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

 Package: msa

 Type: Package

 Title: Multiple Sequence Alignment

-Version: 1.1.1

-Date: 2015-06-12

+Version: 1.1.2

+Date: 2015-10-10

 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

@@ -17,15 +17,18 @@ URL: http://www.bioinf.jku.at/software/msa/

 License: GPL (>= 2)

 Copyright: See file inst/COPYRIGHT

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

-Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors,

-	 tools

+Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),

+        S4Vectors, tools

 Suggests: Biobase, knitr

 LinkingTo: Rcpp

 SystemRequirements:

 VignetteBuilder: knitr

 LazyLoad: yes

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

-         helperFunctions.R inputChecks.R convertRows.R msaPrettyPrint.R

-	 print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R 

-         msaClustalOmega.R

-biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison, Sequencing

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

+        helperFunctions.R inputChecks.R convertRows.R msaPrettyPrint.R

+        print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R

+        msaClustalOmega.R

+biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,

+        Sequencing

+NeedsCompilation: yes

+Packaged: 2015-10-07 16:20:45 UTC; bodenhof

@@ -110,11 +110,11 @@ msaClustalOmega <- function(inputSeqs,

     if (is.null(substitutionMatrix) ||

             identical(substitutionMatrix, "default")) {

             substitutionMatrix <- NULL

-    } else if (is.character(substitutionMatrix) &&

-                   !is.matrix(substitutionMatrix)) {

+    } else {

             possibleValues <- c("BLOSUM30", "BLOSUM40", "BLOSUM50",

                                 "BLOSUM65", "BLOSUM80", "Gonnet")

-            if (!(substitutionMatrix %in% possibleValues)){

+            if (!is.character(substitutionMatrix) ||

+                 !(substitutionMatrix %in% possibleValues)){

                 ##create a string with all possible Values named text

                 text <- ""

                 text <- paste(possibleValues, collapse=", ")

@@ -129,6 +129,8 @@ msaClustalW <- function(inputSeqs,

             ##name of a matrix that should be used

         !is.matrix(substitutionMatrix)) {

         ##check whether value is BLOSUM, PAM, GONNET, or ID;

+        if (type == "protein")

+        {

             possibleValues <- c("blosum", "pam", "gonnet", "id")

             if (!(substitutionMatrix %in% possibleValues)){

                 ##create a string with all possible Values named text

@@ -138,15 +140,69 @@ msaClustalW <- function(inputSeqs,

                      "only can have the values: \n", text)

             }

             params[["substitutionMatrixIsStringFlag"]] <- TRUE

+        }

+        else

+        {

+            possibleValues <- c("iub", "clustalw")

+            if (!(substitutionMatrix %in% possibleValues)){

+                ##create a string with all possible Values named text

+                text <- ""

+                text <- paste(possibleValues, collapse=", ")

+                stop("The parameter substitutionMatrix ",

+                     "only can have the values: \n", text)

+            }

+

+            params[["substitutionMatrixIsStringFlag"]] <- FALSE

+            params[["substitutionMatrixIsDefaultFlag"]] <- TRUE

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

+            substitutionMatrix <- "default"

+        }

     } else {

         ##real matrix

-        if (isSymmetric(substitutionMatrix)) {

-            if (nrow(substitutionMatrix) <=20 ||

-                nrow(substitutionMatrix) >26 ) {

-                    stop("substitutionMatrix has wrong dimensions!")

-            }

-        } else {

-            stop("substitutionMatrix should be a symmetric matrix!")

+        reqNames <- c("A", "R", "N", "D", "C", "Q", "E", "G", "H", "I",

+                      "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V",

+                      "B", "Z", "X", "*")

+

+        if (type == "protein")

+        {

+            rowPerm <- match(reqNames, rownames(substitutionMatrix))

+            if (any(is.na(rowPerm)))

+                stop("substitutionMatrix does not contain all necessary rows")

+

+            colPerm <- match(reqNames, colnames(substitutionMatrix))

+            if (any(is.na(colPerm)))

+                stop("substitutionMatrix does not contain all necessary columns")

+

+            substitutionMatrix <- substitutionMatrix[rowPerm, colPerm]

+

+            if (!isSymmetric(substitutionMatrix))

+                stop("substitutionMatrix should be a symmetric matrix!")

