[adegenet-commits] r936 - in pkg: R man

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

Author: jombart
Date: 2011-06-29 17:46:17 +0200 (Wed, 29 Jun 2011)
New Revision: 936

Modified:
   pkg/R/seqTrack.R
   pkg/man/seqTrack.Rd
Log:
Removed conversion to graphNEL class: check passes, but FAQ #4 still there.
Fuck sake!


Modified: pkg/R/seqTrack.R
===================================================================
--- pkg/R/seqTrack.R	2011-06-29 15:12:56 UTC (rev 935)
+++ pkg/R/seqTrack.R	2011-06-29 15:46:17 UTC (rev 936)
@@ -337,21 +337,21 @@
 ##########################
 ## as("seqTrack", "graphNEL")
 ##########################
-if(require(graph)){
-setOldClass("seqTrack")
-setAs("seqTrack", "graphNEL", def=function(from){
-    ##    if(!require(ape)) stop("package ape is required")
-    if(!require(graph)) stop("package graph is required")
+## if(require(graph)){
+## setOldClass("seqTrack")
+## setAs("seqTrack", "graphNEL", def=function(from){
+##     ##    if(!require(ape)) stop("package ape is required")
+##     if(!require(graph)) stop("package graph is required")
 
-    ori.labels <- rownames(from)
-    from <- from[!is.na(from$ances),,drop=FALSE]
+##     ori.labels <- rownames(from)
+##     from <- from[!is.na(from$ances),,drop=FALSE]
 
 
-     ## CONVERT TO GRAPH
-    res <- ftM2graphNEL(ft=cbind(ori.labels[from$ances], ori.labels[from$id]), W=from$weight, edgemode = "directed", V=ori.labels)
-    return(res)
-})
-}
+##      ## CONVERT TO GRAPH
+##     res <- ftM2graphNEL(ft=cbind(ori.labels[from$ances], ori.labels[from$id]), W=from$weight, edgemode = "directed", V=ori.labels)
+##     return(res)
+## })
+## }
 
 
 

Modified: pkg/man/seqTrack.Rd
===================================================================
--- pkg/man/seqTrack.Rd	2011-06-29 15:12:56 UTC (rev 935)
+++ pkg/man/seqTrack.Rd	2011-06-29 15:46:17 UTC (rev 936)
@@ -167,6 +167,24 @@
 ## PLOT RESULTS
 \dontrun{
 if(require(graph) && require(Rgraphviz)){
+## quick convertion method to graphNEL ##
+setOldClass("seqTrack")
+setAs("seqTrack", "graphNEL", def=function(from){
+    ##    if(!require(ape)) stop("package ape is required")
+    if(!require(graph)) stop("package graph is required")
+
+    ori.labels <- rownames(from)
+    from <- from[!is.na(from$ances),,drop=FALSE]
+
+
+     ## CONVERT TO GRAPH
+    res <- ftM2graphNEL(ft=cbind(ori.labels[from$ances], ori.labels[from$id]), W=from$weight, edgemode = "directed", V=ori.labels)
+    return(res)
+})
+## end conversion function ##
+
+
+
 dat.g <- as(dat, "graphNEL")
 res.g <- as(res, "graphNEL")