R/AllClasses.R

In tidytree: A Tidy Tool for Phylogenetic Tree Data Manipulation

#' @importFrom methods setOldClass
#' @importFrom methods isClass
if (!isClass("phylo")) setOldClass("phylo")
## setOldClass("multiPhylo")
if (!isClass("DNAbin")) setOldClass("DNAbin")
if (!isClass("AAbin")) setOldClass("AAbin")

#' @importFrom methods setClassUnion
setClassUnion("DNAbin_Or_AAbin", c("DNAbin", "AAbin", "NULL"))

#' Class "treedata"
#' This class stores phylogenetic tree with associated data
#'
#'
#' @name treedata-class
#' @aliases treedata-class
#'   show,treedata-method
#' @docType class
#' @slot file tree file
#' @slot treetext newick tree string
#' @slot phylo phylo object for tree structure
#' @slot data associated data
#' @slot extraInfo extra information, reserve for merge_tree
#' @slot tip_seq tip sequences
#' @slot anc_seq ancestral sequences
#' @slot seq_type sequence type, one of NT or AA
#' @slot tipseq_file tip sequence file
#' @slot ancseq_file ancestral sequence file
#' @slot info extra information, e.g. metadata, software version etc.
#' @importFrom methods setClass
#' @importFrom methods representation
#' @importFrom ape as.DNAbin
#' @exportClass treedata
#' @author Guangchuang Yu <https://guangchuangyu.github.io>
#' @keywords classes
setClass("treedata",
         representation = representation(
             file        = "character",
             treetext    = "character",
             phylo       = "phylo",
             data        = "tbl_df",
             extraInfo   = "tbl_df",
             tip_seq     = "DNAbin_Or_AAbin",
             anc_seq     = "DNAbin_Or_AAbin",
             seq_type    = "character",
             tipseq_file = "character",
             ancseq_file = "character",
             info        = "list"
         ),
         prototype = prototype(
             data      = tibble(),
             extraInfo = tibble(),
             anc_seq = NULL,#ape::as.DNAbin(character(0)),
             tip_seq = NULL#ape::as.DNAbin(character(0))
         )
         )

#' treedata object contructor
#'
#'
#' @title treedata
#' @param ... parameters
#' @return treedata object
#' @importFrom methods new
#' @export
#' @author guangchuang yu
treedata <- function(...) {
    new("treedata", ...)
}