+        }

+        else

+        {

+            reqNuc <- if (type == "dna") c("A", "G", "C", "T")

+                      else c("A", "G", "C", "U")

+

+            if (any(is.na(match(reqNuc, rownames(substitutionMatrix)))))

+                    stop("substitutionMatrix does not contain all necessary rows")

+

+            if (any(is.na(match(reqNuc, colnames(substitutionMatrix)))))

+                stop("substitutionMatrix does not contain all necessary columns")

+

+            rowSel <- which(rownames(substitutionMatrix) %in% reqNames)

+            colSel <- which(colnames(substitutionMatrix) %in% reqNames)

+

+            substitutionMatrix <- substitutionMatrix[rowSel, colSel]

+

+            fakeAAmat <- matrix(0, length(reqNames), length(reqNames))

+            rownames(fakeAAmat) <- reqNames

+            colnames(fakeAAmat) <- reqNames

+            fakeAAmat[rownames(substitutionMatrix), colnames(substitutionMatrix)] <-

+                substitutionMatrix

+

+            substitutionMatrix <- fakeAAmat

+

+            params[["dnamatrix"]] <- NULL

         }

     }

@@ -148,111 +148,48 @@ msaMuscle <- function(inputSeqs,

         substitutionMatrix <- NULL;

     }

-

     ##check if substitutionMatrix is a matrix

-    if (!is.null(substitutionMatrix) & !is.matrix(substitutionMatrix)) {

+    if ((!is.null(substitutionMatrix) && !is.matrix(substitutionMatrix)) ||

+        identical(mode(substitutionMatrix), "list"))

         stop("The parameter substitutionMatrix should be a matrix!")

-    }

-

-    ## Attention, the upper check does NOT detect the

-    ## difference between matrices build as

-    ## a) y <- list()

-    ##    length(y) <- 3^2

-    ##    dim(y) <- c(3,3)

-    ## b) x <- matrix(...)

-    ##

-    ## is.matrix(x)==is.matrix(y)==TRUE !!!!

-    ## class(x)==class(y)=="matrix"

-    ## so another is necessary:

-    ## mode(x)==numeric

-    ## mode(y)==list

-

-    ##case a)

-    if (identical(mode(substitutionMatrix), "list")) {

-        ##check if there are any NA-Values

-        if (length(which(is.na(substitutionMatrix)))!=0) {

-            stop("The parameter substitutionMatrix is not valid. \n",

-                 "There are NA-values in the substitutionMatrix! ")

-        }

-

-        ##check if there are any NaN-Values

-        if (length(which(is.element(substitutionMatrix, NaN)))!=0) {

-            stop("The parameter substitutionMatrix is not valid. \n",

-                 "There are NaN-values in the substitutionMatrix! ")

-        }

-

-        ##check if there are any Inf-Values

-        if (length(which(is.element(substitutionMatrix, Inf)))!=0) {

-            stop("The parameter substitutionMatrix is not valid.\n",

-                 "There are Inf-values in the substitutionMatrix! ")

-        }

-

-        ##check if there are any NULL-Values

-        if (length(which(unlist(lapply(substitutionMatrix,is.null))))!=0) {

-            stop("The parameter substitutionMatrix is not valid. \n",

-                 "There are NULL-values in the substitutionMatrix! ")

-        }

-

-

-        ##after having checked all,

-        ##create a real matrix of type b)

-        ##nasty, but should work

+    if (!is.null(substitutionMatrix))

+    {

+        headerNames <- c("A", "C", "D", "E", "F",

+                         "G", "H", "I", "K", "L",

+                         "M", "N", "P", "Q", "R",

+                         "S", "T",  "V","W", "Y")

+

+        if (type == "protein")

+            reqNames <- headerNames

+        else if (type == "dna")

+            reqNames <- c("A", "C", "G", "T")

+        else

+            reqNames <- c("A", "C", "G", "U")

-        ##mode(substitutionMatrix)=list()

-        helpMatrix = matrix(nrow=nrow(substitutionMatrix),

-                            ncol=ncol(substitutionMatrix))

-        colnames(helpMatrix)=colnames(substitutionMatrix)

