lcmsmatching: MsDb.R annotate

annotate MsDb.R @ 6:b8f70d8216b3 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty

author	prog
date	Mon, 27 Mar 2017 06:27:29 -0400
parents	1ba222315fd5
children

rev	line source
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	1 if ( ! exists('MsDb')) { # Do not load again if already loaded
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	2
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	3 library('methods')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	4 source('msdb-common.R')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	5 source('MsDbObserver.R')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	6 source('MsDbOutputStream.R')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	7
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	8 #####################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	9 # CLASS DECLARATION #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	10 #####################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	11
4 1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	12 MsDb <- setRefClass("MsDb", fields = list(.observers = "ANY", .prec = "list", .output.streams = "ANY", .input.stream = "ANY", .mz.tol.unit = "character", .rt.unit = "character"))
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	13
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	14 ###############
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	15 # CONSTRUCTOR #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	16 ###############
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	17
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	18 MsDb$methods( initialize = function(...) {
4 1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	19
1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	20 callSuper(...)
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	21
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	22 .observers <<- NULL
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	23 .output.streams <<- NULL
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	24 .input.stream <<- NULL
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	25 .prec <<- MSDB.DFT.PREC
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	26 .mz.tol.unit <<- MSDB.DFT.MZTOLUNIT
4 1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	27 .rt.unit <<- MSDB.RTUNIT.SEC
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	28 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	29
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	30 ####################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	31 # SET INPUT STREAM #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	32 ####################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	33
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	34 MsDb$methods( setInputStream = function(stream) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	35
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	36 # Check types of input stream
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	37 if ( ! inherits(stream, "MsDbInputStream") && ! is.null(stream))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	38 stop("Input stream must inherit from MsDbInputStream class.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	39
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	40 # Save current stream
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	41 cur.stream <- .self$.input.stream
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	42
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	43 # Set stream
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	44 .input.stream <<- stream
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	45
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	46 return(cur.stream)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	47 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	48
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	49 ######################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	50 # ADD OUTPUT STREAMS #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	51 ######################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	52
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	53 MsDb$methods( addOutputStreams = function(stream) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	54
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	55 # Check types of output streams
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	56 if ( ( ! is.list(stream) && ! inherits(stream, "MsDbOutputStream")) \|\| (is.list(stream) && any( ! vapply(stream, function(s) inherits(s, "MsDbOutputStream"), FUN.VALUE = TRUE))))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	57 stop("Output streams must inherit from MsDbOutputStream class.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	58
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	59 # Add streams to current list
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	60 .output.streams <<- if (is.null(.self$.output.streams)) c(stream) else c(.self$.output.streams, stream)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	61 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	62
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	63 #########################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	64 # REMOVE OUTPUT STREAMS #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	65 #########################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	66
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	67 MsDb$methods( removeOutputStreams = function(stream) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	68
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	69 # Check types of output streams
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	70 if ( ( ! is.list(stream) && ! inherits(stream, "MsDbOutputStream")) \|\| (is.list(stream) && any( ! vapply(stream, function(s) inherits(s, "MsDbOutputStream"), FUN.VALUE = TRUE))))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	71
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	72 # Remove streams from current list
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	73 .output.streams <<- .self$.output.streams[ ! stream %in% .self$.output.streams]
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	74 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	75
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	76 ########################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	77 # RESET OUTPUT STREAMS #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	78 ########################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	79
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	80 MsDb$methods( resetOutputStreams = function(stream) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	81 .output.streams <<- NULL
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	82 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	83
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	84 #################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	85 # ADD OBSERVERS #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	86 #################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	87
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	88 MsDb$methods( addObservers = function(obs) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	89
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	90 # Check types of observers
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	91 if ( ( ! is.list(obs) && ! inherits(obs, "MsDbObserver")) \|\| (is.list(obs) && any( ! vapply(obs, function(o) inherits(o, "MsDbObserver"), FUN.VALUE = TRUE))))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	92 stop("Observers must inherit from MsDbObserver class.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	93
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	94 # Add observers to current list
