allow del.gaps, del.rowgapsonly, del.colgapsonly to work on AAbin obj…

[KlausVigo]

Hello Emmanuel, small change to allow del.gaps, del.rowgapsonly and del.colgapsonly also working on AAbin objects. Regards, Klaus

[emmanuelparadis]

Hello Klaus, Sounds like a great idea! I had a quick look at the suggested additions. You propose

cl <- ifelse(inherits(x, "DNAbin"), "DNAbin", "AAbin")

and at then set the class of the returned object with class(x) <- cl. That would "loose" composite classes (e.g., c("haplotype", "DNAbin") as used in pegas). Why not have simply instead:

cl <- class(x)

Another thing is the internal function deleteGaps which could be:

deleteGaps <- function(x, gapcode) {
        i <- which(x == gapcode)
        if (length(i)) x[-i] else x
}

Then we'll have something like this somewhere in the main body:

gapcode <- ifelse(inherits(x, "DNAbin"), 4, 45)

and add the additional argument each time the internal function is called. What do you think? Cheers, Emmanuel

[KlausVigo]

Hi Emmanuel, all your your suggestion make total sense. I was just trying to fast subset some AA sequence and did some hacks without giving it too much thought. Cheers, Klaus

[emmanuelparadis]

I've pushed a new version here (5.7-1.5) that should do it. Cheers, Emmanuel