######## UnFinished ########

# The output file
learn.file.novorOutput = trap-trypsin.novor

# The base directory of the data files
learn.file.dataBaseDir = /u4/binma/data/novor/nistHuman/

# The data file used to learn
learn.file.trainingData = 1.msp, 2.msp, 3.msp, 4.msp, 5.msp, 6.msp, 7.msp, 8.msp
#learn.file.trainingData = 1.msp

# Number of concurrent threads for learning
learn.nThreads = 8

# Decision tree learning parameters
learn.minLeafWeight = 500
learn.minEntropyReduction = 10

#used for comparing the target sequence with the de novo sequence
learn.error.prefix = 0.5Da
learn.error.aa = 0.1Da

# Algorithm parameters.
alg.algResolution = 50
alg.maxAnchorPeaks = 250
alg.maxShortTagMass = 400
alg.backtraceQueueSize = 50
alg.massAnalyzer = Trap
alg.enzyme = Nonspecific

# User controlled parameters
user.error.product = 0.5Da
user.error.precursor = 15ppm

# Variable modifications will make algorithm to consider both modified and the original residue
user.modification.var = Carbamidomethyl (C), Oxidation (M)

# Fixed modifications will turn off the unmodified residue from consideration
#user.modification.fix = Carbamidomethyl (C),

# Do not use the following simple residues
user.residue.forbidden = I,U

