@@ -179,7 +179,6 @@ importFrom(magrittr,equals)

 importFrom(methods,is)

 importFrom(methods,missingArg)

 importFrom(methods,setGeneric)

-importFrom(methods,setOldClass)

 importFrom(rvcheck,get_fun_from_pkg)

 importFrom(scales,alpha)

 importFrom(tibble,data_frame)

deleted file mode 100644

@@ -1,388 +0,0 @@

-## setOldClass("phylo")

-## setOldClass("multiPhylo")

-##' @importFrom methods setOldClass

-setOldClass("ggtree")

-

-

-## setClassUnion("phyloOrmultiPhylo", c("phylo", "multiPhylo"))

-

-

-supported_tree_object <- function() {

-    c("apeBootstrap",

-      "beast",

-      "codeml_mlc",

-      "codeml",

-      "hyphy",

-      "jplace",

-      "nhx",

-      "paml_rst",

-      "phangorn",

-      "phylip",

-      "r8s",

-      "raxml")

-}

-

-## ##' Class "apeBootstrap"

-## ##' This class stores ape bootstrapping analysis result

-## ##'

-## ##'

-## ##' @name apeBootstrap-class

-## ##' @docType class

-## ##' @slot phylo phylo object of treetext

-## ##' @slot fields available features

-## ##' @slot bootstrap bootstrap value

-## ##' @slot extraInfo extra information

-## ##' @exportClass apeBootstrap

-## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}

-## ##' @keywords classes

-## setClass("apeBootstrap",

-##          representation = representation(

-##              phylo = "phylo",

-##              fields = "character",

-##              bootstrap = "data.frame",

-##              extraInfo = "data.frame"

-##          )

-##          )

-

-## ##' Class "beast"

-## ##' This class stores information of beast output

-## ##'

-## ##'

-## ##' @name beast-class

-## ##' @aliases beast-class

-## ##'      get.tree,beast-method

-## ##'

-## ##' @docType class

-## ##' @slot fields beast statistic variables

-## ##' @slot treetext tree text in beast file

-## ##' @slot phylo tree phylo object

-## ##' @slot translation tip number to name translation in beast file

-## ##' @slot stats beast statistics

-## ##' @slot file beast file, nexus format

-## ##' @slot extraInfo extra information

-## ##' @exportClass beast

-## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}

-## ##' @seealso \code{\link{show}} \code{\link{get.fields}}

-## ##'           \code{\link{ggtree}}

-## ##' @keywords classes

-## setClass("beast",

-##          representation  = representation(

-##              fields      = "character",

-##              treetext    = "character",

-##              phylo       = "phylo",

-##              translation = "matrix",

-##              stats       = "data.frame",

-##              file        = "character",

-##              extraInfo   = "data.frame"

-##              )

-##          )

-

-

-## ##' Class "codeml_mlc"

-## ##' This class stores information of mlc file frm codeml output

-## ##'

-## ##'

-## ##' @name codeml_mlc-class

-## ##' @docType class

-## ##' @slot fields available features

-## ##' @slot treetext tree text

-## ##' @slot phylo phylo object

-## ##' @slot dNdS dN dS information

-## ##' @slot mlcfile mlc file

-## ##' @slot extraInfo extra information

-## ##' @exportClass codeml_mlc

-## ##' @author Guangchuang Yu

-## ##' @seealso \linkS4class{paml_rst} \linkS4class{codeml}

-## ##' @keywords classes

-## setClass("codeml_mlc",

-##          representation = representation(

-##              fields     = "character",

-##              treetext   = "character",

-##              phylo      = "phylo",

-##              dNdS       = "matrix",

-##              ## seq_type   = "character",

-##              ## tip_seq    = "character",

-##              mlcfile    = "character",

-##              extraInfo  = "data.frame"

-##              )

-##          )

-

-## ##' Class "paml_rst"

-## ##' This class stores information of rst file from PAML output

-## ##'

-## ##'

-## ##' @name paml_rst-class

-## ##' @aliases paml_rst-class

-## ##'   set.subs,paml_rst-method

-## ##'   set.subs<-,paml_rst-method

-## ##'

-## ##' @docType class

-## ##' @slot fields availabel attributes

-## ##' @slot treetext tree text

-## ##' @slot phylo phylo object

-## ##' @slot seq_type one of "NT" and "AA"

