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Commit 2f4032d3 authored by Michele Stravs's avatar Michele Stravs
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First fixes. Vignette not working

parent beb9c78d
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......@@ -1685,19 +1685,21 @@ setMethod("toMassbank", "RmbSpectrum2", function(o, addAnnotation = getOption("R
#'
#' @export
exportMassbank <- function(compiled, molfile = NULL)
exportMassbank_recdata(
accessions = unlist(lapply(X = compiled, FUN = "[", "ACCESSION")),
files,
recDataFolder = file.path(getOption("RMassBank")$annotations$entry_prefix, "recdata")
)
{
exportMassbank_recdata(
compiled,
recDataFolder = file.path(getOption("RMassBank")$annotations$entry_prefix, "recdata")
)
if(!is.null(molfile)) {
exportMassbank_moldata(
cpdID = as.numeric(compiled[[1]][["COMMENT"]][[getOption("RMassBank")$annotations$internal_id_fieldname]][[1]]),
molfile,
molDataFolder = file.path(getOption("RMassBank")$annotations$entry_prefix, "moldata")
compiled,
molfile,
molDataFolder = file.path(getOption("RMassBank")$annotations$entry_prefix, "moldata")
)
}
}
exportMassbank_recdata <- function(accessions, files, recDataFolder)
exportMassbank_recdata <- function(compiled, recDataFolder)
{
#mb@mbfiles <- lapply(mb@compiled_ok, function(cpd) toMassbank(cpd, mb@additionalPeaks))
......@@ -1707,32 +1709,30 @@ exportMassbank_recdata <- function(accessions, files, recDataFolder)
molnames <- c()
for(file in seq_len(length(files)))
{
# Read the accession no. from the corresponding "compiled" entry
filename <- names(files)[[file]]
# use this accession no. as filename
filename <- paste(filename, ".txt", sep="")
write(files[[file]],
file.path(getOption("RMassBank")$annotations$entry_prefix, "recdata",filename)
)
filePath <- file.path(recDataFolder,filename)
write(files[[file]], filePath)
}
if(!is.null(molfile))
{
}
exportMassbank_moldata <- function(compiled, molfile, molDataFolder)
{
# Use internal ID for naming the molfiles
if(findLevel(compiled@id,TRUE)=="standard"){
molname <- sprintf("%04d", as.numeric(
compiled@id))
molname <- paste(molname, ".mol", sep="")
write(molfile,
file.path(getOption("RMassBank")$annotations$entry_prefix, "moldata",molname)
)
}
# Use internal ID for naming the molfiles
if(findLevel(compiled@id,TRUE)=="standard"){
molname <- sprintf("%04d", as.numeric(compiled@id))
molname <- paste(molname, ".mol", sep="")
write(molfile, file.path(molDataFolder, "moldata",molname))
}
return(files)
}
# Makes a list.tsv with molfile -> massbank ch$name attribution.
#' Write list.tsv file
......
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