## setOldClass("phylo")
## setOldClass("multiPhylo")
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"
##          )