[Phylobase-commits] r833 - pkg/R

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

Author: francois
Date: 2012-01-11 18:00:24 +0100 (Wed, 11 Jan 2012)
New Revision: 833

Modified:
   pkg/R/readNCL.R
Log:
between brackets annotations at nodes are not being removed by NCL (as generated by BEAST), they are now being removed by phylobase before parsing the tree strings

Modified: pkg/R/readNCL.R
===================================================================
--- pkg/R/readNCL.R	2011-03-24 20:05:33 UTC (rev 832)
+++ pkg/R/readNCL.R	2012-01-11 17:00:24 UTC (rev 833)
@@ -130,10 +130,13 @@
    if (!experimental) {
      for (i in 1:length(ncl$trees)) {
        if (length(grep(":", ncl$trees[i]))) {
-         listTrees[[i]] <- tree.build(ncl$trees[i])
+         ## remove comments from the string, they are not being removed if they are part of the node labels
+         tStr <- gsub("\\[.*?\\]", "", ncl$trees[i])
+         listTrees[[i]] <- tree.build(tStr)
        }
        else {
-         listTrees[[i]] <- clado.build(ncl$trees[i])
+         tStr <- gsub("\\[.*?\\]", "", ncl$trees[i])
+         listTrees[[i]] <- clado.build(tStr)
        }
      }
      listTrees <- lapply(listTrees, function(tr) {