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chore: lint with jarl #21

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Merged
davidbenncsiro merged 1 commit into from
Jan 15, 2026
Merged

chore: lint with jarl #21

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2 changes: 1 addition & 1 deletion R/asd_sco_binary_format.R
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ ASDScoBinary <- R6::R6Class("ASDScoBinary",

spec.df <-
data.frame(wavenumber=as.integer(rownames(spec.data)),
intensity=spec.data[1:length(spec.data)])
intensity=spec.data[seq_along(spec.data)])
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@davidbenncsiro davidbenncsiro Jan 15, 2026

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This and seq_len are nice. Admit that I have not seen them before.


meta.list <- list()
meta.list[["name"]] <- colnames(spec.data)
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4 changes: 2 additions & 2 deletions R/nicolet_spa_format.R
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Expand Up @@ -66,9 +66,9 @@ key.value.pairs <- function(path) {

for (str in strings.from.spa(path)) {
delimiter <- NULL
if (grepl(str, pattern="=")) {
if (grepl(str, pattern="=", fixed = TRUE)) {
delimiter <- "="
} else if (grepl(str, pattern=":")) {
} else if (grepl(str, pattern=":", fixed = TRUE)) {
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@davidbenncsiro davidbenncsiro Jan 15, 2026

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Yes, fair point.

delimiter <- ":"
}

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10 changes: 5 additions & 5 deletions R/parse_raw_file_for_reading.R
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Expand Up @@ -26,7 +26,7 @@ if(!dir.exists(out.directory)){dir.create(out.directory)}

SpecSets <- unique(indf$SampleSpectrumSetId)

for(i in 1:length(SpecSets)){
for(i in seq_along(SpecSets)){
print(paste0('Processing Spectral Set ', i, ' of ', length(SpecSets)))
specid <- SpecSets[i]
idxs <- which(indf$SampleSpectrumSetId==specid)
Expand All @@ -39,11 +39,11 @@ if(!dir.exists(out.directory)){dir.create(out.directory)}
idxS <- which(specdf$Type=='SAMPLE')
sampDF <- specdf[idxS,]

for (j in 1:nrow(sampDF)) {
srec = sampDF[j,]
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@davidbenncsiro davidbenncsiro Jan 15, 2026

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I can at least say that this was not code I wrote. :) Easy to do though.

for (j in seq_len(nrow(sampDF))) {
srec <- sampDF[j,]
#brec = specdf[1,]

fname = paste0(srec$'Sample ID', '_', srec$SampleSpectrumSetId, '_', srec$SpectrumId)
fname <- paste0(srec$'Sample ID', '_', srec$SampleSpectrumSetId, '_', srec$SpectrumId)
odf <- rbind(bkgDF, srec)
write.csv(odf, paste0(out.directory, '/', fname, '.hlr'), row.names = F)

Expand Down Expand Up @@ -93,7 +93,7 @@ parse.scans <- function(path, out.directory) {

indf <- read.csv(path, header = T, check.names=F)

for(i in 1:nrow(indf)){
for(i in seq_len(nrow(indf))){
rec <- indf[i,]
print(paste0('Processing Spectra ', i, ' of ', nrow(indf)))
specid <- paste0( rec$core.label, '_', rec$core_position)
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