-        rownames(helpMatrix)=rownames(substitutionMatrix)

-        for (i in 1:length(t(sapply(substitutionMatrix, unlist)))) {

-            helpMatrix[i]=  unlist(t(sapply(substitutionMatrix, unlist))[i])

-        }

-        substitutionMatrix = helpMatrix

-        ##mode(substitutionMatrix)=numeric =>now: case b)

-    }

+        rowPerm <- match(reqNames, rownames(substitutionMatrix))

+        if (any(is.na(rowPerm)))

+            stop("substitutionMatrix does not contain all necessary rows")

+        colPerm <- match(reqNames, colnames(substitutionMatrix))

+        if (any(is.na(colPerm)))

+            stop("substitutionMatrix does not contain all necessary columns")

-    ## case b)

-    if(!is.null(substitutionMatrix)){

-    ##check, if matrix is symmetric

-    if (isSymmetric(substitutionMatrix)) {

-        ##check dimensions according to NCBI-BLAST

-        if (nrow(substitutionMatrix) !=24) {

-            stop("The parameter substitutionMatrix has wrong dimensions! \n",

-                 "Should be a 24x24 matrix!" )

-        }

-        ##check order according to NCBI-BLAST

-        if (!(identical(toString(tolower(rownames(substitutionMatrix))),

-    "a, r, n, d, c, q, e, g, h, i, l, k, m, f, p, s, t, w, y, v, b, z, x, *"))){

-                stop("The parameter substitutionMatrix has wrong ",

-                     "order or no names! \n",

-                     "Should be in order <abcdefghiklmnpqrstvwxyz>!")

-        }

-        ##check if there are any NA-Values

-        if (length(which(is.na(substitutionMatrix)))!=0) {

-            stop("The parameter substitutionMatrix is not valid. \n",

-                 "There are NA-values in the substitutionMatrix!")

-        }

+        substitutionMatrix <- substitutionMatrix[rowPerm, colPerm]

-        ##check if there are any NaN-Values

-        if (length(which(is.nan(substitutionMatrix)))!=0) {

-            stop("The parameter substitutionMatrix is not valid. \n",

-                 "There are NaN-values in the substitutionMatrix! ")

-        }

+        auxMat <- matrix(0, length(headerNames), length(headerNames))

+        rownames(auxMat) <- headerNames

+        colnames(auxMat) <- headerNames

+        auxMat[reqNames, reqNames] <- substitutionMatrix

+        substitutionMatrix <- auxMat

-        ##check if there are any Inf-Values

-        if (length(which(is.element(substitutionMatrix, Inf)))!=0) {

-            stop("The parameter substitutionMatrix is not valid. \n",

-                 "There are Inf-values in the substitutionMatrix! ")

-        }

+        if (!isSymmetric(substitutionMatrix))

+            stop("substitutionMatrix should be a symmetric matrix!")

-        ##check if there are any NULL-Values:

-        ##by definition not allowed and not possible!

-        ##You can't assign NULL-values to Matrices as well as to Vectors!

-    } else {

-        stop("The parameter substitutionMatrix should be symmetric!")

-    }

-    }

+        if (any(is.na(substitutionMatrix)) || any(is.na(substitutionMatrix)) ||

+            any(is.infinite(substitutionMatrix)))

+            stop("substitutionMatrix contains invalid values!")

+     }

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

     # gapOpening #

@@ -57,24 +57,24 @@ msaPrettyPrint <- function(x, y, output=c("pdf", "tex", "dvi", "asis"),

         stop("The parameter alFile has an invalid argument!")

     if (!is(x, "MultipleAlignment"))

-        stop("The parameter x has an invalid argument! \n", 

+        stop("The parameter x has an invalid argument! \n",

              "x must be a multiple alignment object!")

-    

+

     if (output != "asis")

     {

         if (!is.numeric(paperWidth) || length(paperWidth) != 1 ||

             paperWidth <= 0)

-            stop("The parameter paperWidth must be ", 

+            stop("The parameter paperWidth must be ",

                  "single positive number (unit: inches)!")

         if (!is.numeric(paperHeight) || length(paperHeight) != 1 ||

             paperHeight <= 0)

-            stop("The parameter paperHeight must be ", 

+            stop("The parameter paperHeight must be ",

                  "single positive number (unit: inches)!")

         if (!is.numeric(margins) || length(margins) != 2)

-            stop("The parameter margins must be ", 

+            stop("The parameter margins must be ",

                  "two positive numbers (unit: inches)!")

