@@ -2,6 +2,8 @@ CHANGES IN VERSION 1.3.16

 ------------------------

  o update fortify.phylo to work with phylo that has missing value of edge length <2016-04-21, Thu>

    + https://github.com/GuangchuangYu/ggtree/issues/54

+ o support passing textConnection(text_string) as a file <2016-04-21, Thu>

+   + https://github.com/GuangchuangYu/ggtree/pull/55#issuecomment-212859693

 CHANGES IN VERSION 1.3.15

 ------------------------

@@ -52,7 +52,7 @@ read.nhx <- function(file) {

     nhx_stats$node <- node

     new("nhx",

-        file = file,

+        file = filename(file),

         fields = fields,

         phylo = phylo,

         nhx_tags = nhx_stats

@@ -32,7 +32,7 @@ read.beast <- function(file) {

         phylo       = phylo,

         translation = read.trans_beast(file),

         stats       = stats,

-        file        = file

+        file        = filename(file)

         )

 }

@@ -20,7 +20,7 @@ read.codeml_mlc <- function(mlcfile) {

         dNdS     = dNdS,

         ## seq_type = get_seqtype(tip_seq),

         ## tip_seq  = tip_seq,

-        mlcfile  = mlcfile)

+        mlcfile  = filename(mlcfile))

 }

@@ -49,24 +49,6 @@ setMethod("scale_color", signature(object="codeml_mlc"),

               scale_color_(object, by, ...)

           })

-##' @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")

-          }

-          )

 ##' @rdname get.fields-methods

@@ -79,7 +79,7 @@ read.hyphy <- function(nwk, ancseq, tip.fasfile=NULL) {

                phylo = tr,

                seq_type = type,

                ancseq = seq,

-               tree.file = nwk,

+               tree.file = filename(nwk),

                ancseq.file = ancseq

                )

@@ -21,7 +21,7 @@ read.jplace <- function(file) {

              placements = placements,

              version    = version,

              metadata   = metadata,

-             file       = file

+             file       = filename(file)

              )

          )

 }

@@ -27,6 +27,25 @@ setMethod("show", signature(object = "codeml"),

               print_fields(object, len=4)

           })

+##' @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")

+          }

+          )

+

 ##' show method for \code{jplace} instance

 ##'

 ##' 

@@ -94,3 +113,48 @@ setMethod("show", signature(object = "phylip"),

               cat(msg)

           })

+##' @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)

+          })

@@ -46,7 +46,7 @@ read.paml_rst <- function(rstfile) {

                seq_type        = type,

                marginal_ancseq = ms,

                joint_ancseq    = read.ancseq_paml_rst(rstfile, by = "Joint"),

-               rstfile = rstfile

+               rstfile = filename(rstfile)

                )

     ## if (!is.null(tip.fasfile)) {

     ##     seqs <- readBStringSet(tip.fasfile)

@@ -86,36 +86,6 @@ setMethod("get.tipseq", signature(object="paml_rst"),

               }

           })

-##' @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 get.fields-methods

 ##' @exportMethod get.fields

@@ -34,7 +34,7 @@ read.phylip <- function(file) {

     }

     new("phylip",

-        file = file,

+        file = filename(file),

         phylo = trees,

         ntree = ntree,

         sequence = seq_obj

@@ -21,26 +21,13 @@ read.r8s <- function(file) {

     names(trees) <- label

     new("r8s",

-        file = file,

+        file = filename(file),

         fields = label,

         phylo = trees)

 }

-##' @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)

-          })

-

 ##' @rdname groupClade-methods

 ##' @exportMethod groupClade

@@ -1,3 +1,13 @@

+filename <- function(file) {

+    ## textConnection(text_string) will work just like a file

+    ## in this case, just set the filename as ""

+    file_name <- ""

+    if (is.character(file)) {

+        file_name <- file

+    }

+    return(file_name)

+}

+

 ##' @importFrom ggplot2 last_plot

 get_tree_view <- function(tree_view) {

@@ -1,5 +1,5 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/RAxML.R, R/ape.R, R/codeml_mlc.R, R/hyphy.R, R/method-show.R, R/paml_rst.R, R/phangorn.R, R/r8s.R

+% Please edit documentation in R/RAxML.R, R/ape.R, R/hyphy.R, R/method-show.R, R/phangorn.R

 \docType{methods}

 \name{show,raxml-method}

 \alias{show}

@@ -20,14 +20,14 @@

 \S4method{show}{apeBootstrap}(object)

-\S4method{show}{codeml_mlc}(object)

-

 \S4method{show}{hyphy}(object)

 \S4method{show}{beast}(object)

 \S4method{show}{codeml}(object)

+\S4method{show}{codeml_mlc}(object)

+

 show(object)

 \S4method{show}{nhx}(object)

@@ -36,9 +36,9 @@ show(object)

 \S4method{show}{paml_rst}(object)

-\S4method{show}{phangorn}(object)

-

 \S4method{show}{r8s}(object)

+

+\S4method{show}{phangorn}(object)

 }

 \arguments{

 \item{object}{one of \code{jplace}, \code{beast} object}