AAString does not convert strings to upper case

[stitam]

Hi,

I have noticed the following small inconsistency:

While DNAString automatically converts a lower case strings to upper case:

Biostrings::DNAString("atgc")
#> 4-letter DNAString object
#> seq: ATGC

^{Created on 2022-09-27 with reprex v2.0.2}

AAString (and AAStringSet) does not:

Biostrings::AAString("mkig")
#> 4-letter AAString object
#> seq: mkig

^{Created on 2022-09-27 with reprex v2.0.2}

The impact of this inconsistency is that some other packages seem to depend on upper case characters and may fail sporadically if I am not careful. I understand this issue can be fixed from multiple sides but I am wondering if it would be possible for AAString() and AAStringset() to enforce upper case characters, similarly to DNAString() and DNAStringSet()? Many thanks.

[ahl27]

Fix for this is in PR #97