public void Initialize()
{
EmptyBasePeakRun = new Run
{
AnalysisSettings = new AnalysisSettings
{
RtTolerance = 2.5
}
};
Basepeak1Run = new Run
{
AnalysisSettings = new AnalysisSettings
{
RtTolerance = 2.5
}
};
var spectrumpoint1 = new SpectrumPoint(2000, 150, 2.58F);
var spectrumpoint2 = new SpectrumPoint(3000, 150.01F, 3.00F);
var basePeak1 = new BasePeak(150, 2.5, 150)
{
BpkRTs = new List <double>()
{
2.5
},
Spectrum = new List <SpectrumPoint>()
{
spectrumpoint1, spectrumpoint2
}
};
var EmptyBasePeak = new BasePeak(1, 1, 1)
{
Spectrum = new List <SpectrumPoint>()
{
}
};
Basepeak1Run.BasePeaks = new ConcurrentBag <BasePeak>()
{
basePeak1
};
BasePeak1ChromatogramGenerator = new ChromatogramMetricGenerator();
BasePeak1ChromatogramGenerator.GenerateChromatogram(Basepeak1Run);
EmptyBasePeakRun.BasePeaks = new ConcurrentBag <BasePeak>()
{
EmptyBasePeak
};
EmptyCMG = new ChromatogramMetricGenerator();
EmptyCMG.GenerateChromatogram(EmptyBasePeakRun);
}
public void Initialize()
{
///<summary>The Metric Generator is the main tree from which the other metric calculatingfunction groups are run.
///Therefore most tests will not be run here, but in the function branches RTGrouper/SWATHGrouper etc. There are however a few
///functions that are run here and they are also tested here.</summary>
Scan ms2scan1 = new Scan(false, 1, 1, 0, 2, 2, 1, 1000);
Scan ms2scan2 = new Scan(false, 1, 1, 0, 2, 2, 1, 5000);
Scan ms2scan3 = new Scan(false, 5, 5, 0, 2, 4, 1, 1000);
Scan ms2scan4 = new Scan(false, 1, 1, 0, 2, 4, 2, 51000);
Scan ms2scan5 = new Scan(false, 1, 1, 0, 2, 5, 2, 1000);
Scan ms2scan6 = new Scan(false)
{
ScanStartTime = 0,
MsLevel = 2,
Density = 5
};
var spectrumpoint1 = new SpectrumPoint(2000, 150, 2.58F);
var spectrumpoint2 = new SpectrumPoint(3000, 150.01F, 3.00F);
var basePeak1 = new BasePeak(150, 2.5, 150)
{
BpkRTs = new List <double>()
{
2.5
},
Spectrum = new List <SpectrumPoint>()
{
spectrumpoint1, spectrumpoint2
}
};
Contains5ms2ScansRun = new Run
{
AnalysisSettings = new AnalysisSettings
{
RtTolerance = 2.5
},
Ms2Scans = new ConcurrentBag <Scan>()
{
ms2scan1, ms2scan2, ms2scan3, ms2scan4, ms2scan5
},
LastScanTime = 70,
StartTime = 2.5
};
Contains5ms2ScansRun.BasePeaks.Add(basePeak1);
Contains5ms2ScansRun.SourceFileNames.Add(" ");
Contains5ms2ScansRun.SourceFileChecksums.Add(" ");
Emptyms2scansRun = new Run
{
AnalysisSettings = new AnalysisSettings
{
RtTolerance = 2.5
},
Ms2Scans = new ConcurrentBag <Scan>()
{
ms2scan1, ms2scan2, ms2scan3, ms2scan4, ms2scan6
}, //6 does not have upper and lower offsets
LastScanTime = 0,
StartTime = 1000000
};
Emptyms2scansRun.BasePeaks.Add(basePeak1);
Emptyms2scansRun.SourceFileNames.Add(" ");
Emptyms2scansRun.SourceFileChecksums.Add(" ");
MetricGenerator = new MetricGenerator();
}
