# Init file content: each item should be placed in one single row.
# The current implementation of the model is developed and tested
# based on label free ESI-LC-MS data. Lines with "#" at the begining
# are comments and they will not be parsed by the program.

# Note: the following keywords are case sensitive. Please specify the path
# of each resource below.

# xtandem database search result
xtandemXML=mouse.2011_03_10_02_52_50.t.xml

# The file can be generated by Trans-Proteomic Pipeline (TPP)
prophetFile=interact.pep.xml

# Save the xtandem search xml parsing result
tandemSaveName=xtandem_identified_list.txt

# EvaluationResult obtained from xtandem search result
evaXtandemSaveName=xtandemroc.txt

# Raw mzXML file
mzXMLFileName=LQ20060327_s_dbaHMPre10_14.mzXML

# MS1 spectra save dir
outputDir=raw_data\

# model data directory: Save the regression model build by the program. If
# regression parameter (e.g. lambda) changes, the model does not need to rebuild 
# and thus it saves time.
modelSaveDir=model_data\

# the program will save the protein peptide map here
ProteinPeptideMapSave=pp_map.txt

# protein peptide map excel file contains proteins. This file is generated for debugging.
# Use "ProteinPeptideLinker.setcsvstate("no")" to turn this function off.
PPMapProteinCSV=proteins.csv

# protein peptide map excel file contains pp_map. This file is generated for debugging.
# Use "ProteinPeptideLinker.setcsvstate("no")" to turn this function off.
PPMapContentCSV=pp_map.csv

# output re-ranking result
rerankedSeqList=re_ranked_seq.txt

# output q-value vs num_of_hit curve
rerankedEvaSaveName=mouse_curve.txt

# ------------- parameters of the program ---------------
# define the decoy key word used in decoy database construction. This is just used for
# the performance evaluation purpose.
decoyKeyWord=decoy

# ------------- parameters used to build the model ------
# regularized parameter, the maximal value could be "max(abs(protein_basis'*target_data))"
# the ratio below should be within [0, 1]. Generally, this parameter can be set around
# 0.05
regularizedParameterRatio=0.06

# data mz range
mzRangesLow=210
mzRangesHigh=1980

# when the following parameter is true and there exists "model.mat" in the directory
# modelSaveDir, then the program will not try to generate a new model by loading ms
# spectra, estimating isotopic distribution and preparing bases for the model. This
# choice could be a way to speed up your program when you only have to change 
# "scoreCombineWeight" and "regularizedParameter"
regenerateModel=false

# low resolution or not
lowResolutionData=true

# enable log tranform on raw intensity.
enableLogTranform=true

# the number of isotopes considered. For high resolution data, this could be 3 or 4;
# for low resolution data, this could be 1
numOfIsotopes=1

# mass error in Da. For high resolution data, this could be 0.1Da
massError=0.6

# charges considered, each charge is separated by ",". When you only want to consider
# charge state "1, 2, 3", then "chargeList=1,2,3". Note: "chargeList=,1,2,3" and 
# "chargeList=1,2,3," are invalid and will produce "NaN" in the program. "," can only be
# placed between numbers.
chargeList=1,2,3

# -------------- parameters used to recompute scores -------
# Typical values can be 0.8 ~ 0.99. The default value is 0.99 (please do not use 1).
# Generally, you do not have to change this parameter.
sigValue=0.99