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	95 .observers <<- if (is.null(.self$.observers)) c(obs) else c(.self$.observers, obs)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	96 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	97
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	98 ##################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	99 # SET PRECURSORS #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	100 ##################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	101
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	102 MsDb$methods( setPrecursors = function(prec) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	103 .prec <<- prec
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	104 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	105
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	106 #################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	107 # SET DB FIELDS #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	108 #################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	109
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	110 MsDb$methods( areDbFieldsSettable = function() {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	111 return(FALSE)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	112 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	113
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	114 MsDb$methods( setDbFields = function(fields) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	115 stop("Method setDbFields() not implemented in concrete class.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	116 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	117
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	118 ################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	119 # SET MS MODES #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	120 ################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	121
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	122 MsDb$methods( areDbMsModesSettable = function() {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	123 return(FALSE)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	124 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	125
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	126 MsDb$methods( setDbMsModes = function(modes) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	127 stop("Method setDbMsModes() not implemented in concrete class.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	128 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	129
4 1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	130 ###################
1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	131 # SET MZ TOL UNIT #
1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	132 ###################
1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	133
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	134 MsDb$methods( setMzTolUnit = function(mztolunit) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	135
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	136 if ( ! mztolunit %in% MSDB.MZTOLUNIT.VALS)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	137 stop(paste0("M/Z tolerance unit must be one of: ", paste(MSDB.MZTOLUNIT.VALS, collapse = ', '), "."))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	138
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	139 .mz.tol.unit <<- mztolunit
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	140 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	141
4 1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	142 ###############
1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	143 # SET RT UNIT #
1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	144 ###############
1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	145
1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	146 MsDb$methods( setRtUnit = function(unit) {
1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	147
1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	148 if ( ! unit %in% MSDB.RTUNIT.VALS)
1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	149 stop(paste0("RT unit must be one of: ", paste(MSDB.RTUNIT.VALS, collapse = ', '), "."))
1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	150
1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	151 .rt.unit <<- unit
1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	152 })
1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	153
6 b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty prog parents: 4 diff changeset	154 ###############
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty prog parents: 4 diff changeset	155 # GET RT UNIT #
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty prog parents: 4 diff changeset	156 ###############
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty prog parents: 4 diff changeset	157
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty prog parents: 4 diff changeset	158 MsDb$methods( getRtUnit = function(unit) {
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty prog parents: 4 diff changeset	159 return(.self$.rt.unit)
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty prog parents: 4 diff changeset	160 })
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty prog parents: 4 diff changeset	161
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	162 ####################
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	163 # HANDLE COMPOUNDS #
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	164 ####################
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	165
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	166 # Returns TRUE if this database handles compounds directly (by IDs)
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	167 MsDb$methods( handleCompounds = function() {
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	168 return(TRUE)
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	169 })
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	170
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	171 ####################
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	172 # GET MOLECULE IDS #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	173 ####################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	174
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	175 # Returns an integer vector of all molecule IDs stored inside the database.
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	176 MsDb$methods( getMoleculeIds = function(max.results = NA_integer_) {
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	177 stop("Method getMoleculeIds() not implemented in concrete class.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	178 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	179
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	180 ####################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	181 # GET NB MOLECULES #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	182 ####################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	183
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	184 # Returns the number of molecules in the database.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	185 MsDb$methods( getNbMolecules = function() {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	186 stop("Method getNbMolecules() not implemented in concrete class.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	187 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	188
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	189 #################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	190 # GET MZ VALUES #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	191 #################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	192
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	193 # Returns a numeric vector of all masses stored inside the database.