public void Initialize()
{
Scan ms2scan1 = new Scan(false, 1, 1, 0, 2, 2, 1, 100.00)
{
};
Scan ms2scan2 = new Scan(false, 1, 1, 20, 2, 2, 1, 100000.02)
{
};
Scan ms2scan3 = new Scan(false, 5, 5, 30, 2, 4, 2, 30)
{
};
Scan ms2scan4 = new Scan(false, 5, 5, 32, 2, 4, 2, 20010.33)
{
};
Scan ms2scan5 = new Scan(false, 5, 5, 34, 2, 4, 2, 50.33)
{
};
Scan ms2scan6 = new Scan(false, 1, 1, 35, 2, 4, 2, 4000)
{
};
Scan ms2scan7 = new Scan(false, 1, 1, 70, 2, 5, 3, 60000)
{
};
Scan ms2scan8 = new Scan(false, 1, 1, 70, 2, 5, 3, 6000)
{
};
Scan ms2scan9 = new Scan(false)
{
ScanStartTime = 0,
MsLevel = 2,
Density = 5,
TotalIonCurrent = 8000
};
//MS1scans
Scan ms1scan1 = new Scan(false)
{
IsolationWindowLowerOffset = 1,
IsolationWindowUpperOffset = 1,
ScanStartTime = 0,
MsLevel = 1,
Density = 2,
Cycle = 1,
TotalIonCurrent = 1000,
BasePeakIntensity = 1000,
BasePeakMz = 1058
};
Scan ms1scan2 = new Scan(false)
{
IsolationWindowLowerOffset = 5,
IsolationWindowUpperOffset = 5,
ScanStartTime = 30,
MsLevel = 1,
Density = 4,
Cycle = 2,
TotalIonCurrent = 3050,
BasePeakIntensity = 1500,
BasePeakMz = 459
};
Scan ms1scan3 = new Scan(false)
{
IsolationWindowLowerOffset = 5,
IsolationWindowUpperOffset = 5,
ScanStartTime = 70,
MsLevel = 1,
Density = 4,
Cycle = 3,
TotalIonCurrent = 3050,
BasePeakIntensity = 5000,
BasePeakMz = 150
};
//BasePeaks:
var spectrumpoint1 = new SpectrumPoint(2000, 150, 2.58F)
{
};
var spectrumpoint2 = new SpectrumPoint(3000, 150.01F, 3.00F)
{
};
var spectrumpoint3 = new SpectrumPoint(3000, 150.01F, 60F)
{
};
var basePeak1 = new BasePeak(150, 2.5, 150)
{
BpkRTs = new List <double>()
{
2.5
},
Spectrum = new List <SpectrumPoint>()
{
spectrumpoint1, spectrumpoint2
},
Mz = 150
};
basePeak1.FWHMs.Add(1);
basePeak1.FWHMs.Add(2);
basePeak1.Peaksyms.Add(1);
basePeak1.Peaksyms.Add(2);
basePeak1.Intensities.Add(1);
basePeak1.Intensities.Add(2);
basePeak1.FullWidthBaselines.Add(1);
basePeak1.FullWidthBaselines.Add(2);
var basePeak2 = new BasePeak(300, 60, 150)
{
BpkRTs = new List <double>()
{
60
},
Spectrum = new List <SpectrumPoint>()
{
spectrumpoint3
}
};
basePeak2.FWHMs.Add(2);
basePeak2.Peaksyms.Add(1);
basePeak2.Intensities.Add(2);
basePeak2.FullWidthBaselines.Add(1);
//Runs:
Ms2andms1Run = new Run
{
AnalysisSettings = new AnalysisSettings
{
RtTolerance = 2.5
},
Ms2Scans = new ConcurrentBag <Scan>()
{
ms2scan1, ms2scan2, ms2scan3, ms2scan4, ms2scan5, ms2scan6, ms2scan7, ms2scan8
},
Ms1Scans = new List <Scan>()
{
ms1scan1, ms1scan2, ms1scan3
},
LastScanTime = 100,
StartTime = 0
};
Ms2andms1Run.BasePeaks.Add(basePeak1);
Ms2andms1Run.BasePeaks.Add(basePeak2);
Ms2andms1Run.SourceFileNames.Add(" ");
Ms2andms1Run.SourceFileChecksums.Add(" ");
Emptyms2scansRun = new Run
{
AnalysisSettings = new AnalysisSettings
{
RtTolerance = 2.5
},
