@@ -1,8 +1,8 @@

 Package: msa

 Type: Package

 Title: Multiple Sequence Alignment

-Version: 1.11.0

-Date: 2017-04-17

+Version: 1.11.1

+Date: 2018-04-23

 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer

 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>

 Description: The 'msa' package provides a unified R/Bioconductor interface to

@@ -154,7 +154,7 @@ msaClustalW <- function(inputSeqs,

             params[["substitutionMatrixIsStringFlag"]] <- FALSE

             params[["substitutionMatrixIsDefaultFlag"]] <- TRUE

-            params[["dnamatrix"]] <- substitutionMatrix

+            params[["pwdnamatrix"]] <- substitutionMatrix

             substitutionMatrix <- "default"

         }

     } else {

@@ -334,8 +334,7 @@ msaClustalW <- function(inputSeqs,

     ###########

     # convert #

-    ###########

-    ##output the input sequences in a different file format.

+    ###########    ##output the input sequences in a different file format.

     params[["convert"]] <- checkLogicalParams("convert", params, FALSE)

     ##delete param in copy

@@ -655,7 +654,7 @@ msaClustalW <- function(inputSeqs,

     } else {

         posVal <- c("iub", "clustalw")

         params[["pwdnamatrix"]] <- checkSingleValParamsNew("pwdnamatrix",

-                                    params, posVal)

+                                                           params, posVal)

     }

     ##delete param in copy

@@ -729,16 +728,16 @@ msaClustalW <- function(inputSeqs,

     #############

     ##DNA weight matrix=IUB, CLUSTALW or filename

-    ##if filename (seperated with ".") check and use file;

+    ##if filename (separated with ".") check and use file;

     ##else check whether value is iub or clustalw;

     ##if nothing is given, use iub

     if (!is.null(params[["dnamatrix"]]) &&

             grepl("\\.", params[["dnamatrix"]], perl=TRUE)) {

         checkInFile("dnamatrix", params)

-    } else {

+    } else if (is.null(params[["pwdnamatrix"]])) {

         posVal <- c("iub", "clustalw")

-        params[["dnamatrix"]] <- checkSingleValParamsNew("dnamatrix",

-                                    params, posVal)

+        params[["pwdnamatrix"]] <- checkSingleValParamsNew("dnamatrix",

+                                                           params, posVal)

     }

     ##delete param in copy

@@ -1,6 +1,24 @@

 Change history of package msa:

 ==============================

+Version 1.12.0:

+- release as part of Bioconductor 3.7

+

+Version 1.11.1:

+- fix of code for using custom substitution matrices in ClustalW

+

+Version 1.11.0:

+- new branch for Bioconductor 3.7 devel

+

+Version 1.10.0:

+- release as part of Bioconductor 3.6

+

+Version 1.9.0:

+- new branch for Bioconductor 3.6 devel

+

+Version 1.8.0:

+- release as part of Bioconductor 3.5

+

 Version 1.7.2:

 - fix for new clang 4 compiler on Mac OS

@@ -116,6 +116,16 @@ SEXP RClustalW(SEXP rInputSeqs,

             args.push_back(std::string(numiter));

         }

+        //type

+        if (!Rf_isNull(rType)) {

+            string type = as<string>(rType);

+            string autoType = "auto";

+            //clustalW don't know type == "rna"

+            if (autoType.compare(type) != 0 && type != "rna") {

+                args.push_back(" TYPE=" + type);

+            }

+        }

+

         //rSubstitutionMatrix

         bool defaultFlag = false;

         if (hasClustalWEntry(rparam, "substitutionMatrixIsDefaultFlag")) {

@@ -127,8 +137,13 @@ SEXP RClustalW(SEXP rInputSeqs,

         }

         if (defaultFlag) {

-            //do nothing

-            Rprintf("use default substitution matrix\n");

+            if (hasClustalWEntry(rparam, "pwdnamatrix")) {

+		string pwDnaMat = as<string>(rparam["pwdnamatrix"]);

+		Rprintf("use DNA substitution matrix: %s\n", pwDnaMat.c_str());

+	    }

+	    else {

+		Rprintf("use default substitution matrix\n");

+	    }

         } else if (stringFlag) {

             /*FIXME TODO change hardcoded rows and numbers*/

             string inputMatrixFile = as<string>(rSubstitutionMatrix);

@@ -145,16 +160,6 @@ SEXP RClustalW(SEXP rInputSeqs,

             input.substitutionMatrix = substitutionMatrix;

         }

-        //type

-        if (!Rf_isNull(rType)) {

-            string type = as<string>(rType);

-            string autoType = "auto";

-            //clustalW don't know type == "rna"

-            if (autoType.compare(type) != 0 && type != "rna") {

-                args.push_back(" TYPE=" + type);

-            }

-        }

-

         //verbose

         bool verbose = false;

         if (!Rf_isNull(rVerbose)) {

@@ -465,6 +470,10 @@ SEXP RClustalW(SEXP rInputSeqs,

             string pwdnamatrix = as<string>(rparam["pwdnamatrix"]);

             args.push_back(" PWDNAMATRIX=" + pwdnamatrix);

         }

+	else if (hasClustalWEntry(rparam, "dnamatrix")) {

+            string pwdnamatrix = as<string>(rparam["dnamatrix"]);

+            args.push_back(" PWDNAMATRIX=" + pwdnamatrix);

+	}

         //params$pwgapext

         if (hasClustalWEntry(rparam, "pwgapext")) {

@@ -889,6 +889,14 @@ bibliography below).

 \section{Change Log}

 \begin{description}

+\item[Version 1.12.0:] release as part of Bioconductor 3.7

+\item[Version 1.11.1:] \mbox{ }  \begin{itemize}

+   \item fix of code for using custom substitution matrices in ClustalW

+  \end{itemize}

+\item[Version 1.11.0:] new branch for Bioconductor 3.7 devel

+\item[Version 1.10.0:] release as part of Bioconductor 3.56

+\item[Version 1.9.0:] new branch for Bioconductor 3.6 devel

+\item[Version 1.8.0:] release as part of Bioconductor 3.5

 \item[Version 1.7.2:] \mbox{ }  \begin{itemize}

    \item fix for new \verb+clang+ 4 compiler on Mac OS

   \end{itemize}