[Phylobase-commits] r156 - pkg/R

[noreply at r-forge.r-project.org]

Author: pdc
Date: 2008-03-08 02:39:36 +0100 (Sat, 08 Mar 2008)
New Revision: 156

Modified:
   pkg/R/methods-phylo4.R
   pkg/R/phylo4.R
Log:
Move a couple last methods

Modified: pkg/R/methods-phylo4.R
===================================================================
--- pkg/R/methods-phylo4.R	2008-03-08 01:16:11 UTC (rev 155)
+++ pkg/R/methods-phylo4.R	2008-03-08 01:39:36 UTC (rev 156)
@@ -1,3 +1,10 @@
+## accessor functions for all internal bits
+## HORRIBLE KLUGE
+nTips <- function(x,...)  { }  ## mask ape::nTips
+setGeneric("nTips", function(x,...) {
+    standardGeneric("nTips")
+})
+
 setMethod("nTips", "phylo4", function(x, ...) {
     E <- edges(x)
     res <- sum(!E[, 2] %in% E[, 1])
@@ -4,6 +11,15 @@
     return(res)
 })
 
+## hack to ensure ape compatibility
+setMethod("nTips","ANY", function(x) {
+    if (class(x)=="phylo") {
+        Ntip(x)
+    } else stop(paste("no 'nTips' method available for",
+                      deparse(substitute(x)),
+                      "(class",class(x),")"))
+})
+
 setMethod("nNodes", "phylo4", function(x) {
     x at Nnode
 })
@@ -100,6 +116,12 @@
     return(x)
 })
 
+
+printphylo4 <- function(x, printall = TRUE){
+    if (printall)
+      print(as(x, 'data.frame'))
+    else print(head(as(x, 'data.frame')))
+}
 ## hack for print/show 
 ## from http://tolstoy.newcastle.edu.au/R/e2/devel/06/12/1363.html
 #setMethod("print", "phylo4", printphylo)
@@ -110,12 +132,6 @@
 # Alternative print method for phylo4, showing the contents of the tree data.
 ##  Not sure if it works for unrooted trees
 
-printphylo4 <- function(x, printall = TRUE){
-    if (printall)
-      print(as(x, 'data.frame'))
-    else print(head(as(x, 'data.frame')))
-}
-
 printphylo <- function (x,printlen=6,...) {
     printlen <- max(1,printlen)
     nb.tip <- length(x$tip.label)

Modified: pkg/R/phylo4.R
===================================================================
--- pkg/R/phylo4.R	2008-03-08 01:16:11 UTC (rev 155)
+++ pkg/R/phylo4.R	2008-03-08 01:39:36 UTC (rev 156)
@@ -1,22 +1,6 @@
 require(methods)
 require(ape)
-         
-## accessor functions for all internal bits
-## HORRIBLE KLUGE
-nTips <- function(x,...)  { }  ## mask ape::nTips
-setGeneric("nTips", function(x,...) {
-    standardGeneric("nTips")
-})
 
-## hack to ensure ape compatibility
-setMethod("nTips","ANY", function(x) {
-    if (class(x)=="phylo") {
-        Ntip(x)
-    } else stop(paste("no 'nTips' method available for",
-                      deparse(substitute(x)),
-                      "(class",class(x),")"))
-})
-
 setGeneric("nNodes", function(x) {
     standardGeneric("nNodes")
 })