library("Biostrings")
library("cleaver")
setClass("ProteinsIRL",
slots = list(
aa = "AAStringSet",
pfeatures = "CompressedIRangesList"))
setClass("ProteinsAASSL",
slots = list(
aa = "AAStringSet",
pfeatures = "AAStringSetList"))
pir <- new("ProteinsIRL")
pal <- new("ProteinsAASSL")
f <- readAAStringSet("swissprot_human_canonical_19_09_12.fasta")
tracemem(f)
pir@aa <- f
pal@aa <- f
## no copy
tracemem(pir@aa)
tracemem(pal@aa)
system.time(
pir@pfeatures <- cleavageRanges(pir@aa)
)
system.time(
pal@pfeatures <- cleave(pal@aa)
)
object.size(pir)
object.size(pal)
str(pir)
str(pal)
## here the data are copied
system.time(
pirpetides <- extractAt(pir@aa, unname(pir@pfeatures))
)
## here not
system.time(
palpeptides <- pal@pfeatures
)
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