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	194 MsDb$methods( getMzValues = function(mode = NULL, max.results = NA_integer_) {
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	195 stop("Method getMzValues() not implemented in concrete class.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	196 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	197
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	198 #####################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	199 # GET MOLECULE NAME #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	200 #####################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	201
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	202 # Get molecule names
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	203 # molid An integer vector of molecule IDs.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	204 # Returns a character vector containing the names of the molecule IDs, in the same order as the input vector.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	205 MsDb$methods( getMoleculeName = function(molid) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	206 stop("Method getMoleculeName() not implemented in concrete class.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	207 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	208
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	209 ###############################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	210 # GET CHROMATOGRAPHIC COLUMNS #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	211 ###############################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	212
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	213 # Get chromatographic columns.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	214 # Returns a vector of character listing the chromatographic column names. The name must be formatted in lowercase as following: uplc(-c8)?(-20min)?.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	215 MsDb$methods( getChromCol = function(molid = NULL) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	216 stop("Method getChromCol() not implemented in concrete class.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	217 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	218
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	219 ################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	220 # FIND BY NAME #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	221 ################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	222
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	223 # Find a molecule by name
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	224 # name A vector of molecule names to search for.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	225 # Return an integer vector of the same size as the name input vector, containing the found molecule IDs, in the same order.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	226 MsDb$methods( findByName = function(name) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	227 stop("Method findByName() not implemented in concrete class.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	228 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	229
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	230 #######################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	231 # GET RETENTION TIMES #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	232 #######################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	233
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	234 # Get the retention times of a molecule.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	235 # Returns a list of numeric vectors. The list has for keys/names the columns, and for values vectors of numerics (the retention times). If no retention times are registered for this molecule, then returns an empty list.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	236 MsDb$methods( getRetentionTimes = function(molid, col = NA_character_) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	237 stop("Method getRetentionTimes() not implemented in concrete class.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	238 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	239
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	240 ################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	241 # GET NB PEAKS #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	242 ################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	243
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	244 # Get the total number of MS peaks stored inside the database.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	245 # molid The ID of the molecule.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	246 # type The MS type.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	247 MsDb$methods( getNbPeaks = function(molid = NA_integer_, type = NA_character_) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	248 stop("Method getNbPeaks() not implemented in concrete class.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	249 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	250
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	251 ##################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	252 # GET PEAK TABLE #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	253 ##################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	254
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	255 MsDb$methods( getPeakTable = function(molid = NA_integer_, mode = NA_character_) {
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	256 stop("Method getPeakTable() not implemented in concrete class.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	257 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	258
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	259 ##########
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	260 # SEARCH #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	261 ##########
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	262
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	263 # Find molecule MS peaks whose m/z matches the submitted m/z in the tolerance specified.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	264 # mode The mode to use: either MSDB.TAG.POS or MSDB.TAG.NEG.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	265 # shift The m/z shift to use, in ppm.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	266 # prec The m/z precision to use, in ppm.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	267 # col The chromatographic column used.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	268 # rt.tol Simple retention tolerance parameter: rtinf = rt - rt.tol and rtsup = rt + rt.tol
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	269 # rt.tol.x Tolerance parameter for the equations : rtinf = rt - rt.tol.x - rt ^ rt.tol.y and rtsup = rt + rt.tol.x + rt ^ rt.tol.y
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	270 # rt.tol.y Tolerance parameter. See rt.tol.x parameter.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	271 # attribs Only search for peaks whose attribution is among this set of attributions.
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	272 # molids Only search for peaks whose molecule ID is among this vector of integer molecule IDs. Can also be a data frame with a retention time column x.colnames$rt and a molecule ID column MSDB.TAG.MOLID.