-## ##' @slot tip_seq sequences of tips

-## ##' @slot marginal_ancseq Marginal reconstruction of ancestral sequences

-## ##' @slot joint_ancseq Joint reconstruction of ancestral sequences

-## ##' @slot marginal_subs sequence substitutions based on marginal_ancseq

-## ##' @slot joint_subs sequence substitutions based on joint_ancseq

-## ##' @slot marginal_AA_subs Amino acid sequence substitutions based on marginal_ancseq

-## ##' @slot joint_AA_subs Amino acid sequence substitutions based on joint_ancseq

-## ##' @slot rstfile rst file

-## ##' @slot extraInfo extra information

-## ##' @exportClass paml_rst

-## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}

-## ##' @seealso \linkS4class{codeml} \linkS4class{codeml_mlc}

-## ##' @keywords classes

-## setClass("paml_rst",

-##          representation       = representation(

-##              fields           = "character",

-##              treetext         = "character",

-##              phylo            = "phylo",

-##              seq_type         = "character",

-##              tip_seq          = "character",

-##              marginal_ancseq  = "character",

-##              joint_ancseq     = "character",

-##              marginal_subs    = "data.frame",

-##              joint_subs       = "data.frame",

-##              marginal_AA_subs = "data.frame",

-##              joint_AA_subs    = "data.frame",

-##              rstfile          = "character",

-##              extraInfo        = "data.frame"

-##          )

-##          )

-

-## ##' Class "codeml"

-## ##' This class stores information of output from codeml

-## ##'

-## ##'

-## ##' @name codeml-class

-## ##' @docType class

-## ##' @slot mlc A \code{code_mlc} object

-## ##' @slot rst A \code{paml_rst} object

-## ##' @slot extraInfo extra information

-## ##' @exportClass codeml

-## ##' @seealso \linkS4class{codeml_mlc} \linkS4class{paml_rst}

-## ##' @keywords codeml

-## setClass("codeml",

-##          representation = representation(

-##              mlc       = "codeml_mlc",

-##              rst       = "paml_rst",

-##              extraInfo = "data.frame"

-##              )

-##          )

-

-

-

-## ##' Class "hyphy"

-## ##' This class stores information of HYPHY output

-## ##'

-## ##'

-## ##' @name hyphy-class

-## ##' @docType class

-## ##' @slot fields available features

-## ##' @slot treetext tree text

-## ##' @slot phylo phylo object

-## ##' @slot seq_type one of "NT" and "AA"

-## ##' @slot subs sequence substitutions

-## ##' @slot AA_subs Amino acid sequence substitution

-## ##' @slot ancseq ancestral sequences

-## ##' @slot tip_seq tip sequences

-## ##' @slot tip.fasfile fasta file of tip sequences

-## ##' @slot tree.file tree file

-## ##' @slot ancseq.file ancestral sequence file, nexus format

-## ##' @slot extraInfo extra information

-## ##' @exportClass hyphy

-## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}

-## ##' @seealso \linkS4class{paml_rst}

-## ##' @keywords classes

-## setClass("hyphy",

-##          representation  = representation(

-##              fields      = "character",

-##              treetext    = "character",

-##              phylo       = "phylo",

-##              seq_type    = "character",

-##              subs        = "data.frame",

-##              AA_subs     = "data.frame",

-##              ancseq      = "character",

-##              tip_seq     = "character",

-##              tip.fasfile = "character",

-##              tree.file   = "character",

-##              ancseq.file = "character",

-##              extraInfo   = "data.frame"

-##              )

-##          )

-

-## ##' Class "jplace"

-## ##' This class stores information of jplace file.

-## ##'

-## ##'

-## ##' @name jplace-class

-## ##' @aliases jplace-class

-## ##'   show,jplace-method

-## ##'   get.placements,jplace-method

-## ##'   get.treeinfo,jplace-method

-## ##'   get.fields,jplace-method

-## ##'   get.treetext,jplace-method

-## ##'

-## ##' @docType class

-## ##' @slot fields colnames of first variable of placements

-## ##' @slot treetext tree text

-## ##' @slot phylo tree phylo object

-## ##' @slot placements placement information

-## ##' @slot version version

-## ##' @slot metadata metadata

-## ##' @slot file jplace file

-## ##' @slot extraInfo extra information

-## ##' @exportClass jplace

-## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}

-## ##' @seealso \code{\link{show}} \code{\link{get.tree}}

-## ##'          \code{\link{ggtree}}

-## ##' @keywords classes

-## setClass("jplace",

-##          representation = representation(

-##              fields     = "character",

-##              treetext   = "character",

-##              phylo      = "phylo",

-##              placements = "data.frame",

-##              version    = "numeric",

-##              metadata   = "list",

-##              file       = "character",

-##              extraInfo  = "data.frame"

