#' Describe a new method for analyzing gene position data.
#'
#' @param id Unique identifier for the method.
#' @param name Human readable name.
#' @param description Slightly longer description.
#' @param func Function to apply the method. The function should accept two
#'   parameters: an object of class `geposan_preset` as input and a function to
#'   report progress information to as a numeric value. The return value should
#'   be an object of class `geposan_result`.
#'
#' @return An object of class `geposan_method`.
#'
#' @export
method <- function(id, name, description, func) {
    stopifnot(is.character(id) & length(id) == 1)
    stopifnot(is.character(name) & length(name) == 1)
    stopifnot(is.character(description) & length(description) == 1)
    stopifnot(is.function(func))

    structure(
        list(
            id = id,
            name = name,
            description = description,
            func = func
        ),
        class = "geposan_method"
    )
}

#' Get a list of all available methods.
#'
#' @export
all_methods <- function() {
    list(
        clustering(),
        correlation(),
        neural(),
        adjacency(),
        species_adjacency()
    )
}

#' Print a method object.
#'
#' @param x The method to print.
#' @param ... Other parameters.
#'
#' @seealso [method()]
#'
#' @export
print.geposan_method <- function(x, ...) {
    cat(sprintf(
        paste0(
            "geposan method:",
            "\n  Method ID: %s",
            "\n  Name: %s",
            "\n  Description: %s",
            "\n"
        ),
        x$id,
        x$name,
        x$description
    ))

    invisible(x)
}