# PowerGetBatch 
# Base settings of peak detection parameters

# job selection -------------------------

job.peakdetection.new         = true
job.peakselection.new         = true
job.peakcharacterization.new  = true
job.peakeditor.new            = true

job.peakeditor.autoDbSearch   = false
job.peakeditor.annotation     = false
job.peakeditor.togomdOutput   = true
job.peakeditor.recalcAdduct   = true
job.peakeditor.rejectAlonePeak= true
job.peakeditor.overwrite      = false
job.peakeditor.checkFileOutput= true
job.peakselection.checkFileOutputAllPeak = true
job.peakselection.overwriteCheckFileAllPeak = false
job.peakselection.outputAllMsn = true
job.peakeditor.outputAllMsn   = true
job.peakeditor.outputBestAllMsn   = true
job.peakeditor.peakFileIsoExOutput= false
job.peakeditor.dbSearchDataOutput = false


# peak detection ---------------------------------

peakdetection.ms1FileIntensityCutoff  = 0

# ion grouping --------

peakdetection.isNeighbor              = true
peakdetection.roundDecimal            = 4
peakdetection.neighborMargin          = 20
peakdetection.isNeighborPpm           = true
peakdetection.neighborGap             = 2
peakdetection.isEnabledIntensityLimit = true

peakdetection.AutoIntensityLimit         = false
peakdetection.AutoIntensityLimitCenter   = 1
peakdetection.AutoIntensityLimitSdFactor = 1
peakdetection.intensityLimit          = 0

peakdetection.perScanIntensityCutoffRatio = 0.000

# group merging -------

peakdetection.mergeMargin             = 5
peakdetection.isMergePpm              = true
peakdetection.mergeGap                = 2

# peak detection ------
peakdetection.isSummation             = false

## settings for chromatogram smoothing
peakdetection.isSavitzky              = true
peakdetection.numSmoothing            = 21
peakdetection.numSmoothingMin         = 5
peakdetection.sgNL                    = 20
peakdetection.sgNR                    = 20
peakdetection.sgNLMin                 = 3
peakdetection.sgNRMin                 = 3
peakdetection.sgM                     = 4
peakdetection.numSmoothingTrial       = 20

## settings for noise estimation
peakdetection.numAveCalc              = 20
peakdetection.sdFactorStrongPeakDetection = 0.5
peakdetection.sdFactorNoisePeakRejection = 1

## settings for peak detection

peakdetection.method                   = 1
peakdetection.numGradient              = 5
peakdetection.thresholdAccumulator     = 2
peakdetection.sensitivitySlope         = 100
peakdetection.sdFactorSlopeSensitivity = 0
peakdetection.doMinMaxCutoffSensitivitySlope = false
peakdetection.minSensitivitySlope         = 100
peakdetection.maxSensitivitySlope         = 10000
peakdetection.neighborScopeValley         = 2
peakdetection.modeCalcSensitivitySlope    = 0
peakdetection.maxPeakWidthFactor          = 3
peakdetection.maxScanAsNoSegWithoutStartEnd = 3
peakdetection.ratioHeightShareBackGround = 0.2

peakdetection.minPeakHeight              = 1000
peakdetection.minPeakTopHeight           = 1000
peakdetection.maxMinTopRatio             = 0.2
peakdetection.minPearsonCor              = 0

peakdetection.maxHighestNumber   = 10
peakdetection.maxHighestValue    = 0.01
peakdetection.minScanNo          = 4

peakdetection.maxDeconvNeighborMarginPpm = 15

# peak selection --------------------------------

peakselection.fMinIonNo  = 4
peakselection.fMinInt    = 40
peakselection.fMinCor    = 0.4

peakselection.fMaxPValue = -1
peakselection.fMinRt     = -1
peakselection.fMaxRt     = -1
peakselection.fMinMz     = -1
peakselection.fMaxMz     = -1

peakselection.fMinCorCos    = -1
peakselection.fMaxPValueCos = -1

peakselection.fMinIonValidRatio = 0.6
peakselection.fMaxNeighborDifPpm = 10

peakselection.removeConstantPeaks      = true
peakselection.removeConstantOnlyValid  = false
peakselection.removeConstantPpm        = 3
peakselection.removeConstantRt         = 2
peakselection.removeConstantLimitNum   = 8
peakselection.removeConstantLimitRatio = 0.01
peakselection.removeConstantLimitCor   = 0.6

peakselection.minPeakTopHeight = 2000
peakselection.maxMinTopRatio   = 0.4

# peak characterization ---------------------------------

peakcharacter.maxChargeFind13C = 6
peakcharacter.marginMzFind13C  = 7
peakcharacter.isPpmFind13C     = true

peakcharacter.maxPeakNum13C    = 10

peakcharacter.dsMaxDist        = 6
peakcharacter.dsMaxPvalueTTest = 100
peakcharacter.dsMinCC          = 0.6
peakcharacter.dsMaxPvalueCC    = 0.0001

peakcharacter.removeGhostPeaks    = false
peakcharacter.removeGhostPpm      = 60
peakcharacter.removeGhostIntRatio = 0.8
peakcharacter.removeGhostCor      = 0.90
peakcharacter.removeGhostRt       = 6

# peak editor -------------------------------------------

peakeditor.defaultIonizationMode       = [M+H]+

peakeditor.exactMassCalc_minIonNum     = 5
peakeditor.exactMassCalc_confInterval  = 99.9999

peakeditor.exactMassCalc_usedCorrectedMass = false

peakeditor.ratio13CCalc_minPairNum     = 5
peakeditor.ratio13CCalc_confInterval   = 99.999
peakeditor.exactMassCalc.method        = 1

peakeditor.exactMassCalc_1_marginPpm   = 1

peakeditor.recalcAdduct.marginPpm      = 5
peakeditor.recalcAdduct.limitRatioToGroupMax   = 0.05
peakeditor.recalcAdduct.limitRatioBetweenPeaks = 0.05

peakeditor.rejectAlonePeak.minPeakTopHeight = 1000
peakeditor.rejectAlonePeak.maxMinTopRatio   = 0.3

peakeditor.overwrite.rt                = false
peakeditor.overwrite.mass              = false
peakeditor.overwrite.valid             = false
peakeditor.overwrite.componentIds      = false
peakeditor.overwrite.charge            = false
peakeditor.overwrite.adducts           = false