     }

@@ -85,14 +85,14 @@ msaPrettyPrint <- function(x, y, output=c("pdf", "tex", "dvi", "asis"),

             if (max(subset) < .Machine$integer.max)

                 subset <- as.integer(subset)

             else

-               stop("One or more values for parameter subset ", 

+               stop("One or more values for parameter subset ",

                     "are larger than integer!")

         }

         else if (!is.integer(subset))

             stop("The parameter subset has an invalid argument!")

         if (length(subset) < 2)

-            stop("The parameter subset is expected to be \n", 

+            stop("The parameter subset is expected to be \n",

                  " a vector with at least 2 entries!")

         if (!all(subset %in% 1:nrow(x)))

@@ -122,7 +122,7 @@ msaPrettyPrint <- function(x, y, output=c("pdf", "tex", "dvi", "asis"),

     if (!is.numeric(consensusThreshold) || length(consensusThreshold) != 1 ||

         consensusThreshold < 0 || consensusThreshold > 100)

-        stop("The parameter consensusThreshold must be \n", 

+        stop("The parameter consensusThreshold must be \n",

              "a single numeric between 0 and 100 !")

     if (shadingMode %in% c("identical", "similar"))

@@ -151,9 +151,9 @@ msaPrettyPrint <- function(x, y, output=c("pdf", "tex", "dvi", "asis"),

                                          "accessible area"))

         else

             stop("Missing shadingModeArg for functional shading mode. \n",

-                 "Valid values are: \n", 

-                 "\"charge\", \n", 

-                 "\"hydropathy\", \n", 

+                 "Valid values are: \n",

+                 "\"charge\", \n",

+                 "\"hydropathy\", \n",

                  "\"structure\", \n",

                  "\"chemical\",\n",

                  " \"rasmol\",\n",

@@ -203,7 +203,7 @@ msaPrettyPrint <- function(x, y, output=c("pdf", "tex", "dvi", "asis"),

     if (output != "asis")

     {

         if (!is.character(file) || length(file) > 1)

-            stop("The argument for parameter file must be \n", 

+            stop("The argument for parameter file must be \n",

                  "a single character string!")

         if (substr(file, nchar(file) - 2, nchar(file)) != output)

@@ -241,6 +241,11 @@ msaPrettyPrint <- function(x, y, output=c("pdf", "tex", "dvi", "asis"),

     texOutput <- paste0("\\begin{texshade}{", stratifyFilenames(alFile), "}")

+    if (is(x, "AAMultipleAlignment"))

+        texOutput <- c(texOutput, "\\seqtype{P}")

+    else

+        texOutput <- c(texOutput, "\\seqtype{N}")

+

     if (length(toShow) == 1)

     {

         if (sum(width(toShow)) < ncol(x))

@@ -45,21 +45,191 @@ print.MsaMetaData <- function(x, show)

     }

 }

+print.MsaMultipleAlignmentChunk <- function(str, names=NULL, halfNrow=9, pos="",

+                                            addOne=FALSE)

+{

+    lx <- length(str)

+    iW <- nchar(as.character(lx - if (addOne) 1 else 0)) + 2

+

+    cat(format("", width=iW), sep = "")

+

+    if (length(names) > 0)

+        cat(format(paste(" aln", pos), width=nchar(str)[1]), " names\n")

+    else

+        cat(paste(" aln", pos), "\n", sep="")

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

-                                                 "call"))

+    if (addOne)

+        str <- paste0(format(c(paste("[", 1:(lx - 1), "]", sep=""), "Con"),

+                             width=iW, justify="right"), " ",

+                      str, if (is.null(names)) "" else paste0(" ", names))

+    else

+        str <- paste0(format(paste("[", 1:lx, "]", sep=""), width=iW,

+                             justify="right"), " ",

+                      str, if (is.null(names)) "" else paste0(" ", names))

+

+    if (lx <= 2 * halfNrow + 1)

+        cat(paste(str, collapse="\n"), "\n")

