@@ -1,18 +1,18 @@

 Package: msa

 Type: Package

 Title: Multiple Sequence Alignment

-Version: 0.99.2

-Date: 2015-04-09

+Version: 0.99.3

+Date: 2015-04-10

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

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

-Description: This package provides a unified R/Bioconductor interface

-        to the multiple sequence alignment algorithms ClustalW,

-        ClustalOmega, and Muscle. All three algorithms are integrated

-        in the package, therefore, they do not depend on any external

-        software tools and are available for all major platforms. The

-        multiple sequence alignment algorithms are complemented by a

-        function for pretty-printing multiple sequence alignments using

-        the LaTeX package TeXshade.

+Description: This package provides a unified R/Bioconductor interface to the

+	     multiple sequence alignment algorithms ClustalW, ClustalOmega,

+	     and Muscle. All three algorithms are integrated in the package,

+	     therefore, they do not depend on any external software tools

+	     and are available for all major platforms. The multiple sequence

+	     alignment algorithms are complemented by a function for

+	     pretty-printing multiple sequence alignments using the LaTeX

+	     package TeXshade.

 License: GPL (>= 2)

 Copyright: See file inst/COPYRIGHT

 Depends: R (>= 3.1.0), methods, Biostrings (>= 2.30.0)

@@ -20,6 +20,7 @@ Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),

         S4Vectors, tools

 Suggests: Biobase, knitr

 LinkingTo: Rcpp

+SystemRequirements: GNU make

 VignetteBuilder: knitr

 LazyLoad: yes

 Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R

@@ -29,3 +30,4 @@ Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R

 biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,

         Sequencing

 NeedsCompilation: yes

+Packaged: 2015-04-10 22:07:02 UTC; bodenhof

@@ -1,13 +1,14 @@

-setClass("MsaMetaData", 

-        representation(version="character", 

-                       params="list", 

-                       call="character"))

+setClass("MsaMetaData",

+         slots=c(version="character",

+                 params="list",

+                 call="character"),

+         contains="VIRTUAL")

-setClass("MsaDNAMultipleAlignment", 

-        contains=c("DNAMultipleAlignment", "MsaMetaData"))

+setClass("MsaDNAMultipleAlignment",

+         contains=c("DNAMultipleAlignment", "MsaMetaData"))

-setClass("MsaRNAMultipleAlignment", 

-        contains=c("RNAMultipleAlignment", "MsaMetaData"))

+setClass("MsaRNAMultipleAlignment",

+         contains=c("RNAMultipleAlignment", "MsaMetaData"))

-setClass("MsaAAMultipleAlignment", 

-        contains=c("AAMultipleAlignment", "MsaMetaData"))

+setClass("MsaAAMultipleAlignment",

+         contains=c("AAMultipleAlignment", "MsaMetaData"))

@@ -1,8 +1,5 @@

-print.MsaMetaData <- function(x, show=c("version", "standardParams",

-                                        "algParams", "call"))

+print.MsaMetaData <- function(x, show)

 {

-    show <- match.arg(show, several.ok=TRUE)

-

     sep <- FALSE

     if ("version" %in% show)

@@ -48,14 +45,22 @@ print.MsaMetaData <- function(x, show=c("version", "standardParams",

     }

 }

-setMethod("print", signature("MsaMetaData"), print.MsaMetaData)

-

-print.MsaMultipleAlignment <- function(x, show=c("version", "call"))

+print.MsaMultipleAlignment <- function(x, show=c("alignment", "version",

+                                                 "call"))

 {

-    print(as(x, "MsaMetaData"), show=show)

-    cat("\n")

-    print(as(x, substr(class(x), 4, nchar(class(x)))))

+    show <- match.arg(show,

+                      choices=c("alignment", "version", "call",

+                                "standardParams", "algParams"),

+                      several.ok=TRUE)

+

+    print.MsaMetaData(x, show=show)

+

+    if ("alignment" %in% show)

+    {

+        cat("\n")

+        print(as(x, substr(class(x), 4, nchar(class(x)))))

