Mercurial > repos > prog > lcmsmatching

comparison MsDbOutputDataFrameStream.R @ 5:fb9c0409d85c draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 608d9e59a0d2dcf85a037968ddb2c61137fb9bce
author prog
date Wed, 19 Apr 2017 10:00:05 -0400
parents 20d69a062da3
children
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4:b34c14151f25 5:fb9c0409d85c
6 6
7 ##################### 7 #####################
8 # CLASS DECLARATION # 8 # CLASS DECLARATION #
9 ##################### 9 #####################
10 10
11 MsDbOutputDataFrameStream <- setRefClass("MsDbOutputDataFrameStream", contains = 'MsDbOutputStream', fields = list( .df = "ANY")) 11 MsDbOutputDataFrameStream <- setRefClass("MsDbOutputDataFrameStream", contains = 'MsDbOutputStream', fields = list( .df = "ANY", .output.fields = "ANY"))
12 12
13 ############### 13 ###############
14 # CONSTRUCTOR # 14 # CONSTRUCTOR #
15 ############### 15 ###############
16 16
17 MsDbOutputDataFrameStream$methods( initialize = function(keep.unused = FALSE, one.line = FALSE, match.sep = MSDB.DFT.MATCH.SEP, output.fields = msdb.get.dft.output.fields(), multval.field.sep = MSDB.DFT.OUTPUT.MULTIVAL.FIELD.SEP, first.val = FALSE, ascii = FALSE, noapostrophe = FALSE, noplusminus = FALSE, nogreek = FALSE, ...) { 17 MsDbOutputDataFrameStream$methods( initialize = function(keep.unused = FALSE, one.line = FALSE, match.sep = MSDB.DFT.MATCH.SEP, output.fields = NULL, multval.field.sep = MSDB.DFT.OUTPUT.MULTIVAL.FIELD.SEP, first.val = FALSE, ascii = FALSE, noapostrophe = FALSE, noplusminus = FALSE, nogreek = FALSE, ...) {
18
19 callSuper(keep.unused = keep.unused, one.line = one.line, match.sep = match.sep, multval.field.sep = multval.field.sep, first.val = first.val, ascii = ascii, noapostrophe = noapostrophe, noplusminus = noplusminus, nogreek = nogreek, ...)
18 20
19 .df <<- data.frame() 21 .df <<- data.frame()
20 22 .output.fields <<- output.fields
21 callSuper(keep.unused = keep.unused, one.line = one.line, match.sep = match.sep, output.fields = output.fields, multval.field.sep = multval.field.sep, first.val = first.val, ascii = ascii, noapostrophe = noapostrophe, noplusminus = noplusminus, nogreek = nogreek, ...)
22 }) 23 })
23 24
24 ################## 25 ##################
25 # GET DATA FRAME # 26 # GET DATA FRAME #
26 ################## 27 ##################
55 x <- data.frame(mz = mz) 56 x <- data.frame(mz = mz)
56 colnames(x) <- MSDB.TAG.MZ 57 colnames(x) <- MSDB.TAG.MZ
57 if ( ! is.null(rt)) { 58 if ( ! is.null(rt)) {
58 x.rt <- data.frame(rt = rt) 59 x.rt <- data.frame(rt = rt)
59 colnames(x.rt) <- MSDB.TAG.RT 60 colnames(x.rt) <- MSDB.TAG.RT
61 if (.self$.rtunit == MSDB.RTUNIT.MIN)
62 x.rt[[MSDB.TAG.RT]] <- x.rt[[MSDB.TAG.RT]] / 60
60 x <- cbind(x, x.rt) 63 x <- cbind(x, x.rt)
61 } 64 }
65
62 66
63 # Merge input values with matched peaks 67 # Merge input values with matched peaks
64 if ( ! is.null(peaks)) { 68 if ( ! is.null(peaks)) {
65 69
66 # No rows 70 # No rows
67 if (nrow(peaks) == 0) 71 if (nrow(peaks) == 0) {
68 # Add NA values 72 # Add NA values
69 peaks[1, ] <- NA 73 peaks[1, ] <- NA
70 74
71 # Process existing rows 75 # Process existing rows
72 else { 76 } else {
77
78 # Convert RT
79 if (.self$.rtunit == MSDB.RTUNIT.MIN)
80 if (MSDB.TAG.COLRT %in% colnames(peaks))
81 peaks[[MSDB.TAG.COLRT]] <- peaks[[MSDB.TAG.COLRT]] / 60
82
73 # Process multi-value fields 83 # Process multi-value fields
74 for (c in colnames(peaks)) 84 for (c in colnames(peaks))
75 if (c %in% MSDB.MULTIVAL.FIELDS) { 85 if (c %in% MSDB.MULTIVAL.FIELDS) {
76 86
77 # Keep only first value in multi-value fields 87 # Keep only first value in multi-value fields