+    else

+    {

+        cat(paste(str[1:halfNrow], collapse="\n"), "\n")

+        cat(format("...", width = iW, justify = "right"), "...\n")

+        cat(paste(str[(lx - halfNrow + 1):lx], collapse="\n"), "\n")

+    }

+}

+

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

+                                       showNames=TRUE, showConsensus=TRUE,

+                                       halfNrow=9, nameWidth=20)

 {

     show <- match.arg(show,

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

-                                "standardParams", "algParams"),

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

+                                "standardParams", "algParams", "all"),

                       several.ok=TRUE)

+    if ("all" %in% show)

+        show <- c("complete", "version", "call", "standardParams", "algParams")

+

     print.MsaMetaData(x, show=show)

-    if ("alignment" %in% show)

+    if (any(c("alignment", "complete") %in% show))

     {

-        cat("\n")

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

+        nr <- nrow(x)

+        nc <- ncol(x)

+

+        if (identical(halfNrow, NA) || identical(halfNrow, -1))

+            halfNrow <- nr

+

+        if (!is.numeric(halfNrow) || length(halfNrow) != 1 ||

+             round(halfNrow) != halfNrow || halfNrow < 1)

+            stop("halfNrow must be a single whole number or NA")

+

+        if (!is.numeric(nameWidth) || length(nameWidth) != 1 ||

+             round(nameWidth) != nameWidth || nameWidth < 5)

+            stop("nameWidth must be a single whole number at least as large as 5")

+

+        if (nameWidth > getOption("width") - 20)

+        {

+            nameWidth <- getOption("width") - 20

+            warning("nameWidth must be at least width - 20")

+        }

+

+        cat("\n", class(x), " with ", nr,

+            ifelse(nr == 1, " row and ", " rows and "),

+            nc, ifelse(nc == 1, " column\n", " columns\n"), sep = "")

+

+        if (nr > 0)

+        {

+            strings <- unmasked(x)

+            mdim <- maskeddim(x)

+

+            if (sum(mdim) > 0)

+            {

+                if (mdim[1] > 0)

+                {

+                    strings <- BStringSet(strings)

+

+                    maskStrings <- rep(BStringSet(paste(rep.int("#", nc),

+                                                        collapse = "")),

+                                       mdim[1])

+

+                    i <- as.integer(rowmask(x))

+

+                    if (!is.null(rownames(x)))

+                        names(maskStrings) <- rownames(x)[i]

+                    strings[i] <- maskStrings

+                }

+

+                if (mdim[2] > 0)

+                {

+                    strings <- as.matrix(strings)

+                    strings[, as.integer(colmask(x))] <- "#"

+                    strings <- BStringSet(apply(strings, 1, paste,

+                                                collapse = ""))

+                }

+            }

+

+            strings <- as.character(strings)

+

+            iw <- nchar(as.character(length(strings))) + 2

+

+            if (showConsensus)

+            {

+                cons <- consensusString(consensusMatrix(unmasked(x)))

+                strings <- c(strings, cons)

+

+                if (length(names(strings)) > 0)

+                    names(strings)[length(strings)] <- "Consensus"

+

+                addOne <- TRUE

+            }

+            else

+                addOne <- FALSE

+

+            names <- names(strings)

+

+            if (showNames && length(names) > 0)

+            {

+                names <- names(strings)

+

+                names <- ifelse(nchar(names) <= nameWidth,

+                                names,

+                                paste0(substr(names, 1, nameWidth - 3), "..."))

+

+                chunkSize <- getOption("width") - iw - nameWidth - 3

+            }

+            else

+            {

+                names <- NULL

+                chunkSize <- getOption("width") - iw - 2

+            }

+

+            seqLen <- nchar(strings)[1]

+

+            if (seqLen < 7)

+                strings <- format(strings, width=7, justify="left")

+

+            if (nchar(strings)[1] <= chunkSize)

+                print.MsaMultipleAlignmentChunk(strings, names, halfNrow=halfNrow,

+                                                addOne=addOne)

+            else if ("complete" %in% show)

+            {

+                starts <- seq(from=1, to=seqLen, by=chunkSize)

+                stops <- pmin(starts + chunkSize - 1, seqLen)

+

+                n <- length(starts)

+

+                for (i in 1:n)

+                {

+                    aln <- substr(strings, starts[i], stops[i])

+

+                    pos <- paste0("(", starts[i], "..", stops[i], ")")

+

+                    if (nchar(pos) + 4 > chunkSize)

+                        pos <- paste0(substr(pos, 1, chunkSize - 7), "...")