-##              )

-##          )

-

-

-## ##' Class "nhx"

-## ##' This class stores nhx tree

-## ##'

-## ##'

-## ##' @name nhx-class

-## ##' @rdname nhx-class

-## ##' @docType class

-## ##' @slot file input file

-## ##' @slot fields available feature

-## ##' @slot phylo phylo object

-## ##' @slot nhx_tags tag information in nhx file

-## ##' @slot extraInfo extra information

-## ##' @exportClass nhx

-## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}

-## ##' @keywords classes

-## setClass("nhx",

-##          representation = representation(

-##              file = "character",

-##              fields = "character",

-##              phylo = "phylo",

-##              nhx_tags = "data.frame",

-##              extraInfo = "data.frame"

-##          )

-##          )

-

-

-## ##' Class "phangorn"

-## ##' This class stores ancestral sequences inferred from 'phangorn'

-## ##'

-## ##'

-## ##' @name phangorn-class

-## ##' @docType class

-## ##' @slot fields available attributes

-## ##' @slot phylo phylo object

-## ##' @slot seq_type one of "NT" and "AA"

-## ##' @slot tip_seq sequences of tips

-## ##' @slot ancseq ancenstral sequences

-## ##' @slot subs sequence substitution

-## ##' @slot AA_subs Amino acid sequence substitution

-## ##' @slot extraInfo extra information

-## ##' @exportClass phangorn

-## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}

-## ##' @seealso \linkS4class{paml_rst}

-## ##' @keywords classes

-## setClass("phangorn",

-##          representation = representation(

-##              fields = "character",

-##              phylo = "phylo",

-##              seq_type = "character",

-##              tip_seq = "character",

-##              ancseq = "character",

-##              subs = "data.frame",

-##              AA_subs = "data.frame",

-##              extraInfo = "data.frame")

-##          )

-

-

-

-## ##' Class "phylip"

-## ##' This class stores phylip tree(s)

-## ##'

-## ##'

-## ##' @name phylip-class

-## ##' @docType class

-## ##' @slot file input file

-## ##' @slot fields available feature

-## ##' @slot phylo phylo or multiPhylo

-## ##' @slot ntree number of trees

-## ##' @slot sequence sequences

-## ##' @slot extraInfo extra information

-## ##' @exportClass phylip

-## ##' @author Guangchuang Yu

-## ##' @keywords classes

-## setClass("phylip",

-##          representation = representation(

-##              file = "character",

-##              fields = "character",

-##              phylo = "phyloOrmultiPhylo",

-##              ntree = "numeric",

-##              sequence = "character",

-##              extraInfo = "data.frame")

-##          )

-

-

-## ##' Class "r8s"

-## ##' This class stores output info from r8s

-## ##'

-## ##'

-## ##' @name r8s-class

-## ##' @docType class

-## ##' @slot file input file

-## ##' @slot fields available feature

-## ##' @slot treetext tree text

-## ##' @slot phylo multiPhylo, time tree, rate tree and absolute substitution tree

-## ##' @slot extraInfo extra information

-## ##' @exportClass r8s

-## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}

-## ##' @keywords classes

-## setClass("r8s",

-##          representation = representation(

-##              file      = "character",

-##              fields    = "character",

-##              treetext  = "character",

-##              phylo     = "multiPhylo",

-##              extraInfo = "data.frame"

-##              )

-##          )

-

-

-## ##' Class "raxml"

-## ##' This class stores RAxML bootstrapping analysis result

-## ##'

-## ##'

-## ##' @name raxml-class

-## ##' @docType class

-## ##' @slot file input file

-## ##' @slot fields available features

-## ##' @slot treetext tree text

-## ##' @slot phylo phylo object of treetext

-## ##' @slot bootstrap bootstrap value

-## ##' @slot extraInfo extra information

-## ##' @exportClass raxml

-## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}

-## ##' @keywords classes

-## setClass("raxml",

-##          representation = representation(

-##              file       = "character",

-##              treetext   = "character"

