan, int stopScan)
{
Check.Require(iqResult != null, "ChromCorrelator failed. IqResult is null.");
Check.Require(iqResult.ObservedIsotopicProfile != null, "ChromCorrelator failed. ObservedIsotopicProfile is null for IqResult");
return(CorrelatePeaksWithinIsotopicProfile(run, iqResult.ObservedIsotopicProfile, startScan, stopScan));
}
protected void GetBasicIqResultData(ref IqResult result, List <string> rowData)
{
result.Target.ID = ParseIntField(rowData, TargetIDHeaders, 0);
result.Target.ChargeState = ParseIntField(rowData, ChargeStateHeaders, 0);
result.Target.MonoMassTheor = ParseDoubleField(rowData, MonoMassTheorHeaders, 0);
result.Target.MZTheor = ParseDoubleField(rowData, MzTheorHeaders, 0);
result.Target.ScanLC = ParseIntField(rowData, TargetScanHeaders);
result.Target.ElutionTimeTheor = ParseDoubleField(rowData, ElutionTimeTheorHeaders, 0);
result.Target.Code = ParseStringField(rowData, CodeHeaders);
result.Target.EmpiricalFormula = ParseStringField(rowData, EmpiricalFormulaHeaders);
result.Abundance = ParseFloatField(rowData, AbundanceHeaders, 0);
result.ElutionTimeObs = ParseDoubleField(rowData, ElutionTimeObsHeaders, 0);
result.FitScore = ParseDoubleField(rowData, FitScoreHeaders, 1);
result.InterferenceScore = ParseDoubleField(rowData, InterferenceScoreHeaders, 1);
result.LcScanObs = ParseIntField(rowData, LcScanObsHeaders);
result.MZObs = ParseDoubleField(rowData, MZObsHeaders, 0);
result.MonoMassObs = ParseDoubleField(rowData, MonomassObsHeaders, 0);
result.MZObsCalibrated = ParseDoubleField(rowData, MZObsCalibratedHeaders, 0);
result.MonoMassObsCalibrated = ParseDoubleField(rowData, MonomassObsCalibratedHeaders, 0);
result.NumChromPeaksWithinTolerance = ParseIntField(rowData, ChromPeaksWithinTolHeaders);
result.MassErrorBefore = (result.MonoMassObs - result.Target.MonoMassTheor) / result.Target.MonoMassTheor * 1e6;
result.MassErrorAfter = (result.MonoMassObsCalibrated - result.Target.MonoMassTheor) / result.Target.MonoMassTheor * 1e6;
}
public virtual string GetResultAsString(IqResult result, bool includeHeader = false)
{
var sb = new StringBuilder();
var delim = "\t";
if (includeHeader)
{
var header = GetHeader();
sb.Append(header);
sb.Append(Environment.NewLine);
}
sb.Append(result.Target.ID);
sb.Append(delim);
sb.Append(result.Target.Code);
sb.Append(delim);
sb.Append(result.Target.EmpiricalFormula);
sb.Append(delim);
sb.Append(result.Target.ChargeState);
sb.Append(delim);
sb.Append(result.Target.MonoMassTheor.ToString("0.00000"));
sb.Append(delim);
sb.Append(result.Target.MZTheor.ToString("0.00000"));
sb.Append(delim);
sb.Append(result.Target.ElutionTimeTheor.ToString("0.00000"));
sb.Append(delim);
sb.Append(result.Target.ScanLC);
sb.Append(delim);
sb.Append(result.MonoMassObs.ToString("0.00000"));
sb.Append(delim);
sb.Append(result.MZObs.ToString("0.00000"));
sb.Append(delim);
sb.Append(result.MonoMassObsCalibrated.ToString("0.00000"));
sb.Append(delim);
sb.Append(result.MZObsCalibrated.ToString("0.00000"));
sb.Append(delim);
sb.Append(result.ElutionTimeObs.ToString("0.00000"));
sb.Append(delim);
sb.Append(result.NumChromPeaksWithinTolerance);
sb.Append(delim);
sb.Append(result.LcScanObs);
sb.Append(delim);
sb.Append(result.Abundance.ToString("0.#"));
sb.Append(delim);
sb.Append(result.FitScore.ToString("0.000"));
sb.Append(delim);
sb.Append(result.InterferenceScore.ToString("0.000"));
var outString = sb.ToString();
return(outString);
}
/// <summary>
/// Gets charge results as strings, 1 line per result
/// </summary>
/// <param name="result"></param>
/// <param name="includeHeader"></param>
/// <returns></returns>
public string GetChargeResultAsString(IqResult result, bool includeHeader = false)
{
if (!(result.Target.ChargeState == 0 || result.Abundance <= 0))
{
var sb = new StringBuilder();
if (includeHeader)
{
var header = GetHeader();
sb.Append(header);
sb.Append(Environment.NewLine);
}
sb.Append(result.Target.ID);
sb.Append(Delimiter);
sb.Append(result.Target.Code);
sb.Append(Delimiter);
sb.Append(result.Target.EmpiricalFormula);
sb.Append(Delimiter);
sb.Append(result.Target.ChargeState);
sb.Append(Delimiter);
sb.Append(result.Target.MonoMassTheor.ToString("0.000"));
sb.Append(Delimiter);
sb.Append(result.Target.MZTheor.ToString("0.000"));
sb.Append(Delimiter);
sb.Append(result.Target.ElutionTimeTheor.ToString("0.000"));
sb.Append(Delimiter);
sb.Append(result.MonoMassObs.ToString("0.000"));
sb.Append(Delimiter);
sb.Append(result.MZObs.ToString("0.000"));
sb.Append(Delimiter);
sb.Append(result.ElutionTimeObs.ToString("0.0000"));
sb.Append(Delimiter);
sb.Append(result.NumChromPeaksWithinTolerance);
sb.Append(Delimiter);
sb.Append(result.LcScanObs);
sb.Append(Delimiter);
sb.Append(result.Abundance.ToString("0.#"));
sb.Append(Delimiter);
sb.Append(result.FitScore.ToString("0.000"));
sb.Append(Delimiter);
sb.Append(result.CorrelationData.RSquaredValsMedian);
var outString = sb.ToString();
return(outString);
}
else
{
return(null);
}
}
protected override void ConvertTextToDataObject(ref IqResult iqResult, List <string> rowData)
{
GetBasicIqResultData(ref iqResult, rowData);
}
public virtual string GetHeader(IqResult result)
{
return(GetHeader());
}
public virtual ChromCorrelationData CorrelateData(Run run, IqResult iqResult, int startScan, int stopScan)
{
throw new NotImplementedException();
}
protected abstract void ConvertTextToDataObject(ref IqResult iqResult, List <string> rowData);