+

+                    if (nchar(aln)[1] < nchar(pos) + 4)

+                        aln <- format(aln, width=nchar(pos) + 4, justify="left")

+

+                    print.MsaMultipleAlignmentChunk(aln, names, halfNrow=halfNrow,

+                                                    pos=pos, addOne=addOne)

+

+                    if (i < n)

+                        cat("\n")

+                }

+            }

+           else

+            {

+                w1 <- (chunkSize - 2) %/% 2

+                w2 <- (chunkSize - 3) %/% 2

+

+                strings <- paste0(substr(strings, start=1, stop=w1),

+                                  "...",

+                                  substr(strings, start=seqLen - w2 + 1, stop=seqLen))

+

+                print.MsaMultipleAlignmentChunk(strings, names, halfNrow=halfNrow,

+                                                addOne=addOne)

+            }

+        }

     }

 }

@@ -1,27 +1,21 @@

 ##345678901234567890123456789012345678901234567890123456789012345678901234567890

 citHeader("To cite package 'msa' in publications use:")

-#year <- sub(".*(2[[:digit:]]{3})-.*", "\\1", meta$Date, perl = TRUE) 

-#vers <- paste("R package version", meta$Version)

-desc <- packageDescription("msa")

-year <- sub(".*(2[[:digit:]]{3})-.*", "\\1", desc$Date)

-vers <- paste("R package version", desc$Version)

-url  <- desc$URL

-

-

-citEntry(entry="Manual", 

-         title = "msa -- An R Package for Multiple Sequence Alignment.", 

-         author = personList(as.person("Enrico Bonatesta"), as.person("Christoph Horejs-Kainrath"), as.person("Ulrich Bodenhofer")),

-         year = year, 

-         note = vers,

-         organization=paste("Institute of Bioinformatics",

-                            "Johannes Kepler University", sep=", "),

-         address="Linz, Austria",

-         url=url,

-         textVersion = 

-             paste("Enrico Bonatesta, Christoph Horejs-Kainrath and Ulrich Bodenhofer (", year, "). ",

-                   "msa -- An R Package for Multiple Sequence Alignment. ",

-                   vers, ".", sep="")

+citEntry(entry="Article",

+         title = "msa: an R package for multiple sequence alignment",

+         author = personList(as.person("Ulrich Bodenhofer"),

+                             as.person("Enrico Bonatesta"),

+                             as.person("Christoph Horejs-Kainrath"),

+                             as.person("Sepp Hochreiter")),

+         journal="Bioinformatics",

+         note="(accepted)",

+         year="2015",

+         doi="10.1093/bioinformatics/btv494",

+         textVersion =

+             paste("U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter (2015)",

+                   "msa: an R package for multiple sequence alignment.",

+                   "Bioinformatics (accepted).",

+                   "DOI: 10.1093/bioinformatics/btv176.")

 )

 citFooter(

@@ -1,6 +1,23 @@

 Change history of package msa:

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

+Version 1.2.0:

+- new branch for Bioconductor 3.2 release

+

+Version 1.1.2:

+- new print() function for multiple alignments that also

+  allows for displaying alignments in their entirety (plus additional

+  customizations)

+- strongly improved handling of custom substitution matrices by

+  msaClustalW(): now custom matrices can also be supplied for nucleotide

+  sequences which can also be passed via the 'substitutionMatrix' argument.

+  The 'dnamatrix' argument is still available for the sake of backwards

+  compatibility.

+- strongly improved handling of custom substitution matrices by

+  msaMuscle()

+- fix of improperly aligned sequence logos produced by msaPrettyPrint()

+- updated citation information

+

 Version 1.1.1:

 - fix of msa() function

@@ -37,6 +37,14 @@ The following slots are defined for \code{MsaMetaData} objects:

 \author{Enrico Bonatesta and Christoph Horejs-Kainrath

   <msa@bioinf.jku.at>

 }

+\references{

+  \url{http://www.bioinf.jku.at/software/msa}

+  

+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

+  (2015). msa: an R package for multiple sequence alignment. 