+    }

 }

 setMethod("print", signature("MsaDNAMultipleAlignment"),

@@ -1,7 +1,3 @@

-setMethod("show", signature("MsaMetaData"),

-          function(object) print(object, show=c("version", "standardParams",

-                                                "algParams", "call")))

-

 setMethod("show", signature("MsaDNAMultipleAlignment"),

           function(object) print(object))

 setMethod("show", signature("MsaRNAMultipleAlignment"),

@@ -2,16 +2,15 @@

 \docType{class}

 \alias{class:MsaMetaData}

 \alias{MsaMetaData-class}

-\alias{show,MsaMetaData-method}

+\alias{MsaMetaData}

 \alias{params,MsaMetaData-method}

-\alias{print,MsaMetaData-method}

 \alias{version}

 \alias{version,MsaMetaData-method}

 \title{Class \code{MsaMetaData}}

 \description{S4 class for storing metadata about multiple sequence

   alignment results}

 \section{Objects}{

-  Objects of these classes are not be created and used directly. This

+  Objects of this virtual class are not be created and used directly. This

   is an auxiliary class used by the classes

   \code{\linkS4class{MsaAAMultipleAlignment}},

   \code{\linkS4class{MsaDNAMultipleAlignment}}, and

@@ -31,20 +30,6 @@ The following slots are defined for \code{MsaMetaData} objects:

 }

 \section{Methods}{

   \describe{

-    \item{\code{print(x, show=c("version", "standardParams",

-	"algParams", "call"))}:}{displays the object; the \code{show}

-      parameter can be used to determine which information should be

-      present in the output. If \code{show} contains \code{"version"},

-      the \code{version} slot is shown. If \code{show} contains

-      \code{"call"}, the \code{call} slot is shown.

-      If \code{show} contains \code{"standardParams"}, the

-      settings of the the parameters that are common to all three

-      multiple sequence alignment algorithms. If \code{show}

-      contains \code{"algParams"}, the

-      algorith-specific parameters are shown. 

-    }

-    \item{\code{show(object)}:}{displays the object; synonymous to

-      calling  \code{print} with default \code{show} argument}

     \item{\code{version(object)}:}{accessor to the \code{version} slot}

     \item{\code{params(x)}:}{accessor to the \code{params} slot}

   }

@@ -73,10 +58,10 @@ version(myAlignment)

 show(myAlignment)

 ## print the results

-print(myAlignment, show="version")

+print(myAlignment, show="alignment")

+print(myAlignment, show=c("alignment", "version"))

 print(myAlignment, show="standardParams")

 print(myAlignment, show="algParams")

-print(myAlignment, show="call")

 print(myAlignment, show=c("call", "version"))

 ## show the params

@@ -45,17 +45,37 @@

 }

 \section{Methods}{

   \describe{

-    \item{\code{print(x, show=c("version", "call"))}:}{displays the

-      alignment in the same way as \code{show}, but allows for

-      specifying which metadata should be displayed (determined by the

-      \code{show} argument).}

+    \item{\code{print(x, show=c("alignment", "version", "call"))}:}{

+      prints information about the object \code{x}; the \code{show}

+      argument allows for determining what should be printed.

+      The \code{show} must be a character vector and may contain any

+      combination of the following five strings:

+      if \code{show} contains \code{"alignment"}, the multiple

+      sequence alignment is printed using the corresponding method

+      from the \pkg{Biostrings} package.

+      If \code{show} contains \code{"version"},

+      the \code{version} slot is shown. If \code{show} contains

+      \code{"call"}, the \code{call} slot is shown.

+      If \code{show} contains \code{"standardParams"}, the

+      settings of the parameters that are common to all three

+      multiple sequence alignment algorithms are shown. If \code{show}

+      contains \code{"algParams"}, the

+      algorithm-specific parameters are shown. 

+      The order in which the strings are placed in the \code{show}

+      argument does not have an effect on the order in which

+      data are printed. The default is

+      \code{show=c("alignment", "version", "call")}, i.e. by default,

+      the multiple sequence alignment is shown along with version and

+      call information.