-##          ),

-##          contains = "apeBootstrap"

-##          )

-

-

@@ -12,7 +12,7 @@ as.binary <- function(tree, ...) {

 ##' @name reroot

 ##' @rdname reroot-methods

 ##' @title reroot method

-##' @param object one of \code{phylo}, \code{nhx}, \code{phangorn}, \code{jplace}, \code{beast}, \code{hyphy}, \code{codeml}, \code{codeml_mlc}, \code{paml_rst} object

+##' @param object \code{treedata} object

 ##' @param node internal nnode number

 ##' @param ... additional parameter

 ##' @return tree object

@@ -20,6 +20,7 @@ as.binary <- function(tree, ...) {

 ##' @export

 setGeneric("reroot", function(object, node, ...) standardGeneric("reroot"))

+## may change to implement ape::root method

 ##' @docType methods

 ##' @name scale_color

@@ -13,13 +13,7 @@ MRCA <- function(obj, tip) {

         return(getMRCA.df(obj$data, tip))

     }

-    if(class(obj) %in% supported_tree_object()) {

-        obj <- get.tree(obj)

-    }

-    if (class(obj) == "phylo") {

-        return(getMRCA(obj, tip))

-    }

-    stop("obj is not supported...")

+    getMRCA(as.phylo(obj), tip)

 }

deleted file mode 100644

@@ -1,95 +0,0 @@

-## ##' parse RAxML bootstrapping analysis output

-## ##'

-## ##' 

-## ##' @title read.raxml

-## ##' @param file RAxML bootstrapping analysis output

-## ##' @return raxml object

-## ##' @export

-## ##' @author Guangchuang Yu

-## read.raxml <- function(file) {

-##     tree.text <- readLines(file)

-##     tree_text <- gsub('(:[0-9\\.eE+\\-]+)\\[(\\d+)\\]', '\\@\\2\\1', tree.text)

-##     phylo <- read.tree(text=tree_text)

-##     if(any(grepl('@', phylo$node.label))) {

-##         bootstrap <- as.numeric(gsub("[^@]*@(\\d+)", "\\1", phylo$node.label))

-##         phylo$node.label <- gsub("@\\d+", "", phylo$node.label)

-##     }

-

-##     if (all(phylo$node.label == "")) {

-##         phylo$node.label <- NULL

-##     }

-

-##     bootstrap <- data.frame(node = Ntip(phylo) + 1:phylo$Nnode,

-##                             bootstrap = bootstrap)

-

-##     new("raxml",

-##         file      = file,

-##         fields    = "bootstrap",

-##         treetext  = tree.text,

-##         phylo     = phylo,

-##         bootstrap = bootstrap

-##         )

-## }

-

-

-## ##' @rdname show-methods

-## ##' @importFrom ape print.phylo

-## ##' @exportMethod show

-## setMethod("show", signature(object = "raxml"),

-##           function(object) {

-##               cat("'raxml' 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 groupOTU-methods

-## ##' @exportMethod groupOTU

-## setMethod("groupOTU", signature(object="raxml"),

-##           function(object, focus, group_name="group") {

-##               groupOTU_(object, focus, group_name)

-##           }

-##           )

-

-## ##' @rdname groupClade-methods

-## ##' @exportMethod groupClade

-## setMethod("groupClade", signature(object="raxml"),

-##           function(object, node, group_name="group") {

-##               groupClade_(object, node, group_name)

-##           })

-

-## ##' @rdname scale_color-methods

-## ##' @exportMethod scale_color

-## setMethod("scale_color", signature(object="raxml"),

-##           function(object, by="bootstrap", ...) {

-##               scale_color_(object, by, ...)

-##           })

-

-

-## ##' @rdname gzoom-methods

-## ##' @exportMethod gzoom

-## setMethod("gzoom", signature(object="raxml"),

-##           function(object, focus, subtree=FALSE, widths=c(.3, .7)) {

-##               gzoom.phylo(get.tree(object), focus, subtree, widths)

-##           })

-

-

-## ##' @rdname get.tree-methods

-## ##' @exportMethod get.tree

-## setMethod("get.tree", signature(object="raxml"),

-##           function(object,...) {

-##               object@phylo

-##           }

-##           )

-

-

-## ##' @rdname get.fields-methods

-## ##' @exportMethod get.fields

-## setMethod("get.fields", signature(object="raxml"),

-##           function(object, ...) {

-##               get.fields.tree(object)

