Hi,
Some colleagues and I are currently developing some R packages with the
aim to integrate some existing C/C++ libraries into R. The algorithms we
are trying to integrate, not too surprisingly, expect sequences as "char
*" objects. Of course, we would like our packages to be nicely
interoperable with Biostrings. In particular, since the algorithms do
not change their input data, it would be nice to avoid copying. That is
why I tried to find out how to get pointers to the data hidden inside
XStringSet objects. As far as I understood it, an XStringSet object
consists of one large data container of class "SharedRaw_Pool" and a
"GroupedIRanges" object that defines the views on this container. I had
no problem disecting the GroupedIRanges object in my C++ code, but I
could not yet find a way to get the pointer to the container right. I
searched the web and could not find any information. Biostrings and
IRanges are indeed very well documented, but only on a user level, not
the internals. I also looked at the C code included in these two
packages, but, to be frank, I got lost. So, let me ask you the following
questions:
- Is there a way to get a plain "char *" pointer that points to the
first element of the data container?
- Are sequences actually encoded as plain text or not (it would make
sense to me to encode DNA/RNA sequences as four letters per byte)? If
not, my approach is not reasonable anyway and I will have to resort to a
conversion to character vectors anyway.
Thanks a lot in advance for your inputs!
Best regards,
Ulrich
------------------------------------------------------------------------
*Dr. Ulrich Bodenhofer*
Associate Professor
Institute of Bioinformatics
*Johannes Kepler University*
Altenberger Str. 69
4040 Linz, Austria
Tel. +43 732 2468 4526
Fax +43 732 2468 4539
bodenho...@bioinf.jku.at <mailto:bodenho...@bioinf.jku.at>
http://www.bioinf.jku.at/ <http://www.bioinf.jku.at>
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