[Bioc-devel] AAString validity

[Laurent Gatto]

Dear all,

AAString instances can contain invalid amino acids characters,
although the corresponding documentation says it should not.

> DNAString("AA123") ## positive control
Error in .Call2("new_XString_from_CHARACTER", classname, x,
start(solved_SEW),  :
  key 49 not in lookup table

> AAString("AA123")
  5-letter "AAString" instance
seq: AA123
> alphabet(AAString("AA123"))
 [1] "A" "R" "N" "D" "C" "Q" "E" "G" "H" "I" "L" "K" "M" "F" "P" "S" "T" "W" "Y"
[20] "V" "*" "-" "+"

I suspect that the table in xsbasetype.R explains why it does not work.

Would it be possible to encode the AA_ALPHABET for AAStrings?

Thank you very much in advance.

Laurent

> sessionInfo()
R Under development (unstable) (2012-01-29 r58227)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
other attached packages:
[1] Biostrings_2.23.6  IRanges_1.13.22    BiocGenerics_0.1.4