Ms2Scans = new ConcurrentBag <Scan>()
{
ms2scan1, ms2scan2, ms2scan3, ms2scan4, ms2scan9
}, //9 does not have upper and lower offsets
LastScanTime = 0,
StartTime = 1000000
};
Emptyms2scansRun.BasePeaks.Add(basePeak1);
Emptyms2scansRun.SourceFileNames.Add(" ");
Emptyms2scansRun.SourceFileChecksums.Add(" ");
RTGrouper = new RTGrouper();
Result = RTGrouper.DivideByRT(Ms2andms1Run, 2, 100);
}
public void Initialize()
{
var spectrumpoint1A = new SpectrumPoint(2000, 550, 2.58F)
{
};
var spectrumpoint2A = new SpectrumPoint(3000, 551F, 3.00F)
{
};
List <SpectrumPoint> spectrum = new List <SpectrumPoint>()
{
spectrumpoint1A, spectrumpoint2A
};
string tempPath = Path.GetTempPath();
Scan ms2scan1 = new Scan(false, tempPath)
{
IsolationWindowLowerOffset = 1,
IsolationWindowTargetMz = 550,
IsolationWindowUpperOffset = 1,
ScanStartTime = 0,
MsLevel = 2,
Density = 2,
Cycle = 1,
TotalIonCurrent = 1000
};
Scan ms2scan2 = new Scan(false, tempPath)
{
IsolationWindowLowerOffset = 5,
IsolationWindowTargetMz = 550,
IsolationWindowUpperOffset = 5,
ScanStartTime = 30,
MsLevel = 2,
Density = 4,
Cycle = 2,
TotalIonCurrent = 3050
};
Scan ms2scan3 = new Scan(false, tempPath)
{
IsolationWindowLowerOffset = 1,
IsolationWindowTargetMz = 550,
IsolationWindowUpperOffset = 1,
ScanStartTime = 35,
MsLevel = 2,
Density = 4,
Cycle = 3,
TotalIonCurrent = 4000
};
Scan ms2scan4 = new Scan(false, tempPath)
{
IsolationWindowLowerOffset = 1,
IsolationWindowTargetMz = 550,
IsolationWindowUpperOffset = 1,
ScanStartTime = 70,
MsLevel = 2,
Density = 5,
Cycle = 4,
TotalIonCurrent = 6000
};
Scan ms2scan5 = new Scan(false, tempPath)
{
IsolationWindowLowerOffset = 1,
IsolationWindowTargetMz = 550,
IsolationWindowUpperOffset = 1,
ScanStartTime = 70.002,
MsLevel = 2,
Density = 5,
Cycle = 5,
TotalIonCurrent = 6000
};
Scan ms2scan6 = new Scan(false, tempPath)
{
IsolationWindowLowerOffset = 1,
IsolationWindowTargetMz = 1050,
IsolationWindowUpperOffset = 1,
ScanStartTime = 0,
MsLevel = 2,
Density = 2,
Cycle = 1,
TotalIonCurrent = 1000
};
Scan ms2scan7 = new Scan(false, tempPath)
{
IsolationWindowLowerOffset = 5,
IsolationWindowTargetMz = 1050,
IsolationWindowUpperOffset = 5,
ScanStartTime = 30,
MsLevel = 2,
Density = 4,
Cycle = 2,
TotalIonCurrent = 3050
};
Scan ms2scan8 = new Scan(false, tempPath)
{
IsolationWindowLowerOffset = 1,
IsolationWindowTargetMz = 1050,
IsolationWindowUpperOffset = 1,
ScanStartTime = 35,
MsLevel = 2,
Density = 40,
Cycle = 3,
TotalIonCurrent = 4000
};
Scan ms2scan9 = new Scan(false, tempPath)
{
IsolationWindowLowerOffset = 1,
IsolationWindowTargetMz = 1050,
IsolationWindowUpperOffset = 1,
ScanStartTime = 70,
MsLevel = 2,
Density = 20,
Cycle = 4,
TotalIonCurrent = 20000
};
Scan ms2scan10 = new Scan(false, tempPath)
{
IsolationWindowLowerOffset = 1,
