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annotate MsDbOutputDataFrameStream.R @ 1:45e985cd8e9e draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
author prog
date Tue, 31 Jan 2017 05:27:24 -0500
parents 3afe41d3e9e7
children b8f70d8216b3
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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1 if ( ! exists('MsDbOutputDataFrameStream')) { # Do not load again if already loaded
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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3 library(methods)
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4 source('MsDbOutputStream.R')
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5 source('dfhlp.R', chdir = TRUE)
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7 #####################
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8 # CLASS DECLARATION #
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9 #####################
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11 MsDbOutputDataFrameStream <- setRefClass("MsDbOutputDataFrameStream", contains = 'MsDbOutputStream', fields = list( .df = "ANY"))
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13 ###############
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14 # CONSTRUCTOR #
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15 ###############
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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17 MsDbOutputDataFrameStream$methods( initialize = function(keep.unused = FALSE, one.line = FALSE, match.sep = MSDB.DFT.MATCH.SEP, output.fields = msdb.get.dft.output.fields(), multval.field.sep = MSDB.DFT.OUTPUT.MULTIVAL.FIELD.SEP, first.val = FALSE, ascii = FALSE, noapostrophe = FALSE, noplusminus = FALSE, nogreek = FALSE, ...) {
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19 .df <<- data.frame()
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21 callSuper(keep.unused = keep.unused, one.line = one.line, match.sep = match.sep, output.fields = output.fields, multval.field.sep = multval.field.sep, first.val = first.val, ascii = ascii, noapostrophe = noapostrophe, noplusminus = noplusminus, nogreek = nogreek, ...)
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22 })
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24 ##################
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25 # GET DATA FRAME #
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26 ##################
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27
1
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28 MsDbOutputDataFrameStream$methods( getDataFrame = function() {
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30 # Put at least a column name if empty
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31 if (nrow(.self$.df) == 0)
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32 .self$.df[[.self$.output.fields[[MSDB.TAG.MZ]]]] <- numeric()
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34 return(.self$.df)
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35 })
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37 # Move columns to beginning {{{1
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39 MsDbOutputDataFrameStream$methods( moveColumnsToBeginning = function(cols) {
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40 all.cols <- colnames(.self$.df)
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41 other.cols <- all.cols[ ! all.cols %in% cols]
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42 cols <- cols[cols %in% all.cols]
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43 .df <<- .self$.df[c(cols, other.cols)]
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44 })
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45
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46 #################
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47 # MATCHED PEAKS #
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48 #################
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50 MsDbOutputDataFrameStream$methods( matchedPeaks = function(mz, rt = NULL, unused = NULL, peaks = NULL) {
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51
1
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52 library(plyr)
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53
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54 # Set input values
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55 x <- data.frame(mz = mz)
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56 colnames(x) <- MSDB.TAG.MZ
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57 if ( ! is.null(rt)) {
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58 x.rt <- data.frame(rt = rt)
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59 colnames(x.rt) <- MSDB.TAG.RT
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60 x <- cbind(x, x.rt)
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61 }
0
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62
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63 # Merge input values with matched peaks
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64 if ( ! is.null(peaks)) {
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65
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66 # No rows
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67 if (nrow(peaks) == 0)
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68 # Add NA values
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69 peaks[1, ] <- NA
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70
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71 # Process existing rows
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72 else {
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73 # Process multi-value fields
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74 for (c in colnames(peaks))
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75 if (c %in% MSDB.MULTIVAL.FIELDS) {
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76
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77 # Keep only first value in multi-value fields
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78 if (.self$.first.val)
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79 peaks[[c]] <- vapply(peaks[[c]], function(s) split.str(s, sep = MSDB.MULTIVAL.FIELD.SEP, unlist = TRUE)[[1]], FUN.VALUE = '')
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80
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81 # Change separator
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82 else
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83 peaks[[c]] <- vapply(peaks[[c]], function(s) paste0(split.str(s, sep = MSDB.MULTIVAL.FIELD.SEP, unlist = TRUE), collapse = .self$.multval.field.sep), FUN.VALUE = '')
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84
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85 }
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86
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87 # Concatenate results in one line
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88 if (.self$.one.line) {
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89 # For each column, concatenate all values in one string.
1
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90 for (c in seq(peaks)) {
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91 v <- peaks[[c]]
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92 v <- v[ ! is.na(v)] # remove NA values
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93 v <- v[ ! duplicated(v)] # remove duplicates
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94 peaks[1, c] <- paste0(v, collapse = .self$.match.sep, FUN.VALUE = '')
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95 }
0
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96 peaks <- peaks[1, ] # Keep only first line
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97 }
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98 }
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99
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100 # Merge
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101 x <- cbind(x, peaks, row.names = NULL)
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102 }
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103
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104 # Rename columns for output
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105 x <- rename.col(x, names(.self$.output.fields), .self$.output.fields)
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106
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107 # Add unused columns
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108 if ( .self$.keep.unused && ! is.null(unused)) {
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109 x <- cbind(x, unused, row.names = NULL)
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110 }
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111
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112 # Convert strings to ASCII
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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113 if (.self$.ascii || .self$.noapostrophe || .self$.noplusminus || .self$.nogreek)
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114 for (c in seq(x))
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115 if (class(x[[c]]) == 'character') {
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116 if (.self$.noapostrophe)
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117 x[[c]] <- gsub("'", 'prime', x[[c]], perl = TRUE)
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118 if (.self$.noplusminus)
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119 x[[c]] <- gsub('±', '+-', x[[c]], perl = TRUE)
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120 if (.self$.nogreek) {
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121 x[[c]] <- gsub('α', 'alpha', x[[c]], perl = TRUE)
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122 x[[c]] <- gsub('β', 'beta', x[[c]], perl = TRUE)
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123 x[[c]] <- gsub('γ', 'gamma', x[[c]], perl = TRUE)
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124 x[[c]] <- gsub('δ', 'delta', x[[c]], perl = TRUE)
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125 }
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126 if (.self$.ascii) {
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127 x[[c]] <- gsub('[^\u0001-\u007F]', '_', x[[c]], perl = TRUE)
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128 }
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129 }
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130
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131 # Add new rows to data frame
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132 .df <<- rbind.fill(.self$.df, x)
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133 })
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134
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135 } # end of load safe guard