#############################################################################
########### OPTIONS AND PARAMETERS FILE FOR BRUKER MS DATA PARSER ###########
#############################################################################
#
#  The Bruker MS Data Parser reads binary fid files (up to 80,000 points per
#  spectra), along with other associated experimental files to create a tofList
#  and tofListMetaData which are saved as .Rdat files.
#  
#    EXPECTED CONTENTS OF INPUT DATA DIRECTORY:
#      spot subdirectories with names like "0_A1" and "0_L5", each containing 
#         EITHER (for Linear mode):   
#	    /1/1SLin/fid  # the binary data file (required)
#	    /1/1SLin/acqu # the acquisition information file (required)
#	    /1/1SLin/pdata/1/proc # the processing file  (required)
#         OR (for Relfector mode):   
#	    /1/1SRef/fid  # the binary data file (required)
#	    /1/1SRef/acqu # the acquisition information file (required)
#	    /1/1SRef/pdata/1/proc # the processing file  (required)
#      a subdirectory with calibration in the name (optional)
#      a file with the extension  (optional)
#      a file with the extension .axe (optional)
#      a file with the extension .isset (optional)
#      a file named sample.xml (optional)
#
#  OPTIONS:
#
#    Data can be parsed for a single "run" or mulitple "runs".
#    Data from multiple runs can be concatenated.
#    Memory and time usage can be printed during parsing
#
#  OUTPUT:
#  
#    tofList - list of time-of-flight mass spectrum 
#              addressable by spectrumName.
#    tofListMetaData - A data.frame containing string values 
#              for experimental meta-data, with rows and columns 
#              addressable by spectrumName and attributeName.
#
#############################################################################


ParserParams<-list()


# Specify laboratory where data was obtained


ParserParams$dataSource <- "EVMS"


# Specify if multiple runs are to be parsed, "yes" or "no"


ParserParams$multipleRuns <- "no" 


# Specify whether or not to concatenate tofLists, "yes" or "no"


ParserParams$concatLists <- "no" 


# Specify the indices of the runs to parse. 
# MUST APPEAR IN DATA DIRECTORY PATH


ParserParams$runIndices <- 1


# Specify data directory path to the left of the index (or complete path if 
# parsing one run)


directory = system.file("Examples", package = "WMBrukerParser")
ParserParams$dataDirLeft <- paste(directory,"/C3ValidationExtractSmall/RobotRun1/2-100kDa",sep="")


# Specify data directory path to the right of the index (if there is one).


ParserParams$dataDirRight <- ""


# Specify whether or not memory and time usage are to printed during parsing


ParserParams$printMemoryUse <- "no"
