From 0eb732cf743bc38c934b860fc6df60aa248b3034 Mon Sep 17 00:00:00 2001
From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Sun, 8 Jun 2008 06:46:38 +0000
Subject: [PATCH] adding del.gaps()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@32 6e262413-ae40-0410-9e79-b911bd7a66b7
---
 Changes         | 10 ++++++++++
 DESCRIPTION     |  4 ++--
 R/DNA.R         | 23 ++++++++++++++++++++++-
 man/corPagel.Rd |  2 +-
 man/del.gaps.Rd | 31 +++++++++++++++++++++++++++++++
 5 files changed, 66 insertions(+), 4 deletions(-)
 create mode 100644 man/del.gaps.Rd

diff --git a/Changes b/Changes
index 05cbfab..4aa9a91 100644
--- a/Changes
+++ b/Changes
@@ -1,3 +1,13 @@
+		CHANGES IN APE VERSION 2.2-1
+
+
+NEW FEATURES
+
+    o The new function del.gaps() removes insertion gaps ("-") in a
+      set of DNA sequences.
+
+
+
 		CHANGES IN APE VERSION 2.2
 
 
diff --git a/DESCRIPTION b/DESCRIPTION
index c4bf8f7..6b2d89a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ape
-Version: 2.2
-Date: 2008-05-07
+Version: 2.2-1
+Date: 2008-06-08
 Title: Analyses of Phylogenetics and Evolution
 Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
   Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
diff --git a/R/DNA.R b/R/DNA.R
index 2482511..e51f252 100644
--- a/R/DNA.R
+++ b/R/DNA.R
@@ -1,4 +1,4 @@
-## DNA.R (2008-04-24)
+## DNA.R (2008-06-08)
 
 ##   Manipulations and Comparisons of DNA Sequences
 
@@ -7,6 +7,27 @@
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
 
+del.gaps <- function(x)
+{
+    deleteGaps <- function(x) {
+        i <- which(x == 4)
+        x[-i]
+    }
+
+    if (class(x) != "DNAbin") x <- as.DNAbin(x)
+    if (is.matrix(x)) {
+        n <- dim(x)[1]
+        y <- vector("list", n)
+        for (i in 1:n) y[[i]] <- x[i, ]
+        x <- y
+        rm(y)
+    }
+    if (!is.list(x)) return(deleteGaps(x))
+    x <- lapply(x, deleteGaps)
+    class(x) <- "DNAbin"
+    x
+}
+
 as.alignment <- function(x)
 {
     if (is.list(x)) n <- length(x)
diff --git a/man/corPagel.Rd b/man/corPagel.Rd
index 7248f65..4509b44 100644
--- a/man/corPagel.Rd
+++ b/man/corPagel.Rd
@@ -35,7 +35,7 @@ corPagel(value, phy, form = ~1, fixed = FALSE)
 \value{
   an object of class \code{"corPagel"}, the coefficients from an object
   of this class, or the correlation matrix of an initialized object of
-  this class. In most situations, only \code{corPagel()} will be called
+  this class. In most situations, only \code{corPagel} will be called
   by the user.
 }
 \author{Emmanuel Paradis}
diff --git a/man/del.gaps.Rd b/man/del.gaps.Rd
new file mode 100644
index 0000000..3a22424
--- /dev/null
+++ b/man/del.gaps.Rd
@@ -0,0 +1,31 @@
+\name{del.gaps}
+\alias{del.gaps}
+\title{
+  Delete Alignment Gaps in DNA Sequences
+}
+\usage{
+del.gaps(x)
+}
+\arguments{
+  \item{x}{a matrix, a list, or a vector containing the DNA sequences.}
+}
+\description{
+  This function removes the insertion gaps (\code{"-"}) in a sample of
+  DNA sequences.
+}
+\details{
+  The sequences can be either in \code{"DNAbin"} or in character format,
+  but the returned object is always of class \code{"DNAbin"}. If
+  \code{x} is a vector, then a vector is returned; if it is a list or a
+  matrix, then a list is returned.
+}
+\value{
+  A vector (if there is only one input sequence) or a list of class
+  \code{"DNAbin"}.
+}
+\author{Emmanuel Paradis \email{Emmanuel.Paradis@ird.fr}}
+\seealso{
+  \code{\link{base.freq}}, \code{\link{GC.content}},
+  \code{\link{theta.s}}, \code{\link{nuc.div}}, \code{\link{seg.sites}}
+}
+\keyword{univar}
-- 
2.39.2