[Phylobase-commits] r663 - branches/slot-mods/R

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

Author: regetz
Date: 2009-09-23 07:44:57 +0200 (Wed, 23 Sep 2009)
New Revision: 663

Modified:
   branches/slot-mods/R/class-phylo4.R
   branches/slot-mods/R/methods-phylo4.R
Log:
addendum to r660: updated 'labels<-' and .createLabels arguments (and
one test) to reflect new default type for label replacement


Modified: branches/slot-mods/R/class-phylo4.R
===================================================================
--- branches/slot-mods/R/class-phylo4.R	2009-09-23 05:09:38 UTC (rev 662)
+++ branches/slot-mods/R/class-phylo4.R	2009-09-23 05:44:57 UTC (rev 663)
@@ -21,12 +21,12 @@
 #####################
 
 .createLabels <- function(value, ntips, nnodes, use.names = TRUE,
-                          type = c("tip", "internal", "allnode")) {
+                          type = c("all", "tip", "internal")) {
 
     type <- match.arg(type)
 
     ## set up final length of object to return
-    lgthRes <- switch(type, tip=ntips, internal=nnodes, allnode=ntips+nnodes)
+    lgthRes <- switch(type, tip=ntips, internal=nnodes, all=ntips+nnodes)
 
     ## create NA character vector of node labels
     res <- character(lgthRes)
@@ -36,7 +36,7 @@
     names(res) <- switch(type,
                          tip = 1:ntips,
                          internal = seq(from=ntips+1, length=lgthRes),
-                         allnode = 1:(ntips+nnodes))
+                         all = 1:(ntips+nnodes))
 
 
     ## if no values are provided

Modified: branches/slot-mods/R/methods-phylo4.R
===================================================================
--- branches/slot-mods/R/methods-phylo4.R	2009-09-23 05:09:38 UTC (rev 662)
+++ branches/slot-mods/R/methods-phylo4.R	2009-09-23 05:44:57 UTC (rev 663)
@@ -265,7 +265,7 @@
 setReplaceMethod("labels",
                  signature(x="phylo4", type="ANY",
                            use.names="ANY", value="character"),
-   function(x, type = c("tip", "internal", "allnode"),
+   function(x, type = c("all", "tip", "internal"),
             use.names, ..., value) {
 
        ## Default options