+    }

     \item{\code{show(object)}:}{displays the alignment along with

       metadata; synonymous to calling \code{print} with default

-      \code{show} argument}

+      \code{show} argument \code{c("alignment", "version", "call")}}

     \item{\code{version(object)}:}{displays the algorithm with which

       the multiple alignment has been computed along with its

-      version number.}

-    \item{\code{params(x)}:}{accessor to the \code{params} slot.}

+      version number (see also \code{\linkS4class{MsaMetaData}}).}

+    \item{\code{params(x)}:}{accessor to the \code{params} slot (see

+      also \code{\linkS4class{MsaMetaData}})}

   }

 }

 \author{Enrico Bonatesta and Christoph Horejs-Kainrath

@@ -80,10 +100,10 @@ version(myAlignment)

 show(myAlignment)

 ## print the results

-print(myAlignment, show="version")

+print(myAlignment, show="alignment")

+print(myAlignment, show=c("alignment", "version"))

 print(myAlignment, show="standardParams")

 print(myAlignment, show="algParams")

-print(myAlignment, show="call")

 print(myAlignment, show=c("call", "version"))

 ## show the params

@@ -31,11 +31,10 @@

 #include <stdlib.h>

 #include <string.h>

-#include <R.h>

-#include <Rinternals.h>

-

 #include "RClustalOmega.h"

+#include <R.h>

+#include <Rinternals.h>

 #include <Rdefines.h>

 extern "C" {

@@ -2,7 +2,6 @@

 #define _RClustalOmega_H

 #include <Rcpp.h>

-#include <R_ext/Rdynload.h>

 /*

  * note : RcppExport is an alias to `extern "C"` defined by Rcpp.

@@ -2,7 +2,6 @@

 #define RCLUSTALW_H

 #include <Rcpp.h>

-#include <R_ext/Rdynload.h>

 /*

  * note : RcppExport is an alias to `extern "C"` defined by Rcpp.

@@ -15,5 +15,5 @@ namespace clustalw {

 			~RClustalWMain();

 			void run(UserArgs args, ClustalWInput *input, ClustalWOutput *output);

 	};

-	#endif

 }

+#endif

@@ -1,8 +1,14 @@

-.PHONY: all mylibs

+OS := $(shell uname)

+ifeq ($(OS), Darwin)

+	PKG_LIBS=`Rscript -e "Rcpp:::LdFlags()"` -Wl,-all_load ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a  -Wl,-noall_load

+else 

+	PKG_LIBS=`Rscript -e "Rcpp:::LdFlags()"` -Wl,--whole-archive ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a  -Wl,--no-whole-archive

+endif

-PKG_LIBS=`Rscript -e "Rcpp:::LdFlags()"` -Wl,--whole-archive ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a  -Wl,--no-whole-archive

 PKG_CXXFLAGS=-I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" `Rscript -e "Rcpp:::CxxFlags()"`

+.PHONY: all mylibs

+

 all: $(SHLIB)

 $(SHLIB): mylibs

@@ -5,7 +5,6 @@

 #include "seqvect.h"

 #include <Rcpp.h>

-#include <R_ext/Rdynload.h>

 /*

  * note : RcppExport is an alias to `extern "C"` defined by Rcpp.

@@ -1,9 +1,10 @@

+#include "RClustalOmega.h"

+#include "RClustalW.h"

+#include "RMuscle.h"

+

 #include <R.h>

 #include <Rinternals.h>

 #include <R_ext/Rdynload.h>

-#include "RClustalW.h"

-#include "RMuscle.h"

-#include "RClustalOmega.h"

 static const R_CallMethodDef callMethods[] = {

     /* RMuscle.cpp */

@@ -8,6 +8,8 @@

     pdftitle={msa - An R Package for Multiple Sequence Alignment},

     pdfauthor={Enrico Bonatesta, Christoph Horejs-Kainrath, and Ulrich Bodenhofer}}

+\usepackage[OT1]{fontenc}

+

 \title{{\Huge msa}\\[5mm] An R Package for Multiple Sequence Alignment}

 \author{Enrico Bonatesta, Christoph Horejs-Kainrath, and Ulrich Bodenhofer}

 \affiliation{Institute of Bioinformatics, Johannes Kepler University