[Seqinr-commits] r1777 - in pkg: . R man src

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

Author: simonpenel
Date: 2014-01-30 15:39:20 +0100 (Thu, 30 Jan 2014)
New Revision: 1777

Modified:
   pkg/DESCRIPTION
   pkg/R/dist.alignment.R
   pkg/man/dist.alignment.Rd
   pkg/src/alignment.c
Log:
In function dist.alignment with nucleotides sequences, if gap option is set to 1, gaps will be counted in the identity measure (thanks to Peter Hraber)


Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2013-10-07 15:11:49 UTC (rev 1776)
+++ pkg/DESCRIPTION	2014-01-30 14:39:20 UTC (rev 1777)
@@ -1,6 +1,6 @@
 Package: seqinr
-Version: 3.0-8
-Date: 2013-10-7
+Version: 3.0-9
+Date: 2014-1-30
 Title: Biological Sequences Retrieval and Analysis 
 Author: Delphine Charif and Jean R. Lobry and Anamaria Necsulea and Leonor Palmeira and Simon Penel and Guy Perriere
 Maintainer: Simon Penel <simon.penel at univ-lyon1.fr>

Modified: pkg/R/dist.alignment.R
===================================================================
--- pkg/R/dist.alignment.R	2013-10-07 15:11:49 UTC (rev 1776)
+++ pkg/R/dist.alignment.R	2014-01-30 14:39:20 UTC (rev 1777)
@@ -2,7 +2,7 @@
 # Pairwise Distances from Aligned Protein or DNA/RNA Sequences
 #
 
-dist.alignment <- function(x, matrix = c("similarity", "identity") )
+dist.alignment <- function(x, matrix = c("similarity", "identity"),gap )
 {
   #
   # Check arguments:
@@ -26,7 +26,12 @@
   #
   # Call the C distance function:
   #
-  dist <- .Call("distance", sequences, nbseq, matNumber, seqtype, PACKAGE = "seqinr")
+  if (missing(gap)) {
+  	dist <- .Call("distance", sequences, nbseq, matNumber, seqtype,0, PACKAGE = "seqinr")
+  	}
+  else {
+  	dist <- .Call("distance", sequences, nbseq, matNumber, seqtype,gap, PACKAGE = "seqinr")
+  	}
   #
   # Convert the result in a object of class dist:
   #

Modified: pkg/man/dist.alignment.Rd
===================================================================
--- pkg/man/dist.alignment.Rd	2013-10-07 15:11:49 UTC (rev 1776)
+++ pkg/man/dist.alignment.Rd	2014-01-30 14:39:20 UTC (rev 1777)
@@ -11,12 +11,13 @@
 
 }
 \usage{
-dist.alignment(x, matrix = c("similarity", "identity"))
+dist.alignment(x, matrix = c("similarity", "identity"),gap)
 }
 \arguments{
   \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 }
 }
 \value{
   The distance matrix, object of class \code{dist}, computed by using the 

Modified: pkg/src/alignment.c
===================================================================
--- pkg/src/alignment.c	2013-10-07 15:11:49 UTC (rev 1776)
+++ pkg/src/alignment.c	2014-01-30 14:39:20 UTC (rev 1777)
@@ -252,11 +252,12 @@
 /*************************************************************************/
 
 
-SEXP distance(SEXP sequences,SEXP nbseq, SEXP matNumber, SEXP seqtype){
+SEXP distance(SEXP sequences,SEXP nbseq, SEXP matNumber, SEXP seqtype, SEXP gapoption){
 
   SEXP d;
   int MAXNSEQS;
   char **seq;
+  int gap_option;
   int i, j, k, n,totseqs, seq_long, nbases;
   int mat_number, seq_type;
   int **ndiff;
@@ -294,6 +295,7 @@
   totseqs = INTEGER_VALUE(nbseq);
   mat_number= INTEGER_VALUE(matNumber);
   seq_type = INTEGER_VALUE(seqtype);
+  gap_option =  INTEGER_VALUE(gapoption);
 
   PROTECT(d=NEW_NUMERIC(totseqs*totseqs));
 
@@ -354,6 +356,23 @@
 			ndiff[i][j]++;
 		      }
 		  }
+		  
+		  if (gap_option == 1)
+		  	{
+			if (seq[i][k] == '-'  && seq[j][k] != '-' && seq[j][k] != 'N' && seq[j][k] != 'X')
+				{
+				nbases++;
+				ndiff[j][i]++;
+				ndiff[i][j]++;
+				}
+			if (seq[j][k] == '-'  && seq[i][k] != '-' && seq[i][k] != 'N' && seq[i][k] != 'X')
+				{
+				nbases++;
+				ndiff[j][i]++;
+				ndiff[i][j]++;
+				}
+			
+			}
 	      }
 
 	      else if(mat_number == 1 && seq_type == 0){