[BioC] alphabetByCycle not working on AAStringSet

[Nicolas Delhomme]

Hej Bioc!

When I want to get the alphabetByCycle for an AAStringSet, I get "Error in alphabetByCycle(aa) : unknown class ‘AAString’".

Here is a toy example:
> aa <- AAStringSet(c("ARN","DCQ"))
> aa
A AAStringSet instance of length 2
    width seq
[1]     3 ARN
[2]     3 DCQ
> alphabetByCycle(aa)
Error in alphabetByCycle(aa) : unknown class ‘AAString'

My sessionInfo()

R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C         LC_TIME=C            LC_COLLATE=C         LC_MONETARY=C        LC_MESSAGES=C       
 [7] LC_PAPER=C           LC_NAME=C            LC_ADDRESS=C         LC_TELEPHONE=C       LC_MEASUREMENT=C     LC_IDENTIFICATION=C 

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RColorBrewer_1.0-5   ShortRead_1.20.0     Rsamtools_1.14.2     lattice_0.20-24      GenomicRanges_1.14.0 Biostrings_2.30.0   
[7] XVector_0.2.0        IRanges_1.20.0       BiocGenerics_0.8.0  

loaded via a namespace (and not attached):
[1] Biobase_2.22.0      bitops_1.0-6        grid_3.0.2          hwriter_1.3         latticeExtra_0.6-26 stats4_3.0.2       
[7] tools_3.0.2         zlibbioc_1.8.0   

Cheers,

Nico

---------------------------------------------------------------
Nicolas Delhomme

Nathaniel Street Lab
Department of Plant Physiology
Umeå Plant Science Center

Tel: +46 90 786 7989
Email: nicolas.delhomme at plantphys.umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden