[Phylobase-commits] r913 - pkg/R

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

Author: francois
Date: 2014-04-08 19:55:55 +0200 (Tue, 08 Apr 2014)
New Revision: 913

Removed:
   pkg/R/phylo4.R
Log:
phylo4.R not needed anymore, all generic defined with their methods.

Deleted: pkg/R/phylo4.R
===================================================================
--- pkg/R/phylo4.R	2014-04-08 17:55:07 UTC (rev 912)
+++ pkg/R/phylo4.R	2014-04-08 17:55:55 UTC (rev 913)
@@ -1,186 +0,0 @@
-## Same order as in methods-phylo4.R
-
-## nTips
-
-
-## depthTips
-setGeneric("depthTips", function(x) {
-  standardGeneric("depthTips")
-})
-
-## nNodes
-setGeneric("nNodes", function(x) {
-    standardGeneric("nNodes")
-})
-
-## nodeType
-setGeneric("nodeType", function(x) {
-    standardGeneric("nodeType")
-})
-
-## nodeId
-setGeneric("nodeId", function(x, type=c("all", "tip", "internal",
-    "root")) {
-    standardGeneric("nodeId")
-})
-
-## nodeDepth
-setGeneric("nodeDepth", function(x, node) {
-  standardGeneric("nodeDepth")
-})
-
-## nEdges
-setGeneric("nEdges", function(x) {
-    standardGeneric("nEdges")
-})
-
-## edges
-setGeneric("edges", function(x, ...) {
-    standardGeneric("edges")
-})
-
-## edgeOrder
-setGeneric("edgeOrder", function(x, ...) {
-  standardGeneric("edgeOrder")
-})
-
-## edgeId
-setGeneric("edgeId", function(x, type=c("all", "tip", "internal",
-    "root")) {
-    standardGeneric("edgeId")
-})
-
-## hasEdgeLength
-setGeneric("hasEdgeLength", function(x) {
-    standardGeneric("hasEdgeLength")
-})
-
-## edgeLength
-setGeneric("edgeLength", function(x, ...) {
-    standardGeneric("edgeLength")
-})
-
-## edgeLength<-
-setGeneric("edgeLength<-", function(x, ..., value) {
-    standardGeneric("edgeLength<-")
-})
-
-## sumEdgeLength
-setGeneric("sumEdgeLength", function(x, node) {
-    standardGeneric("sumEdgeLength")
-})
-
-## isRooted
-setGeneric("isRooted", function(x) {
-    standardGeneric("isRooted")
-})
-
-## rootNode
-setGeneric("rootNode", function(x) {
-    standardGeneric("rootNode")
-})
-
-## rootNode<-
-setGeneric("rootNode<-", function(x, value) {
-    standardGeneric("rootNode<-")
-})
-
-## labels
-setGeneric("labels")
-
-## labels<-
-setGeneric("labels<-",
-           function(x, type, use.names, ..., value) {
-               standardGeneric("labels<-")
-           })
-
-## hasDuplicatedLabels
-setGeneric("hasDuplicatedLabels",
-           function(x, type) {
-               standardGeneric("hasDuplicatedLabels")
-           })
-
-## hasNodeLabels
-setGeneric("hasNodeLabels", function(x) {
-    standardGeneric("hasNodeLabels")
-})
-
-## nodeLabels
-setGeneric("nodeLabels", function(x) {
-    standardGeneric("nodeLabels")
-})
-
-## nodeLabels<-
-setGeneric("nodeLabels<-",
-           function(x, ..., value) {
-               standardGeneric("nodeLabels<-")
-           })
-
-## tipLabels
-setGeneric("tipLabels", function(x) {
-    standardGeneric("tipLabels")
-})
-
-## tipLabels<-
-setGeneric("tipLabels<-",
-   function(x, ..., value) {
-       standardGeneric("tipLabels<-")
-   })
-
-## hasEdgeLabels
-setGeneric("hasEdgeLabels", function(x) {
-    standardGeneric("hasEdgeLabels")
-})
-
-## edgeLabels
-setGeneric("edgeLabels", function(x) {
-    standardGeneric("edgeLabels")
-})
-
-## edgeLabels<-
-setGeneric("edgeLabels<-",
-           function(x, ..., value) {
-               standardGeneric("edgeLabels<-")
-           })
-
-## print
-setGeneric("print")
-
-
-## head
-setGeneric("head")
-
-## tail
-setGeneric("tail")
-
-## isUltrametric
-setGeneric("isUltrametric", function(x, tol=.Machine$double.eps^.5) {
-  standardGeneric("isUltrametric")
-})
-
-
-### ----------- phylo4d methods -----------
-
-##setGeneric("na.omit")
-
-
-
-##setGeneric("rootEdge", function(x, order, ...) {
-##    standardGeneric("rootEdge")
-##})
-
-###################
-## Function .genlab
-###################
-## (formerly) recursive function to have labels of constant length
-## base = a character string
-## n = number of labels
-.genlab <- function(base, n) {
-    if(n <= 0) return("")
-    s <- seq(length.out=n)
-    fw <- max(nchar(as.character(s)))
-    numstr <- formatC(s, flag="0", width=fw)
-    paste(base, numstr, sep="")
-}
-
-