-##           }

-##           )

-

deleted file mode 100644

@@ -1,15 +0,0 @@

-##' merge phylo and output of boot.phylo to 'apeBootstrap' object

-##'

-##'

-##' @title apeBoot

-##' @param phylo phylo

-##' @param boot bootstrap values

-##' @return an instance of 'apeBootstrap'

-##' @importFrom treeio as.treedata

-##' @export

-##' @author Guangchuang Yu

-apeBoot <- function(phylo, boot) {

-    message("this function was deprecated, please use treeio::as.treedata")

-    as.treedata(phylo, boot)

-}

-

@@ -9,240 +9,6 @@ get_tree_view <- function(tree_view) {

     return(tree_view)

 }

-

-

-## has.field <- function(tree_object, field) {

-##     if ( ! field %in% get.fields(tree_object) ) {

-##         return(FALSE)

-##     }

-

-##     if (is(tree_object, "codeml")) {

-##         is_codeml <- TRUE

-##         tree <- tree_object@rst

-##     } else {

-##         is_codeml <- FALSE

-##         tree <- tree_object

-##     }

-

-##     if (.hasSlot(tree, field)) {

-##         has_slot <- TRUE

-##     } else {

-##         has_slot <- FALSE

-##     }

-

-##     if (has_slot == FALSE) {

-##         if (has.extraInfo(tree_object) == FALSE) {

-##             return(FALSE)

-##         }

-

-##         if (nrow(tree_object@extraInfo) == 0) {

-##             return(FALSE)

-##         }

-

-##         if (!field %in% colnames(tree_object@extraInfo)) {

-##             return(FALSE)

-##         }

-##     }

-##     res <- TRUE

-##     attr(res, "has_slot") <- has_slot

-##     attr(res, "is_codeml") <- is_codeml

-##     return(res)

-## }

-

-## append_extraInfo <- function(df, object) {

-##     if (has.extraInfo(object)) {

-##         info <- object@extraInfo

-##         if ("parent" %in% colnames(info)) {

-##             res <- merge(df, info, by.x=c("node", "parent"), by.y=c("node", "parent"))

-##         } else {

-##             res <- merge(df, info, by.x="node", by.y="node")

-##         }

-##     } else {

-##         return(df)

-##     }

-

-##     i <- order(res$node, decreasing = FALSE)

-##     res <- res[i,]

-##     return(res)

-## }

-

-## get.fields.tree <- function(object) {

-##     if (is(object, "codeml")) {

-##         fields <- c(get.fields(object@rst),

-##                     get.fields(object@mlc))

-##         fields <- unique(fields)

-##     } else {

-##         fields <- object@fields

-##     }

-

-##     if (has.slot(object, "extraInfo")) {

-##         extraInfo <- object@extraInfo

-##         if (nrow(extraInfo) > 0) {

-##             cn <- colnames(extraInfo)

-##             i <- match(c("x", "y", "isTip", "node", "parent", "label", "branch", "branch.length"), cn)

-##             i <- i[!is.na(i)]

-##             fields %<>% c(cn[-i])

-##         }

-##     }

-##     return(fields)

-## }

-

-## print_fields <- function(object, len=5) {

-##     fields <- get.fields(object)

-##     n <- length(fields)

-##     i <- floor(n/len)

-##     for (j in 0:i) {

-##         ii <- 1:len + len * j

-##         if (j == i) {

-##             x <- n %% len

-##             if (x == 0) {

-##                 ii <- NULL

-##             } else {

-##                 ii <- ii[1:x]

-##             }

-##         }

-

-##         if (!is.null(ii)) {

-##             cat("\t", paste0("'",

-##                              paste(fields[ii], collapse="',\t'"),

-##                              "'")

-##                 )

-##         }

-##         if ( j == i) {

-##             cat(".\n")

-##         } else {

-##             cat(",\n")

-##         }

-##     }

-## }

-

-## plot.subs <- function(x, layout, show.tip.label,

-##                       tip.label.size,

-##                       tip.label.hjust,

-##                       position, annotation,

-##                       annotation.color = "black",

-##                       annotation.size=3, ...) {

-

-##     p <- ggtree(x, layout=layout, ...)

