| cc06d22b |
##' @rdname show-methods
##' @importFrom ape print.phylo
##' @exportMethod show
setMethod("show", signature(object = "beast"),
function(object) {
cat("'beast' S4 object that stored information of\n\t",
paste0("'", object@file, "'.\n\n"))
cat("...@ tree: ")
print.phylo(get.tree(object))
cat("\nwith the following features available:\n")
print_fields(object)
})
|
| df059d88 |
##' @rdname show-methods
##' @exportMethod show
setMethod("show", signature(object = "codeml"),
function(object) {
cat("'codeml' S4 object that stored information of\n\t",
paste0("'", object@rst@rstfile, "' and \n\t'",
object@mlc@mlcfile, "'."),
"\n\n")
cat("...@ tree:")
print.phylo(get.tree(object))
cat("\nwith the following features available:\n")
print_fields(object, len=4)
})
|
| f2aa6adb |
##' @rdname show-methods
##' @exportMethod show
setMethod("show", signature(object = "codeml_mlc"),
function(object) {
cat("'codeml_mlc' S4 object that stored information of\n\t",
paste0("'", object@mlcfile, "'."),
"\n\n")
cat("...@ tree:")
print.phylo(get.tree(object))
cat("\nwith the following features available:\n")
cat("\t", paste0("'",
paste(get.fields(object), collapse="',\t'"),
"'."),
"\n")
}
)
|
| df059d88 |
##' show method for \code{jplace} instance
##'
##'
##' @name show
##' @docType methods
##' @rdname show-methods
##'
##' @title show method
##' @param object one of \code{jplace}, \code{beast} object
##' @return print info
##' @importFrom methods show
##' @exportMethod show
##' @usage show(object)
##' @author Guangchuang Yu \url{http://ygc.name}
##' @examples
##' jp <- system.file("extdata", "sample.jplace", package="ggtree")
##' jp <- read.jplace(jp)
##' show(jp)
setMethod("show", signature(object = "jplace"),
function(object) {
cat("'jplace' S4 object that stored information of\n\t",
paste0("'", object@file, "'."),
"\n\n")
cat("...@ tree: ")
phylo <- get.tree(object)
phylo$node.label <- NULL
phylo$tip.label %<>% gsub("\\@\\d+", "", .)
print.phylo(phylo)
cat("\nwith the following features availables:\n")
cat("\t", paste0("'",
paste(get.fields(object), collapse="',\t'"),
"'."),
"\n")
}
)
|
| cc06d22b |
##' @rdname show-methods
##' @exportMethod show
setMethod("show", signature(object = "nhx"),
function(object) {
cat("'nhx' S4 object that stored information of\n\t",
paste0("'", object@file, "'.\n\n"))
cat("...@ tree: ")
print.phylo(get.tree(object))
cat("\nwith the following features available:\n")
print_fields(object)
})
|
| df059d88 |
##' @rdname show-methods
##' @exportMethod show
setMethod("show", signature(object = "phylip"),
function(object) {
cat("'phylip' S4 object that stored information of\n\t",
paste0("'", object@file, "'.\n\n"))
cat("...@ tree: ")
print.phylo(get.tree(object))
msg <- paste0("\nwith sequence alignment available (", length(object@sequence),
|
| a90eeffd |
" sequences of length ", nchar(object@sequence)[1], ")\n")
|
| df059d88 |
cat(msg)
})
|
| f2aa6adb |
##' @rdname show-methods
##' @exportMethod show
setMethod("show", signature(object = "paml_rst"),
function(object) {
cat("'paml_rst' S4 object that stored information of\n\t",
paste0("'", object@rstfile, "'.\n\n"))
## if (length(object@tip.fasfile) != 0) {
## cat(paste0(" and \n\t'", object@tip.fasfile, "'.\n\n"))
## } else {
## cat(".\n\n")
## }
fields <- get.fields(object)
if (nrow(object@marginal_subs) == 0) {
fields <- fields[fields != "marginal_subs"]
fields <- fields[fields != "marginal_AA_subs"]
}
if (nrow(object@joint_subs) == 0) {
fields <- fields[fields != "joint_subs"]
fields <- fields[fields != "joint_AA_subs"]
}
cat("...@ tree:")
print.phylo(get.tree(object))
cat("\nwith the following features available:\n")
cat("\t", paste0("'",
paste(fields, collapse="',\t'"),
"'."),
"\n")
})
##' @rdname show-methods
##' @importFrom ape print.phylo
##' @exportMethod show
setMethod("show", signature(object = "r8s"),
function(object) {
cat("'r8s' S4 object that stored information of\n\t",
paste0("'", object@file, "'.\n\n"))
cat("...@ tree: ")
print.phylo(get.tree(object))
## cat("\nwith the following features available:\n")
## print_fields(object)
})
|