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	273 # molids.rt.tol Retention time tolerance used when molids parameter is a data frame (rt, id)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	274 # precursor.match Remove peaks whose molecule precursor peak has not also been matched.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	275 # precursor.rt.tol
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	276 # Returns a data frame, listing m/z values provided in input. Several matches can be found for an m/z value, in which case several lines (the same number as the number of matches found) with the same m/z value repeated will be inserted. The m/z values will be listed in the same order as in the input. The columns of the data.frame are: mz, rt (only if present in the input), id, mztheo, col, colrt, composition, attribution.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	277 MsDb$methods( searchForMzRtList = function(x = NULL, mode, shift = NULL, prec = NULL, col = NULL, rt.tol = NULL, rt.tol.x = NULL, rt.tol.y = NULL, molids = NULL, molids.rt.tol = NULL, attribs = NULL, precursor.match = FALSE, precursor.rt.tol = NULL, same.cols = FALSE, same.rows = FALSE, peak.table = FALSE) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	278
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	279 # Use provided data frame
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	280 old.input <- NULL
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	281 tmp.output <- NULL
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	282 if ( ! is.null(x)) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	283 tmp.input <- MsDbInputDataFrameStream$new(df = x)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	284 tmp.output <- MsDbOutputDataFrameStream$new()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	285 old.input <- .self$setInputStream(tmp.input)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	286 .self$addOutputStreams(tmp.output)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	287 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	288
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	289 if (precursor.match) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	290 # Get IDs of all molecules whose precursor peak matches one of the mz in the list
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	291 precursors.df <- .self$.doSearchForMzRtList(mode = mode, shift = shift, prec = prec, col = col, rt.tol = rt.tol, rt.tol.x = rt.tol.x, rt.tol.y = rt.tol.y, attribs = .self$.prec[[mode]], output.to.stream = FALSE)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	292 cols.to.keep <- if (is.null(col)) MSDB.TAG.MOLID else c(MSDB.TAG.MOLID, MSDB.TAG.COL, MSDB.TAG.COLRT)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	293 precursors.ids <- precursors.df[, cols.to.keep, drop = FALSE]
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	294 precursors.ids <- precursors.ids[ ! is.na(precursors.ids[[MSDB.TAG.MOLID]]), , drop = FALSE]
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	295 precursors.ids <- precursors.ids[ ! duplicated(precursors.ids), ]
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	296
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	297 # Get all matching peaks whose molecule is inside the previously obtained list of molecules
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	298 df <- .self$.doSearchForMzRtList(mode = mode, shift = shift, prec = prec, col = col, rt.tol = NULL, rt.tol.x = NULL, rt.tol.y = NULL, molids = precursors.ids, molids.rt.tol = precursor.rt.tol, same.cols = same.cols, same.rows = same.rows, peak.table = peak.table)
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	299 # TODO
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	300 #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	301 # peaks <- if (peak.table) results[['peaks']] else results
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	302 #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	303 # # Merge results with the column/rt found for precursors.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	304 # if ( ! is.null(col) && ! is.null(peaks)) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	305 # precursors.ids <- precursors.df[, c(MSDB.TAG.MOLID, MSDB.TAG.col, MSDB.TAG.COLRT)]
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	306 # precursors.ids <- precursors.ids[ ! is.na(precursors.ids[[MSDB.TAG.MOLID]]), ]
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	307 #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	308 # # Get rows where ID is NA
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	309 # peaks.na <- peaks[is.na(peaks[[MSDB.TAG.MOLID]]), ]
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	310 #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	311 # # Get rows where ID is found (i.e.: not NA)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	312 # peaks <- peaks[, !(colnames(peaks) %in% c(MSDB.TAG.COL, MSDB.TAG.COLRT))] # drop col and colrt columns
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	313 # peaks.not.na <- peaks[! is.na(peaks[[MSDB.TAG.MOLID]]), ]
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	314 #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	315 # # Add col and colrt values to found peaks
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	316 # peaks <- merge(peaks.not.na, precursors.ids, by = MSDB.TAG.MOLID)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	317 #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	318 # # Put back unfound peaks
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	319 # peaks <- rbind(peaks, peaks.na)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	320 #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	321 # # Sort
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	322 # peaks <- peaks[order(peaks[[x.colnames$mz]], peaks[[x.colnames$rt]], peaks[[MSDB.TAG.MOLID]], peaks[[MSDB.TAG.COL]]), ]
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	323 #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	324 # # Remove rownames
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	325 # rownames(peaks) <- NULL
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	326 #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	327 # # Reorder columns
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	328 # peaks <- peaks[unlist(.self$.output.fields[names(.PEAK.TABLE.COLS)])]
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	329 # }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	330 #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	331 # # Remove duplicates
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	332 # if ( ! is.null(peaks))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	333 # peaks <- peaks[ ! duplicated(peaks), ]
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	334 #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	335 # if (peak.table)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	336 # results[['peaks']] <- peaks
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	337 # else
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	338 # results <- peaks
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	339 #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	340 # return(results)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	341 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	342 else
