[Seqinr-commits] r2121 - in pkg: R man

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

Author: simonpenel
Date: 2021-05-20 11:23:54 +0200 (Thu, 20 May 2021)
New Revision: 2121

Modified:
   pkg/R/dist.alignment.R
   pkg/man/dist.alignment.Rd
Log:
Argument gap is now a boolean

Modified: pkg/R/dist.alignment.R
===================================================================
--- pkg/R/dist.alignment.R	2021-05-20 07:56:36 UTC (rev 2120)
+++ pkg/R/dist.alignment.R	2021-05-20 09:23:54 UTC (rev 2121)
@@ -2,7 +2,7 @@
 # Pairwise Distances from Aligned Protein or DNA/RNA Sequences
 #
 
-dist.alignment <- function(x, matrix = c("identity", "similarity"),gap )
+dist.alignment <- function(x, matrix = c("identity", "similarity"),gap = FALSE )
 {
   #
   # Check arguments:
@@ -26,12 +26,12 @@
   #
   # Call the C distance function:
   #
-  if (missing(gap)) {
-  	dist <- .Call("distance", sequences, nbseq, matNumber, seqtype,0, PACKAGE = "seqinr")
-  	}
+  if (gap == TRUE) {
+    dist <- .Call("distance", sequences, nbseq, matNumber, seqtype,1, PACKAGE = "seqinr")
+  }
   else {
-  	dist <- .Call("distance", sequences, nbseq, matNumber, seqtype,gap, PACKAGE = "seqinr")
-  	}
+    dist <- .Call("distance", sequences, nbseq, matNumber, seqtype,0, PACKAGE = "seqinr")
+  }
   #
   # Convert the result in a object of class dist:
   #

Modified: pkg/man/dist.alignment.Rd
===================================================================
--- pkg/man/dist.alignment.Rd	2021-05-20 07:56:36 UTC (rev 2120)
+++ pkg/man/dist.alignment.Rd	2021-05-20 09:23:54 UTC (rev 2121)
@@ -17,7 +17,7 @@
   \item{x}{an object of class \code{alignment}, as returned by
   \code{read.alignment} for instance}
   \item{matrix}{the matrix distance to be used, partial matching allowed }
-  \item{gap}{-optional- with nucleotides, if set to 1, gaps will be counted in the identity measure }
+  \item{gap}{-optional- logical, with identity matrix, if set to \code{TRUE}, gaps will be counted in the identity measure }
 }
 \value{
   The distance matrix, object of class \code{dist}, computed by using the