@@ -1,12 +1,12 @@

 Package: msa

 Type: Package

 Title: Multiple Sequence Alignment

-Version: 1.3.5

-Date: 2016-04-07

+Version: 1.3.6

+Date: 2016-04-18

 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,

+Description: The 'msa' 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

@@ -60,7 +60,6 @@ msaPrettyPrint <- function(x, y, output=c("pdf", "tex", "dvi", "asis"),

         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 ||

@@ -211,7 +210,7 @@ msaPrettyPrint <- function(x, y, output=c("pdf", "tex", "dvi", "asis"),

         jobname <- substr(file, 1, nchar(file) - 4)

-        if (length(grep("[^\\w/\\\\:.]", jobname, perl=TRUE)) > 0)

+        if (length(grep("[^\\w-/\\\\:.]", jobname, perl=TRUE)) > 0)

         {

             warning("Cannot use file name '", file,

                     "' because it contains invalid characters => \n",

@@ -1,6 +1,11 @@

 Change history of package msa:

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

+Version 1.3.6:

+- msaPrettyPrint() now also accepts dashes in file names

+- added section about pretty-printing wide alignments to package

+  vignette

+

 Version 1.3.5:

 - adaptation of displaying help text by msa() function 

new file mode 100644

Binary files /dev/null and b/vignettes/JKU_EN_noName.pdf differ

@@ -143,6 +143,7 @@ Institute of Bioinformatics\\

 Johannes Kepler University Linz\\

 A-4040 Linz, Austria

 \end{tabular}}}

+\put(9.5,0.4){\makebox(0,0)[cb]{\includegraphics[height=0.8cm]{JKU_EN_noName}}}

 \put(19,0){\makebox(0,0)[rb]{\fontfamily{phv}\normalsize\begin{tabular}[b]{r}

 Tel. +43 732 2468 4520\\

 Fax +43 732 2468 4539\\

@@ -684,6 +684,41 @@ is to check sequence names carefully and to avoid problematic sequence names fro

 Note, moreover, that too long sequence names will lead to less appealing outputs,

 so users are generally advised to consider sequence names carefully.

+\subsection{Pretty-Printing Wide Alignments}

+

+If the alignment to be printed with \verb+msaPrettyPrint()+ is wide

+(thousands of columns or wider), \LaTeX\ may terminate prematurely because of

+exceeded \TeX\ capacity. Unfortunately, this problem remains opaque to the

+user, since \verb+texi2dvi()+ and \verb+texi2pdf()+ do not convey much details

+about \LaTeX\ problems when typesetting a document. We recommend the following

+if a user encounters problems with running \verb+msaPrettyPrint()+'s output

+with \verb+texi2dvi()+ and \verb+texi2pdf()+:

+\begin{enumerate}

+\item Run \verb+pdflatex+ on the generated \verb+.tex+ file to see

+  whether it is actually a problem with \TeX\ capacity.

+\item If so, split the alignment into multiple chunks and run

+  \verb+msaPrettyPrint()+ on each chunk separately.

+\end{enumerate}

+

+The following example

+demonstrates this approach for a multiple aligment object `\verb+aln+':

+<<SplitAlignmentIntoJunks,eval=FALSE>>=

+chunkSize <- 300 ## how much fits on one page depends on the length of

+                 ## names and the number of sequences;

+                 ## change to what suits your needs

+

+for (start in seq(1, ncol(aln), by=chunkSize))

+{

+    end <- min(start + chunkSize - 1, ncol(aln))

+    alnPart <- DNAMultipleAlignment(subseq(unmasked(aln), start, end))

+

+    msaPrettyPrint(x=alnPart, output="pdf", subset=NULL,

+                   file=paste0("aln_", start, "-", end, ".pdf"))

+}

+@

+\noindent This creates multiple PDF files all of which show one part of the alignment.

+Please note, however, that the numbering of columns is restarted for each chunk.

+

 \subsection{Further Caveats}

 \begin{itemize}

@@ -782,6 +817,10 @@ bibliography below).

 \section{Change Log}

 \begin{description}

+\item[Version 1.3.6:] \mbox{ }  \begin{itemize}

+   \item \verb+msaPrettyPrint()+ now also accepts dashes in file names

+   \item added section about pretty-printing wide alignments to package vignette

+  \end{itemize}

 \item[Version 1.3.5:] \mbox{ }  \begin{itemize}

    \item adaptation of displaying help text by \verb+msa()+ function

   \end{itemize}