[adegenet-commits] r275 - pkg/R

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

Author: jombart
Date: 2009-04-01 12:41:58 +0200 (Wed, 01 Apr 2009)
New Revision: 275

Modified:
   pkg/R/handling.R
Log:
Added locNames accessor


Modified: pkg/R/handling.R
===================================================================
--- pkg/R/handling.R	2009-04-01 10:34:24 UTC (rev 274)
+++ pkg/R/handling.R	2009-04-01 10:41:58 UTC (rev 275)
@@ -662,3 +662,39 @@
 
     return(x)
 })
+
+
+
+
+
+###########
+# locNames
+###########
+setGeneric("locNames", function(x,...){
+    standardGeneric("locNames")
+})
+
+
+
+setMethod("locNames","genind", function(x, withAlleles=FALSE, ...){
+    ## return simply locus names
+    if(x at type=="PA" | !withAlleles) return(x at loc.names)
+
+    ## return locus.allele
+    res <- rep(x at loc.names, x at loc.nall)
+    res <- paste(res,unlist(x at all.names),sep=".")
+    return(res)
+})
+
+
+
+setMethod("locNames","genpop", function(x, withAlleles=FALSE, ...){
+    ## return simply locus names
+    if(x at type=="PA" | !withAlleles) return(x at loc.names)
+
+    ## return locus.allele
+    res <- rep(x at loc.names, x at loc.nall)
+    res <- paste(res,unlist(x at all.names),sep=".")
+    return(res)
+})
+