-##     if (show.tip.label) {

-##         p <- p + geom_tiplab(hjust = tip.label.hjust,

-##                              size  = tip.label.size)

-##     }

-##     if (!is.null(annotation) && !is.na(annotation)) {

-##         p <- p + geom_text(aes_string(x=position, label=annotation),

-##                            size=annotation.size,

-##                            color=annotation.color, vjust=-.5)

-##     }

-##     p + theme_tree2()

-## }

-

-## .add_new_line <- function(res) {

-##     ## res <- paste0(strwrap(res, 50), collapse="\n")

-##     ## res %<>% gsub("\\s/\n", "\n", .) %>% gsub("\n/\\s", "\n", .)

-##     if (nchar(res) > 50) {

-##         idx <- gregexpr("/", res)[[1]]

-##         i <- idx[floor(length(idx)/2)]

-##         res <- paste0(substring(res, 1, i-1), "\n", substring(res, i+1))

-##     }

-##     return(res)

-## }

-

-## get.subs_ <- function(tree, fasta, translate=TRUE, removeGap=TRUE) {

-##     N <- getNodeNum(tree)

-##     node <- 1:N

-##     parent <- sapply(node, getParent, tr=tree)

-##     label <- getNodeName(tree)

-##     subs <- sapply(seq_along(node), function(i) {

-##         if (i == getRoot(tree)) {

-##             return(NA)

-##         }

-##         res <- getSubsLabel(fasta, label[parent[i]], label[i], translate, removeGap)

-##         if (is.null(res)) {

-##             return('')

-##         }

-##         .add_new_line(res)

-##     })

-

-##     dd <- data.frame(node=node, parent=parent, label=label, subs=subs)

-##     dd <- dd[dd$parent != 0,]

-##     dd <- dd[, -c(1,2)]

-##     dd[,1] <- as.character(dd[,1])

-##     dd[,2] <- as.character(dd[,2])

-##     return(dd)

-## }

-

-## getSubsLabel <- function(seqs, A, B, translate, removeGap) {

-##     seqA <- seqs[A]

-##     seqB <- seqs[B]

-

-##     if (nchar(seqA) != nchar(seqB)) {

-##         stop("seqA should have equal length to seqB")

-##     }

-

-##     if (translate == TRUE) {

-##         AA <- seqA %>% seq2codon %>% codon2AA

-##         BB <- seqB %>% seq2codon %>% codon2AA

-##     } else {

-##         ## strsplit is faster than substring

-##         ##

-##         ## n <- nchar(seqA) ## should equals to nchar(seqB)

-##         ## AA <- substring(seqA, 1:n, 1:n)

-##         ## BB <- substring(seqB, 1:n, 1:n)

-##         AA <- strsplit(seqA, split="") %>% unlist

-##         BB <- strsplit(seqB, split="") %>% unlist

-##     }

-

-##     ii <- which(AA != BB)

-

-##     if (removeGap == TRUE) {

-##         if (length(ii) > 0 && translate == TRUE) {

-##             ii <- ii[AA[ii] != "X" & BB[ii] != "X"]

-##         }

-

-##         if (length(ii) > 0 && translate == FALSE) {

-##             ii <- ii[AA[ii] != "-" & BB[ii] != "-"]

-##         }

-##     }

-

-##     if (length(ii) == 0) {

-##         return(NULL)

-##     }

-

-##     res <- paste(AA[ii], ii, BB[ii], sep="", collapse=" / ")

-##     return(res)

-## }

-

-## seq2codon <- function(x) {

-##     substring(x, first=seq(1, nchar(x)-2, 3), last=seq(3, nchar(x), 3))

-## }

-

-## ## @importFrom Biostrings GENETIC_CODE

-## codon2AA <- function(codon) {

-##     ## a genetic code name vector

-##     GENETIC_CODE <- get_fun_from_pkg("Biostrings", "GENETIC_CODE")

-##     aa <- GENETIC_CODE[codon]

-##     aa[is.na(aa)] <- "X"

-##     return(aa)

-## }

-

-

-## getPhyInfo <- function(phy) {

-##     line1 <- readLines(phy, n=1)

-##     res <- strsplit(line1, split="\\s")[[1]]

-##     res <- res[res != ""]

-

-##     return(list(num=as.numeric(res[1]), width=as.numeric(res[2])))

-## }

-

-## get_seqtype <- function(seq) {

-##     if (length(grep("[^-ACGT]+", seq[1])) == 0) {

-##         seq_type = "NT" ## NucleoTide

-##     } else {

-##         seq_type = "AA" ## Amino Acid

-##     }

-##     return(seq_type)