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	343 .self$.doSearchForMzRtList(mode = mode, shift = shift, prec = prec, col = col, rt.tol = rt.tol, rt.tol.x = rt.tol.x, rt.tol.y = rt.tol.y, molids = molids, molids.rt.tol = molids.rt.tol, attribs = attribs, same.cols = same.cols, same.rows = same.rows, peak.table = peak.table)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	344
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	345 if ( ! is.null(x)) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	346 results <- tmp.output$getDataFrame()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	347 .self$removeOutputStreams(tmp.output)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	348 .self$setInputStream(old.input)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	349 return(results)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	350 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	351 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	352
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	353 MsDb$methods( .doSearchForMzRtList = function(mode, shift = NULL, prec = NULL, col = NULL, rt.tol = NULL, rt.tol.x = NULL, rt.tol.y = NULL, molids = NULL, molids.rt.tol = NULL, attribs = NULL, same.cols = FALSE, same.rows = FALSE, peak.table = FALSE, output.to.stream = TRUE) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	354
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	355 # # Choose columns to keep from x
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	356 # x.cols <- if (same.cols) colnames(x) else intersect(if (is.null(col)) c(x.colnames$mz) else c(x.colnames$mz, x.colnames$rt), colnames(x))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	357 #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	358 # # Create a peak fake data frame for defining columns
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	359 # peaks.fake <- data.frame(stringsAsFactors = FALSE)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	360 # for (field in names(.PEAK.TABLE.COLS))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	361 # if ( ! is.null(col) \|\| ! field %in% .RT.MATCHING.COLS)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	362 # peaks.fake[.self$.output.fields[[field]]] <- vector(mode = .PEAK.TABLE.COLS[[field]], length = 0)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	363 #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	364 # # Initialize y data frame, so when x contains no rows an empty y data frame is returned with all the columns set with right type.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	365 # if (same.rows) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	366 # y <- peaks.fake[, if (is.null(col)) c(MSDB.TAG.MZ) else c(MSDB.TAG.MZ, MSDB.TAG.RT), drop = FALSE]
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	367 # y[MSDB.TAG.MSMATCHING] <- character()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	368 # }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	369 # else
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	370 # y <- peaks.fake
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	371 # y <- cbind(y, x[NULL, ! x.cols %in% colnames(y), drop = FALSE])
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	372 # if (peak.table) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	373 # z <- peaks.fake
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	374 # z <- cbind(z, x[NULL, ! x.cols %in% colnames(z), drop = FALSE])
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	375 # }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	376
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	377 # Loop on all lines of input
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	378 peaks <- NULL
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	379 .self$.input.stream$reset()
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	380 while (.self$.input.stream$hasNextValues()) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	381
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	382 .self$.input.stream$nextValues()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	383
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	384 # Search for m/z
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	385 results <- .self$searchForMzRtTols(mode = mode, mz = .self$.input.stream$getMz(), shift = shift, prec = prec, rt = .self$.input.stream$getRt(), col = col, rt.tol = rt.tol, rt.tol.x = rt.tol.x, rt.tol.y = rt.tol.y, attribs = attribs, molids = molids, molids.rt.tol = molids.rt.tol)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	386
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	387 # Call output streams
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	388 if (output.to.stream && ! is.null(.self$.output.streams))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	389 for (s in .self$.output.streams)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	390 s$matchedPeaks(mz = .self$.input.stream$getMz(), rt = if (is.null(col)) NULL else .self$.input.stream$getRt(), peaks = results, unused = .self$.input.stream$getAll(but = if (is.null(col)) c(MSDB.TAG.MZ) else c(MSDB.TAG.MZ, MSDB.TAG.RT)))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	391
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	392 # Append to peak list
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	393 peaks <- rbind(peaks, results)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	394
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	395 # # Add results to output
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	396 # r <- nrow(y) + 1
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	397 # x.lines <- x[i, x.cols, drop = FALSE]
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	398 # x.lines <- rename.col(x.lines, unlist(x.colnames), unlist(.self$.output.fields[names(x.colnames)]))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	399 # if (nrow(results) == 0) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	400 # y[r, colnames(x.lines)] <- x.lines
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	401 # }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	402 # else {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	403 # if (same.rows) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	404 # y[r, colnames(x.lines)] <- x.lines
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	405 # ids <- results[[MSDB.TAG.MOLID]]
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	406 # ids <- ids[ ! duplicated(ids)] # Remove duplicated values
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	407 # y[r, MSDB.TAG.msmatching] <- paste(ids, collapse = .self$.molids.sep)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	408 # }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	409 # if ( ! same.rows \|\| peak.table) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	410 # new.rows <- cbind(x.lines, results, row.names = NULL)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	411 # if ( ! same.rows) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	412 # rows <- r:(r+nrow(results)-1)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	413 # y[rows, colnames(new.rows)] <- new.rows
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	414 # }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	415 # if (peak.table) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	416 # zr <- nrow(z) + 1
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	417 # zrows <- zr:(zr+nrow(results)-1)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	418 # z[zrows, colnames(new.rows)] <- new.rows