IsolationWindowTargetMz = 1050,
IsolationWindowUpperOffset = 1,
ScanStartTime = 70.002,
MsLevel = 2,
Density = 18,
Cycle = 5,
TotalIonCurrent = 10000
};
//MS1scans
Scan ms1scan1 = new Scan(false, tempPath)
{
IsolationWindowLowerOffset = 1,
IsolationWindowUpperOffset = 1,
ScanStartTime = 0,
MsLevel = 1,
Density = 2,
Cycle = 1,
TotalIonCurrent = 1000,
BasePeakIntensity = 1000,
BasePeakMz = 1058
};
Scan ms1scan2 = new Scan(false, tempPath)
{
IsolationWindowLowerOffset = 5,
IsolationWindowUpperOffset = 5,
ScanStartTime = 30,
MsLevel = 1,
Density = 4,
Cycle = 2,
TotalIonCurrent = 3050,
BasePeakIntensity = 1500,
BasePeakMz = 459
};
Scan ms1scan3 = new Scan(false, tempPath)
{
IsolationWindowLowerOffset = 5,
IsolationWindowUpperOffset = 5,
ScanStartTime = 70,
MsLevel = 1,
Density = 4,
Cycle = 3,
TotalIonCurrent = 3050,
BasePeakIntensity = 5000,
BasePeakMz = 150
};
//BasePeaks:
var spectrumpoint1 = new SpectrumPoint(2000, 150, 2.58F)
{
};
var spectrumpoint2 = new SpectrumPoint(3000, 150.01F, 3.00F)
{
};
var spectrumpoint3 = new SpectrumPoint(3000, 150.01F, 60F)
{
};
var basePeak1 = new BasePeak(150, 2.5, 150)
{
BpkRTs = new List <double>()
{
2.5
},
Spectrum = new List <SpectrumPoint>()
{
spectrumpoint1, spectrumpoint2
},
Mz = 150
};
basePeak1.FWHMs.Add(1);
basePeak1.FWHMs.Add(2);
basePeak1.Peaksyms.Add(1);
basePeak1.Peaksyms.Add(2);
basePeak1.Intensities.Add(1);
basePeak1.Intensities.Add(2);
basePeak1.FullWidthBaselines.Add(1);
basePeak1.FullWidthBaselines.Add(2);
var basePeak2 = new BasePeak(300, 60, 150)
{
BpkRTs = new List <double>()
{
60
},
Spectrum = new List <SpectrumPoint>()
{
spectrumpoint3
}
};
basePeak2.FWHMs.Add(2);
basePeak2.Peaksyms.Add(1);
basePeak2.Intensities.Add(2);
basePeak2.FullWidthBaselines.Add(1);
//Runs:
ms2andms1Run = new Run <Scan>
{
AnalysisSettings = new AnalysisSettings
{
RtTolerance = 2.5
},
LastScanTime = 100,
StartTime = 0
};
ms2andms1Run.Ms2Scans.AddRange(new Scan[] { ms2scan1, ms2scan2, ms2scan3, ms2scan4, ms2scan5, ms2scan6, ms2scan7, ms2scan8, ms2scan9, ms2scan10 });
ms2andms1Run.Ms1Scans.AddRange(new Scan[] { ms1scan1, ms1scan2, ms1scan3 });
ms2andms1Run.BasePeaks.Add(basePeak1);
ms2andms1Run.BasePeaks.Add(basePeak2);
ms2andms1Run.SourceFileNames.Add(" ");
ms2andms1Run.SourceFileChecksums.Add(" ");
/*
* emptyms2scansRun = new Run
* {
* AnalysisSettings = new AnalysisSettings
* {
* RtTolerance = 2.5
* },
* Ms2Scans = new ConcurrentBag<Scan>() { ms2scan1, ms2scan2, ms2scan3, ms2scan4, ms2scan6 },//9 does not have upper and lower offsets
* LastScanTime = 0,
* StartTime = 1000000
* };
*
* emptyms2scansRun.BasePeaks.Add(basePeak1);
* emptyms2scansRun.SourceFileNames.Add(" ");
* emptyms2scansRun.SourceFileChecksums.Add(" ");*/
swathGrouper = new SwathGrouper();
result = swathGrouper.GroupBySwath(ms2andms1Run);
}