Mercurial > repos > prog > lcmsmatching

annotate PeakforestEntry.R @ 3:abfba8eb1c8d draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 494194bb501d1d7033613131865f7bd68976041c
author prog
date Tue, 14 Mar 2017 12:35:23 -0400
parents 45e985cd8e9e
children
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1 #####################
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2 # CLASS DECLARATION #
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3 #####################
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5 # TODO Create class PeakforestCompoundEntry
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6 PeakForestSpectrumEntry <- methods::setRefClass("PeakForestSpectrumEntry", contains = "BiodbEntry")
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8 PeakForestCompoundEntry <- methods::setRefClass("PeakForestCompoundEntry", contains = "BiodbEntry")
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11 ###########
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12 # FACTORY #
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13 ###########
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16 ###Arg is jcontent ot indicate that the content is already a json.
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17 createPeakforestCompoundFromJSON <- function(contents, drop = FALSE) {
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19 if(is.character(contents))
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20 contents <- jsonlite::fromJSON(contents, simplifyDataFrame=FALSE)
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22 jsonfields <- list()
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23 jsonfields[[BIODB.ACCESSION]] <- "id"
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24 jsonfields[[BIODB.PUBCHEMCOMP.ID]] <- "PubChemCID"
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25 jsonfields[[BIODB.CHEBI.ID]] <- "ChEBI"
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26 jsonfields[[BIODB.HMDB.ID]] <- "HMDB"
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27 jsonfields[[BIODB.KEGG.ID]] <- "KEGG"
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28 jsonfields[[BIODB.FORMULA]] <- "formula"
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29 jsonfields[[BIODB.SMILES]] <- "canSmiles"
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30 jsonfields[[BIODB.AVERAGE.MASS]] <- "averageMass"
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31 jsonfields[[BIODB.MONOISOTOPIC.MASS]] <- "monoisotopicMass"
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32 jsonfields[[BIODB.INCHI]] <- "inChI"
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33 jsonfields[[BIODB.INCHIKEY]] <- "inchiIKey"
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34 jsonfields[[BIODB.NAME]] <- "mainName"
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36 entries <- vector(length(contents),mode="list")
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38 for (i in seq_along(contents)){
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40 jsontree <- contents[[i]]
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41 entry <- PeakForestCompoundEntry$new()
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44 for(field in names(jsonfields)){
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46 tosearch <- jsonfields[[field]]
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47 value <- jsontree$tosearch
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48 entry$setField(field,value)
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49 }
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51 entries[[i]] <- entry
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52 }
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54
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55 if (drop && length(contents) == 1)
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56 entries <- entries[[1]]
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57
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58 entries
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59 }
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60
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61 createPeakforestSpectraFromJSON <- function(contents, drop = FALSE, checkSub = TRUE) {
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62
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63 entries <- vector(length(contents),mode="list")
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64 jsonfields <- character()
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65 jsonfields[[BIODB.ACCESSION]] <- "id" # TODO Use BIODB.ACCESSION instead
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66 jsonfields[[BIODB.MSMODE]] <- "polarity"
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67
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68
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69 ###Checking that it's a list.
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70 if(length(contents) == 1){
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71 if(startsWith(contents[[1]], "<html>") ){
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72 return(NULL)
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73 }else{
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74 contents <- jsonlite::fromJSON(contents[[1]],simplifyDataFrame=FALSE)
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75
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76 }
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77 }
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78
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79 for (i in seq_along(contents)){
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80
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81 content <- contents[[i]]
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82 jsontree <- NULL
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83 if(typeof(content) == "character"){
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84 if(startsWith(content, "<html>")|content=="null"){
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85 entries[[i]] <- NULL
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86 next
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87 }
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88 jsontree <- jsonlite::fromJSON(content,simplifyDataFrame=FALSE)
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89 }else{
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90 jsontree <- content
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91 }
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92 cnames <- c(BIODB.PEAK.MZ, BIODB.PEAK.RELATIVE.INTENSITY, BIODB.PEAK.FORMULA, BIODB.PEAK.MZTHEO, BIODB.PEAK.ERROR.PPM)
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93
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94 entry <- PeakForestSpectrumEntry$new()
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95 #####Setting thz mass analyzer
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96 entry$setField(BIODB.MSDEV,jsontree$analyzerMassSpectrometerDevice$instrumentName)
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97 entry$setField(BIODB.MSDEVTYPE,jsontree$analyzerMassSpectrometerDevice$ionAnalyzerType)
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98
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99
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100
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101 for(field in names(jsonfields)){
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102
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103 tosearch <- jsonfields[[field]]
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104 value <- jsontree$tosearch
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105 entry$setField(field,value)
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106 }
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107
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108 ######################
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109 # TREATING THE PEAKS #
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110 ######################
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111
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112 entry$setField(BIODB.NB.PEAKS,length(jsontree$peaks))
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113 peaks <- data.frame( matrix( 0,ncol = length(cnames), nrow = 0))
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114 colnames(peaks) <- cnames
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115 ###Parsing peaks.
