@@ -1,7 +1,7 @@

 Package: ggtree

 Type: Package

 Title: a phylogenetic tree viewer for different types of tree annotations

-Version: 1.1.13

+Version: 1.1.14

 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -1,3 +1,7 @@

+CHANGES IN VERSION 1.1.14

+------------------------

+ o update paml_rst to compatible with only marginal ancestral sequence or joint ancestral sequence available <2015-08-07, Fri>

+ 

 CHANGES IN VERSION 1.1.13

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

  o implement annotation_image <2015-08-01, Sat>

@@ -322,6 +322,9 @@ set.paml_rst_ <- function(object) {

     types <- get.fields(object)

     for (type in types) {

         value <- subs_paml_rst(object, type)

+        if (all(is.na(value)))

+            next

+        

         if (type == "marginal_subs") {

             object@marginal_subs <- value

         } else if (type == "marginal_AA_subs") {

@@ -364,9 +367,11 @@ subs_paml_rst <- function(x, type, ...) {

         stop("tip sequences is not available...")

     }

     if (type %in% c("marginal_subs", "marginal_AA_subs")) {

-        seqs <- c(seqs, x@marginal_ancseq)

+        ancseq <- x@marginal_ancseq

+        ## seqs <- c(seqs, x@marginal_ancseq)

     } else if (type %in% c("joint_subs", "joint_AA_subs")){

-        seqs <- c(seqs, x@joint_ancseq)

+        ancseq <- x@joint_ancseq

+        ## seqs <- c(seqs, x@joint_ancseq)

     } else {

         stop("type should be one of 'marginal_subs',

                              'marginal_AA_subs', 'joint_subs' or 'joint_AA_subs'. ")

@@ -376,6 +381,10 @@ subs_paml_rst <- function(x, type, ...) {

     } else {

         translate <- TRUE

     }

-    

+

+    if (all(ancseq == "")) {

+        return(NA)

+    }

+    seqs <- c(seqs, ancseq)

     get.subs_(x@phylo, seqs, translate=translate, ...)

 }

@@ -114,11 +114,22 @@ setMethod("show", signature(object = "paml_rst"),

               ## } 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(get.fields(object), collapse="',\t'"),

+                               paste(fields, collapse="',\t'"),

                                "'."),

                   "\n")

           })

@@ -130,7 +141,7 @@ setMethod("get.fields", signature(object = "paml_rst"),

               if (length(object@tip_seq) == 0) {

                   warning("tip sequence not available...\n")

               } else {

-                  get.fields.tree(object)

+                  get.fields.tree(object) 

               }

           }

           )