-## }

-

 reverse.treeview <- function(tv) {

     tv$data <- reverse.treeview.data(tv$data)

     return(tv)

@@ -256,91 +22,6 @@ reverse.treeview.data <- function(df) {

 }

-## jplace_treetext_to_phylo <- function(tree.text) {

-##     ## move edge label to node label separate by @

-##     tr <- gsub('(:[0-9\\.eE\\+\\-]+)\\{(\\d+)\\}', '\\@\\2\\1', tree.text)

-##     phylo <- read.tree(text=tr)

-##     if (length(grep('@', phylo$tip.label)) > 0) {

-##         phylo$node.label[1] %<>% gsub("(.*)\\{(\\d+)\\}", "\\1@\\2", .)

-##         tip.edgeNum <- as.numeric(gsub("[^@]*@(\\d*)", "\\1",phylo$tip.label))

-##         node.edgeNum <- as.numeric(gsub("[^@]*@(\\d*)", "\\1",phylo$node.label))

-##         phylo$tip.label %<>% gsub("@\\d+", "", .)

-##         phylo$node.label %<>% gsub("@\\d+", "", .)

-##         if (all(phylo$node.label == "")) {

-##             phylo$node.label <- NULL

-##         }

-

-##         N <- getNodeNum(phylo)

-##         edgeNum.df <- data.frame(node=1:N, edgeNum=c(tip.edgeNum, node.edgeNum))

-##         ## root node is not encoded with edge number

-##         edgeNum.df <- edgeNum.df[!is.na(edgeNum.df[,2]),]

-##         attr(phylo, "edgeNum") <- edgeNum.df

-##     }

-

-##     ## using :edge_length{edge_num} to match edge_num to node_num

-##     ## this is not a good idea since there may exists identical edge_length.

-##     ## but we can use it to verify our method.

-##     ##

-##     ## en.matches <- gregexpr(":[0-9\\.eE\\+\\-]+\\{\\d+\\}", tree.text)

-##     ## matches <- en.matches[[1]]

-##     ## match.pos <- as.numeric(matches)

-##     ## match.len <- attr(matches, 'match.length')

-

-##     ## edgeLN <- substring(tree.text, match.pos+1, match.pos+match.len-2)

-##     ## edgeLN.df <- data.frame(length=as.numeric(gsub("\\{.+", "", edgeLN)),

-##     ##                         edgeNum = as.numeric(gsub(".+\\{", "", edgeLN)))

-

-##     ## xx <- merge(edgeLN.df, edgeNum.df, by.x="node", by.y="node")

-

-##     return(phylo)

-## }

-

-extract.treeinfo.jplace <- function(object, layout="rectangular", ladderize=TRUE, right=FALSE, ...) {

-

-    tree <- get.tree(object)

-

-    df <- fortify.phylo(tree, layout=layout, ladderize=ladderize, right=right, ...)

-

-    edgeNum.df <- attr(tree, "edgeNum")

-    if (!is.null(edgeNum.df)) {

-        df2 <- merge(df, edgeNum.df, by.x="node", by.y="node", all.x=TRUE)

-        df <- df2[match(df[, "node"], df2[, "node"]),]

-    }

-

-    attr(df, "ladderize") <- ladderize

-    attr(df, "right") <- right

-    return(df)

-}

-

-## ## convert edge number to node number for EPA/pplacer output

-## edgeNum2nodeNum <- function(jp, edgeNum) {

-##     edges <- attr(jp@phylo, "edgeNum")

-

-##     idx <- which(edges$edgeNum == edgeNum)

-##     if (length(idx) == 0) {

-##         return(NA)

-##     }

-

-##     edges[idx, "node"]

-## }

-

-## is.character_beast <- function(stats3, cn) {

-##     for (i in 1:nrow(stats3)) {

-##         if ( is.na(stats3[i,cn]) ) {

-##             next

-##         } else {

-##             ## res <- grepl("[a-df-zA-DF-Z]+", unlist(stats3[i, cn]))

-##             ## return(all(res == TRUE))

-##             res <- grepl("^[0-9\\.eE-]+$", unlist(stats3[i, cn]))

-##             return(all(res == FALSE))

-##         }

-##     }

-##     return(FALSE)

-## }

-

-

-

-

 color_scale <- function(c1="grey", c2="red", n=100) {