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116 if(length(jsontree$peaks) != 0){
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117 peaks <- sapply(jsontree$peaks,function(x){
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118 return(list(as.double(x$mz),
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119 as.integer(x$ri),
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120 as.character(x$composition),
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121 as.double(x$theoricalMass),
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122 as.double(x$deltaPPM)
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123 ))
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124 })
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125 ###Removing all whitespaces from the formule.
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126 peaks[3,]<-vapply(peaks[3,],function(x){
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127 gsub(" ","",trimws(x))
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128 },FUN.VALUE = NA_character_)
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129
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130 peaks<-t(peaks)
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131 colnames(peaks)<-cnames
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132 }
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133
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134 entry$setField(BIODB.PEAKS,peaks)
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135
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136 ##################################
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137 # TREATING THE LIST OF COMPOUNDS #
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138 ##################################
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139
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140 entry$setField(BIODB.NB.COMPOUNDS,length(jsontree$listOfCompounds))
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141 compounds <- list()
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142
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143 ###Parsing compounds.
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144 if( length( jsontree$listOfCompounds) != 0){
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145 compounds <- lapply( jsontree$listOfCompounds, function(x){
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146 createPeakforestCompoundFromJSON(x)
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147 })
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148 }
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149
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150 entry$setField(BIODB.COMPOUNDS, compounds)
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151
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152
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153 entries[[i]] <- entry
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154 }
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155
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156
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157 if (drop && length(contents) == 1)
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158 entries <- entries[[1]]
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159
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160 entries
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161 }
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162
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163
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164 ####TDO CLEAN THIS
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165
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166 createReducedSpectraFromJSON <- function(contents,
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167 drop = FALSE,
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168 checkSub = TRUE) {
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169 entries <- vector(length(contents), mode = "list")
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170 jsonfields <- character()
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171 # jsonfields[[BIODB.ACCESSION]] <-
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172 # "id" # TODO Use BIODB.ACCESSION instead
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173
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174
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175 ###Checking that it's a list.
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176 if (length(contents) == 1) {
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177 if (startsWith(contents[[1]], "<html>")) {
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178 return(NULL)
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179 } else{
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180 contents <- jsonlite::fromJSON(contents[[1]], simplifyDataFrame=FALSE)
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181
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182 }
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183 }
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184
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185 for (i in seq_along(contents)) {
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186 content <- contents[[i]]
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187 jsontree <- NULL
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188 if (typeof(content) == "character") {
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189 if (startsWith(content, "<html>") | content == "null") {
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190 entries[[i]] <- NULL
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191 next
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192 }
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193 jsontree <- jsonlite::fromJSON(content, simplifyDataFrame=FALSE)
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194 } else{
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195 jsontree <- content
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196 }
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197
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198
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199 cnames <-
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200 c(
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201 BIODB.PEAK.MZ,
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202 BIODB.PEAK.RELATIVE.INTENSITY,
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203 BIODB.PEAK.FORMULA,
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204 BIODB.PEAK.MZTHEO,
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205 BIODB.PEAK.ERROR.PPM
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206 )
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207
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208 entry <- PeakForestSpectrumEntry$new()
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209 entry$setField(BIODB.ACCESSION, jsontree$id)
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210
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211 ######################
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212 # TREATING THE PEAKS #
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213 ######################
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214
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215 entry$setField(BIODB.NB.PEAKS, length(jsontree$peaks))
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216 peaks <- data.frame(matrix(0, ncol = length(cnames), nrow = 0))
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217 colnames(peaks) <- cnames
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218 ###Parsing peaks.
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219 if (length(jsontree$peaks) != 0) {
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220 peaks <- sapply(jsontree$peaks, function(x) {
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221 return(
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222 list(
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223 as.double(x$mz),
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224 as.integer(x$ri),
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225 as.character(x$composition),
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226 as.double(x$theoricalMass),
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227 as.double(x$deltaPPM)
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228 )
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229 )
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230 })
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231 ###Removing all whitespaces from the formule.
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232 peaks[3, ] <- vapply(peaks[3, ], function(x) {
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233 gsub(" ", "", trimws(x))
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234 }, FUN.VALUE = NA_character_)
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235
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236 peaks <- as.data.frame(t(peaks))
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237 colnames(peaks) <- cnames
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238 }
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239
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240 entry$setField(BIODB.PEAKS, peaks)
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241
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242 entries[[i]] <- entry
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243 }
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244
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245
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246 if (drop && length(contents) == 1)
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247 entries <- entries[[1]]
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248
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249 entries
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250 }