fix in read.dna and change in write.dna

[ape.git] / man / makeLabel.Rd

diff --git a/man/makeLabel.Rd b/man/makeLabel.Rd
index 5c56dbc12b8a7ad5060dfa59970562835435f8df..be99abdd8ce8944d1b698abc3aa5aa6fd9706371 100644 (file)
--- a/man/makeLabel.Rd
+++ b/man/makeLabel.Rd
@@ -1,6 +1,16 @@
 \name{makeLabel}
 \alias{makeLabel}
+\alias{makeLabel.character}
+\alias{makeLabel.phylo}
+\alias{makeLabel.multiPhylo}
+\alias{makeLabel.DNAbin}
 \title{Label Management}
+\description{
+  This is a generic function with methods for character vectors, trees
+  of class \code{"phylo"}, lists of trees of class \code{"multiPhylo"},
+  and DNA sequences of class \code{"DNAbin"}. All options for the class
+  character may be used in the other methods.
+}
 \usage{
 makeLabel(x, ...)
 \method{makeLabel}{character}(x, len = 99, space = "_", make.unique = TRUE,
@@ -26,13 +36,7 @@ makeLabel(x, ...)
     modified; \code{TRUE} by default.}
   \item{nodes}{a logical specifying whether node labels are to be
     modified; \code{TRUE} by default.}
-  \item{...}{further arguments to be passed to or from other methods.}
-}
-\description{
-  This is a generic function with methods for character vectors, trees
-  of class \code{"phylo"}, lists of trees of class \code{"multiPhylo"},
-  and DNA sequences of class \code{"DNAbin"}. All options for the class
-  character may be used in the other methods.
+  \item{\dots}{further arguments to be passed to or from other methods.}
 }
 \details{
   The option \code{make.unique} does not work exactly in the same way
@@ -44,7 +48,7 @@ makeLabel(x, ...)
   on. The number of digits added preserves the option `len'.
 
   The default for `len' makes labels short enough to be read by
-  PHYML. Clustal accepts labels up to 30 character long.
+  PhyML. Clustal accepts labels up to 30 character long.
 }
 \note{
   The current version does not perform well when trying to make very
@@ -53,10 +57,11 @@ makeLabel(x, ...)
 \value{
   An object of the appropriate class.
 }
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
 \seealso{
-  \code{\link[base]{make.unique}}, \code{\link[base]{make.names}},
-  \code{\link[base]{abbreviate}}
+  \code{\link{makeNodeLabel}}, \code{\link[base]{make.unique}},
+  \code{\link[base]{make.names}}, \code{\link[base]{abbreviate}},
+  \code{\link{mixedFontLabel}}
 }
 \examples{
 x <- rep("a", 3)
@@ -66,3 +71,4 @@ x <- rep("aaaaa", 2)
 makeLabel(x, len = 3) # made unique and of length 3
 makeLabel(x, len = 3, make.unique = FALSE)
 }
+\keyword{manip}