comparison MsXlsDb.R @ 2:20d69a062da3 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8

1:253d531a0193

	###############
	
	MsXlsDb$methods( initialize = function(db_dir = NA_character_, limit = NA_integer_, cache_dir = NA_character_, cache = FALSE, ...) {

		# Initialize members
		.db_dir <<- if ( ! is.null(db_dir)) db_dir else NA_character_
		.limit <<- if ( ! is.null(limit) && ! is.na(limit) && limit > 0) limit else NA_integer_
		cache_dir <- if (cache && is.na(cache_dir) && ! is.na(db_dir)) file.path(db_dir, 'cache') else cache_dir
		.cache_dir <<- if ( cache || ! is.null(cache_dir)) cache_dir else NA_character_
		.files <<- NULL

	#################
	# GET MZ VALUES #
	#################
	
	# Returns a numeric vector of all masses stored inside the database.
	MsXlsDb$methods( getMzValues = function(mode = NULL) {

		mz <- numeric()

		# Get all mz values of all molecules
		for(molid in .self$getMoleculeIds())
			for (m in (if (is.null(mode) || is.na(mode)) c(MSDB.TAG.POS, MSDB.TAG.NEG) else mode))
				mz <- c(mz, .self$.get.peaks(molid, m)[[MSDB.TAG.MZTHEO]])

		# Remove duplicated
		mz <- mz[ ! duplicated(mz)]

		return(mz)
	})
	
	#############

2:20d69a062da3

	###############
	
	MsXlsDb$methods( initialize = function(db_dir = NA_character_, limit = NA_integer_, cache_dir = NA_character_, cache = FALSE, ...) {

		# Initialize members
		                # TODO check that db_dir is not null neither na, and tests that it exists and is a directory.
		.db_dir <<- if ( ! is.null(db_dir)) db_dir else NA_character_
		.limit <<- if ( ! is.null(limit) && ! is.na(limit) && limit > 0) limit else NA_integer_
		cache_dir <- if (cache && is.na(cache_dir) && ! is.na(db_dir)) file.path(db_dir, 'cache') else cache_dir
		.cache_dir <<- if ( cache || ! is.null(cache_dir)) cache_dir else NA_character_
		.files <<- NULL

	#################
	# GET MZ VALUES #
	#################
	
	# Returns a numeric vector of all masses stored inside the database.
	MsXlsDb$methods( getMzValues = function(mode = NULL, max.results = NA_integer_) {

		mz <- numeric()

		# Get all mz values of all molecules
		for(molid in .self$getMoleculeIds())
			for (m in (if (is.null(mode) || is.na(mode)) c(MSDB.TAG.POS, MSDB.TAG.NEG) else mode))
				mz <- c(mz, .self$.get.peaks(molid, m)[[MSDB.TAG.MZTHEO]])

		# Remove duplicated
		mz <- mz[ ! duplicated(mz)]

		# Apply cut-off
		if ( ! is.na(max.results))
			mz <- mz[1:max.results]

		return(mz)
	})
	
	#############