+  \emph{Bioinformatics} (accepted). DOI:

+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

+}

 \seealso{\code{\link{msa}}, \code{\link{msaClustalW}},

   \code{\link{msaClustalOmega}}, \code{\link{msaMuscle}},

   \code{\linkS4class{MsaAAMultipleAlignment}},

@@ -45,14 +45,20 @@

 }

 \section{Methods}{

   \describe{

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

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

+      showNames=TRUE, showConsensus=TRUE, halfNrow=9, nameWidth=20)}:}{

       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:

+      combination of the following strings:

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

-      sequence alignment is printed using the corresponding method

-      from the \pkg{Biostrings} package.

+      sequence alignment is printed in a way similar to the

+      corresponding method from the \pkg{Biostrings} package

+      (except for the consensus sequence, see below).

+      If \code{show} contains \code{"complete"}, the entire width of

+      the alignment is printed by splitting it over multiple blocks of

+      lines if necessary. This overrules \code{"alignment"} if both

+      are contained in the \code{show} argument.

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

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

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

@@ -66,11 +72,33 @@

       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.

+      call information. If \code{show} contains \code{"all"}, the

+      complete alignment is shown along with version information,

+      call, and the complete set of parameters.

+      As said above, by default, printing alignments is similar to

+      the standard \code{print} method provided by the \pkg{Biostrings}

+      package, whereas including \code{"complete"} in the argument

+      \code{show} prints the entire width of the alignment.

+      Unlike the method from the \pkg{Biostrings}

+      package, the appearance can be customized: by default,

+      the consensus sequence is appended below the alignment. To switch

+      this off, use \code{showConsensus=FALSE}. Whether or not sequence

+      names should be printed can be controlled via the

+      \code{showNames} argument. The width reserved for the sequence

+      names can be adjusted using the \code{nameWidth} argument;

+      the default is 20 like in the \pkg{Biostrings} method.

+      If the number of sequences in the alignment is large, output

+      can become quite lengthy. That is why only the first

+      \code{halfNrow} and the last \code{halfNrow} sequences are

+      shown. To show all sequences, set \code{halfNrow} to \code{NA}

+      or -1. Note that \code{print} can also handle masked objects,

+      where the masked sequences/positions are shown as hash marks.

+      However, the consensus sequences are computed from the

+      complete, unmasked alignment and displayed as such.

     }

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

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

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

+      arguments.}

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

       the multiple alignment has been computed along with its

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

@@ -78,8 +106,16 @@

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

   }

 }

-\author{Enrico Bonatesta and Christoph Horejs-Kainrath

-  <msa@bioinf.jku.at>

+\author{Enrico Bonatesta, Christoph Horejs-Kainrath, and

+  Ulrich Bodenhofer <msa@bioinf.jku.at>

+}

+\references{

+  \url{http://www.bioinf.jku.at/software/msa}

+  

+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

+  (2015). msa: an R package for multiple sequence alignment. 

+  \emph{Bioinformatics} (accepted). DOI:

+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

 }

 \seealso{\code{\link{msa}}, \code{\link{msaClustalW}},

   \code{\link{msaClustalOmega}}, \code{\link{msaMuscle}},

@@ -101,6 +137,8 @@ show(myAlignment)

 ## print the results

 print(myAlignment, show="alignment")

+print(myAlignment, show="alignment", showConsensus=FALSE)

+print(myAlignment, show="complete")

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

 print(myAlignment, show="standardParams")

 print(myAlignment, show="algParams")

@@ -17,8 +17,8 @@

   \tabular{ll}{

     Package: \tab msa\cr

     Type: \tab Package\cr

-    Version: \tab 0.99.1\cr

-    Date: \tab 2015-03-29\cr

+    Version: \tab 1.1.2\cr

+    Date: \tab 2015-09-29\cr

     License: \tab GPL-2\cr

   }

 }

@@ -27,6 +27,11 @@

 }

 \references{

   \url{http://www.bioinf.jku.at/software/msa}

+  

+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

+  (2015). msa: an R package for multiple sequence alignment. 

