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annotate MsDbOutputDataFrameStream.R @ 6:b8f70d8216b3 draft

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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 45e985cd8e9e
children
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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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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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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", .output.fields = "ANY"))
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13 ###############
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14 # CONSTRUCTOR #
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15 ###############
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17 MsDbOutputDataFrameStream$methods( initialize = function(keep.unused = FALSE, one.line = FALSE, match.sep = MSDB.DFT.MATCH.SEP, output.fields = NULL, multval.field.sep = MSDB.DFT.OUTPUT.MULTIVAL.FIELD.SEP, first.val = FALSE, ascii = FALSE, noapostrophe = FALSE, noplusminus = FALSE, nogreek = FALSE, ...) {
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19 callSuper(keep.unused = keep.unused, one.line = one.line, match.sep = match.sep, multval.field.sep = multval.field.sep, first.val = first.val, ascii = ascii, noapostrophe = noapostrophe, noplusminus = noplusminus, nogreek = nogreek, ...)
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21 .df <<- data.frame()
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22 .output.fields <<- output.fields
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23 })
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25 ##################
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26 # GET DATA FRAME #
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27 ##################
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29 MsDbOutputDataFrameStream$methods( getDataFrame = function() {
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31 # Put at least a column name if empty
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32 if (nrow(.self$.df) == 0)
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33 .self$.df[[.self$.output.fields[[MSDB.TAG.MZ]]]] <- numeric()
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35 return(.self$.df)
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36 })
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38 # Move columns to beginning {{{1
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40 MsDbOutputDataFrameStream$methods( moveColumnsToBeginning = function(cols) {
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41 all.cols <- colnames(.self$.df)
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42 other.cols <- all.cols[ ! all.cols %in% cols]
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43 cols <- cols[cols %in% all.cols]
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44 .df <<- .self$.df[c(cols, other.cols)]
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45 })
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47 #################
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48 # MATCHED PEAKS #
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49 #################
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51 MsDbOutputDataFrameStream$methods( matchedPeaks = function(mz, rt = NULL, unused = NULL, peaks = NULL) {
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52
1
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53 library(plyr)
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54
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55 # Set input values
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56 x <- data.frame(mz = mz)
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57 colnames(x) <- MSDB.TAG.MZ
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58 if ( ! is.null(rt)) {
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59 x.rt <- data.frame(rt = rt)
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60 colnames(x.rt) <- MSDB.TAG.RT
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61 if (.self$.rtunit == MSDB.RTUNIT.MIN)
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62 x.rt[[MSDB.TAG.RT]] <- x.rt[[MSDB.TAG.RT]] / 60
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63 x <- cbind(x, x.rt)
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64 }
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65
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66
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67 # Merge input values with matched peaks
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68 if ( ! is.null(peaks)) {
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70 # No rows
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71 if (nrow(peaks) == 0) {
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72 # Add NA values
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73 peaks[1, ] <- NA
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74
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75 # Process existing rows
6
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76 } else {
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77
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78 # Convert RT
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79 if (.self$.rtunit == MSDB.RTUNIT.MIN)
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80 if (MSDB.TAG.COLRT %in% colnames(peaks))
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81 peaks[[MSDB.TAG.COLRT]] <- peaks[[MSDB.TAG.COLRT]] / 60
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82
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83 # Process multi-value fields
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84 for (c in colnames(peaks))
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85 if (c %in% MSDB.MULTIVAL.FIELDS) {
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86
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87 # Keep only first value in multi-value fields
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88 if (.self$.first.val)
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89 peaks[[c]] <- vapply(peaks[[c]], function(s) split.str(s, sep = MSDB.MULTIVAL.FIELD.SEP, unlist = TRUE)[[1]], FUN.VALUE = '')
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90
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91 # Change separator
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92 else
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93 peaks[[c]] <- vapply(peaks[[c]], function(s) paste0(split.str(s, sep = MSDB.MULTIVAL.FIELD.SEP, unlist = TRUE), collapse = .self$.multval.field.sep), FUN.VALUE = '')
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94
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95 }
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96
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97 # Concatenate results in one line
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98 if (.self$.one.line) {
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99 # For each column, concatenate all values in one string.
1
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100 for (c in seq(peaks)) {
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101 v <- peaks[[c]]
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102 v <- v[ ! is.na(v)] # remove NA values
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103 v <- v[ ! duplicated(v)] # remove duplicates
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104 peaks[1, c] <- paste0(v, collapse = .self$.match.sep, FUN.VALUE = '')
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105 }
0
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106 peaks <- peaks[1, ] # Keep only first line
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107 }
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108 }
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109
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110 # Merge
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111 x <- cbind(x, peaks, row.names = NULL)
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112 }
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113
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114 # Rename columns for output
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115 x <- rename.col(x, names(.self$.output.fields), .self$.output.fields)
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116
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117 # Add unused columns
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118 if ( .self$.keep.unused && ! is.null(unused)) {
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119 x <- cbind(x, unused, row.names = NULL)
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120 }
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121
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122 # Convert strings to ASCII
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123 if (.self$.ascii || .self$.noapostrophe || .self$.noplusminus || .self$.nogreek)
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124 for (c in seq(x))
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125 if (class(x[[c]]) == 'character') {
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126 if (.self$.noapostrophe)
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127 x[[c]] <- gsub("'", 'prime', x[[c]], perl = TRUE)
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128 if (.self$.noplusminus)
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129 x[[c]] <- gsub('±', '+-', x[[c]], perl = TRUE)
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130 if (.self$.nogreek) {
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131 x[[c]] <- gsub('α', 'alpha', x[[c]], perl = TRUE)
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132 x[[c]] <- gsub('β', 'beta', x[[c]], perl = TRUE)
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133 x[[c]] <- gsub('γ', 'gamma', x[[c]], perl = TRUE)
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134 x[[c]] <- gsub('δ', 'delta', x[[c]], perl = TRUE)
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135 }
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136 if (.self$.ascii) {
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137 x[[c]] <- gsub('[^\u0001-\u007F]', '_', x[[c]], perl = TRUE)
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138 }
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139 }
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140
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141 # Add new rows to data frame
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142 .df <<- rbind.fill(.self$.df, x)
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143 })
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144
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145 } # end of load safe guard