The C++/Bio++ remote acnuc access API

The C++ remote acnuc access API is conceived as a part of the Bio++ libraries. It is scheduled to be included in version 2.0 of Bio++. Pending this release, the Bio++/acnuc interface is available here as an add-on to the current Bio++ library.

Installation.
You should first install the Bio++ libraries if they are not already on your computer.
Then, download file Raa.tgz, and expand it.
In the Makefile therein, edit the line
BPPINCLUDE = ...
to reflect the path to the include directory of the Bio++ libraries on your computer.
Run make. This will build file libbpp-raa.a.

Usage.
The bpp-raa library is used adding
#include "RAA.h"
to your source files, and linking them with libbpp-raa.a (from the Raa directory), libbpp-seq.a, libbpp-utils.a, and libbpp-numcalc.a (from the lib directory of the Bio++ libraries), and with the libz library (add -lz to your link command). Under SunOS, you'll also have to add -lnsl -lsocket to your link command. Bpp-raa defined classes are part of the bpp namespace.

Bpp-raa API.
The Bio++ API for remote acnuc access is performed through five classes. These classes allow:

to open one or several sequence databases (e.g., embl, genbank, swissprot/uniprot),
to extract sequences identified by accession number or name in the form of Bio++ objects (e.g., instances of the Sequence class),
to query the database using the ACNUC query language shared by all ACNUC software and obtain the list of matching sequences,
to translate coding nucleotide sequences to proteins using their database-assigned genetic code and reading frame,
to browse upwards and downwards the biological classification of species and taxa,
to browse the list of database keywords.

All of this requires an internet connection and that the port 5558 is not closed by a firewall. To check whether outbound connection through this port works on your computer, type:
telnet pbil.univ-lyon1.fr 5558
in a terminal. You should obtain this reply:

Trying 134.214.32.76...
Connected to pbil.univ-lyon1.fr.
Escape character is '^]'.
OK acnuc socket started

If nothing happens for a long time, then check your computer's firewall and/or ask your local network manager.

Example.

#include "RAA.h"

using namespace std;
using namespace bpp;

int main(int argc, char **argv)
{
	RAA *myraa = new RAA("embl");
	Sequence *seq = myraa->getSeq("AL391737");
	RaaList *mylist = myraa->processQuery("au=galtier", "galtier");
	myraa->deleteList(mylist);
	delete myraa;
}