R/functions-FragmentViews.R

In sgibb/topdownr: Investigation of Fragmentation Conditions in Top-Down Proteomics

#' @describeIn FragmentViews-class Constructor
#'
#' In general it is not necessary to call the constructor manually. See
#' [readTopDownFiles()] instead.
#'
#' @param sequence `character`/
#' [Biostrings::AAString-class],
#' complete protein/peptide sequence.
#' @param mass `double`,
#' mass of the fragments, same length as `start`/`end`/`width`.
#' @param type `character`,
#' type of the fragments, same length as `start`/`end`/width`.
#' @param z `integer`,
#' charge of the fragments,
#' length one or same length as `start`/`end`/width`.
#' @param start `integer`,
#' start positions of the fragments. At least two of
#' `start`/`end`/width` has to be given.
#' @param end `integer`,
#' end positions of the fragments. At least two of
#' `start`/`end`/width` has to be given.
#' @param width `integer`,
#' width positions of the fragments. At least two of
#' `start`/`end`/width` has to be given.
#' @param names `character`,
#' names of the fragments, same length as `start`/`end`/width`.
#' @param metadata `list`, metadata like modifications.
#' @return An [FragmentViews-class] object.
#' @export
FragmentViews <- function(sequence, mass, type, z=1L,
                          start=NULL, end=NULL, width=NULL, names=NULL,
                          metadata=list()) {
    v <- Views(
        AAString(sequence),
        start=start, end=end, width=width,
        names=names
    )
    d <- DataFrame(mass=mass,
                   type=factor(type, levels=sort(unique(type))),
                   z=Rle(z))
    elementMetadata(v) <- d
    metadata(v) <- metadata
    new("FragmentViews", v[order(d$mass)])
}

#' Validate FragmentViews
#'
#' @param object FragmentViews
#' @return `TRUE` (if valid) else `character` with msg what was incorrect
#' @noRd
.validateFragmentViews <- function(object) {
    msg <- character()

    cols <- c("mass", "type", "z")
    if (!all(cols %in% colnames(elementMetadata(object)))) {
        sel <- !cols %in% colnames(elementMetadata(object))
        msg <- c(msg, paste(paste0("'", cols[sel], "'", collapse=", "),
                            if (sum(sel) == 1L) { "is" } else { "are" },
                            "missing."))
    }

    mass <- elementMetadata(object)[, "mass", drop=TRUE]

    if (!is.double(mass)) {
        msg <- c(msg, "'mass' has to be of type double.")
    }

    if (is.unsorted(mass)) {
        msg <- c(msg, "'mass' has to be sorted.")
    }

    if (length(msg)) {
        msg
    } else {
        TRUE
    }
}