+  \emph{Bioinformatics} (accepted). DOI:

+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

   Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994)

   CLUSTAL W: improving the sensitivity of progressive multiple sequence

@@ -132,6 +132,11 @@

 \references{

   \url{http://www.bioinf.jku.at/software/msa}

+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

+  (2015). msa: an R package for multiple sequence alignment. 

+  \emph{Bioinformatics} (accepted). DOI:

+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

+ 

   \url{http://www.clustal.org/download/clustalw_help.txt}

   \url{http://www.clustal.org/omega/README}

@@ -27,12 +27,11 @@

   \item{maxiters}{maximum number of iterations; the default value is 0

     (no limitation). In the original ClustalOmega implementation, this

     parameter is called \code{iterations}.}

-  \item{substitutionMatrix}{substitution matrix for scoring matches and

-    mismatches; can be a real matrix, a file name, or the name of a

-    built-in substitution matrix. In the latter case, the choices

+  \item{substitutionMatrix}{name of substitution matrix for scoring matches and

+    mismatches; can be one of the choices

     \code{"BLOSUM30"}, \code{"BLOSUM40"}, \code{"BLOSUM50"},

-    \code{"BLOSUM65"}, \code{"BLOSUM80"}, and \code{"Gonnet"} are

-    supported.  This parameter is a new feature - the original ClustalOmega

+    \code{"BLOSUM65"}, \code{"BLOSUM80"}, and \code{"Gonnet"}.

+    This parameter is a new feature - the original ClustalOmega

     implementation does not allow for using a custom substitution matrix.}

   \item{type}{type of the input sequences \code{inputSeqs};

     see \code{\link{msa}}.}

@@ -59,6 +58,10 @@

   specific to ClustalOmega can be passed to ClustalOmega via additional

   arguments (see argument \code{help} above).

+  Since ClustalOmega only allows for using built-in amino acid

+  substitution matrices, it is hardly useful for multiple alignments

+  of nucleotide sequences.

+

   For a note on the order of output sequences and direct reading from

   FASTA files, see \code{\link{msa}}.

 }

@@ -76,6 +79,11 @@

 }

 \references{

   \url{http://www.bioinf.jku.at/software/msa}

+  

+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

+  (2015). msa: an R package for multiple sequence alignment. 

+  \emph{Bioinformatics} (accepted). DOI:

+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

   \url{http://www.clustal.org/omega/README}

@@ -34,7 +34,9 @@

     built-in substitution matrix. In the latter case, the choices

     \code{"blosum"}, \code{"pam"}, \code{"gonnet"}, and \code{"id"} are

     supported for amino acid sequences. For aligning nucleotide

-    sequences, the parameter \code{dnamatrix} must be used instead.

+    sequences, the choices \code{"iub"} and \code{"clustalw"} are

+    possible. The parameter \code{dnamatrix} can also be used instead

+    for the sake of backwards compatibility.

     The valid choices for this parameter are \code{"iub"} and

     \code{"clustalw"}. In the original ClustalW implementation, this

     parameter is called \code{matrix}.}

@@ -79,7 +81,12 @@

 }

 \references{

   \url{http://www.bioinf.jku.at/software/msa}

-  

+   

+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

+  (2015). msa: an R package for multiple sequence alignment. 

+  \emph{Bioinformatics} (accepted). DOI:

+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

+ 

   \url{http://www.clustal.org/download/clustalw_help.txt}

   Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994)

@@ -85,6 +85,11 @@

 }

 \references{

   \url{http://www.bioinf.jku.at/software/msa}

+  

+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

+  (2015). msa: an R package for multiple sequence alignment. 

+  \emph{Bioinformatics} (accepted). DOI:

+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

   \url{http://www.drive5.com/muscle/muscle.html}

@@ -188,9 +188,14 @@

   <msa@bioinf.jku.at>

 }

 \references{

-\url{http://www.bioinf.jku.at/software/msa}

+  \url{http://www.bioinf.jku.at/software/msa}

+  

+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

+  (2015). msa: an R package for multiple sequence alignment. 

+  \emph{Bioinformatics} (accepted). DOI:

+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

-\url{https://www.ctan.org/pkg/texshade}