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	419 # }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	420 # }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	421 # }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	422 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	423
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	424 # results <- if (peak.table) list(main = y, peaks = z) else y
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	425
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	426 # return(results)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	427 return(peaks)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	428 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	429
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	430 # rt Retention time in seconds.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	431 # molids An option vector of molecule IDs, used to restrict the search.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	432 MsDb$methods( searchForMzRtTols = function(mode, mz, rt = NULL, shift = NULL, prec = NULL, col = NULL, rt.tol = NULL, rt.tol.x = NULL, rt.tol.y = NULL, attribs = NULL, molids = NULL, molids.rt.tol = NULL, colnames = MSDB.DFT.INPUT.FIELDS) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	433
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	434 # Set M/Z bounds
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	435 if (.self$.mz.tol.unit == MSDB.MZTOLUNIT.PPM) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	436 mz.low <- mz * (1 + (- shift - prec) * 1e-6)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	437 mz.high <- mz * (1 + (- shift + prec) * 1e-6)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	438 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	439 else { # PLAIN
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	440 mz.low <- mz - shift - prec
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	441 mz.high <- mz - shift + prec
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	442 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	443
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	444 # Set retention time bounds
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	445 rt.low <- NULL
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	446 rt.high <- NULL
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	447 if ( ! is.null(rt.tol)) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	448 low <- rt - rt.tol
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	449 high <- rt + rt.tol
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	450 rt.low <- if (is.null(rt.low)) low else max(low, rt.low)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	451 rt.high <- if (is.null(rt.high)) high else min(high, rt.high)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	452 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	453 if ( ! is.null(rt.tol.x)) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	454 low <- rt - rt.tol.x - rt ^ rt.tol.y
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	455 high <- rt + rt.tol.x + rt ^ rt.tol.y
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	456 rt.low <- if (is.null(rt.low)) low else max(low, rt.low)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	457 rt.high <- if (is.null(rt.high)) high else min(high, rt.high)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	458 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	459
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	460 # List molecule IDs
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	461 if ( ! is.null(molids.rt.tol) && is.data.frame(molids)) {
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	462 ids <- molids[(rt >= molids[[MSDB.TAG.COLRT]] - molids.rt.tol) & (rt <= molids[[MSDB.TAG.COLRT]] + molids.rt.tol), MSDB.TAG.MOLID]
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	463 if (length(ids) == 0)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	464 # No molecule ID match for this retention time
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	465 return(data.frame()) # return empty result set
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	466 } else {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	467 ids <- molids
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	468 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	469
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	470 return(.self$searchForMzRtBounds(mode,
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	471 mz.low = mz * (1 + (- shift - prec) * 1e-6),
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	472 mz.high = mz * (1 + (- shift + prec) * 1e-6),
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	473 rt.low = rt.low,
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	474 rt.high = rt.high,
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	475 col = col,
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	476 attribs = attribs,
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	477 molids = ids))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	478 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	479
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	480 # rt.low Lower bound of the retention time in seconds.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	481 # rt.high Higher bound of the retention time in seconds.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	482 MsDb$methods( searchForMzRtBounds = function(mode, mz.low, mz.high, rt.low = NULL, rt.high = NULL, col = NULL, attribs = NULL, molids = NULL) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	483
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	484 results <- .self$.do.search.for.mz.rt.bounds(mode = mode, mz.low = mz.low, mz.high = mz.high, rt.low = rt.low, rt.high = rt.high, col = col, attribs = attribs, molids = molids)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	485
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	486 return(results)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	487 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	488
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	489 # TODO Write description of output: data frame with which columns ?
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	490 MsDb$methods( .do.search.for.mz.rt.bounds = function(mode, mz.low, mz.high, rt.low = NULL, rt.high = NULL, col = NULL, attribs = NULL, molids = NULL) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	491 stop("Method .do.search.for.mz.rt.bounds() not implemented in concrete class.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	492 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	493
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	494 # DEPRECATED
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	495 MsDb$methods( searchForMz = function(x, mode, tol = 5, col = NULL, rt.tol.x = 5, rt.tol.y = 0.80) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	496 warning("Method searchForMz() is deprecated. Use searchForMzRtList() instead.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	497 .self$searchForMzRtList(x = x, mode = mode, prec = tol, col = col, rt.tol.x = rt.tol.x, rt.tol.y = rt.tol.y)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	498 })
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	499
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	500 } # end of load safe guard

Mercurial > repos > prog > lcmsmatching

annotate MsDb.R @ 6:b8f70d8216b3 draft