Nothing
##' @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", ...)
}
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