[Biojava-l] biojava and STRAP

[Dr. Christoph Gille]

Hi,

I would like to ask whether my program STRAP could benefit from
BioJava and vice versa. Is it worth to develop converters to exchange
objects like protein objects between both?

http://www.charite.de/bioinf/strap/


STRAP is a multi purpose multiple sequences alignment tool.  It
contains wrapper classes for the alignment procedures
SequenceAligner, ClustalW,Mafft5, T_Coffee, Muscle, Dialign, DialignT,
Probcons2, NeoBio, JAligner and for the 3D-superposition program CE/CL
and for transmembrane helix and secondary structure and coiled coil
prediction.

Further it has a very fast PDB and DSSP parsers (30ms per PDB-file).

There is a wrapper for Rasmol and Pymol and a specialized multi-model
3D-wire viewer.

These classes could be made available in BioJava.  I guess one has to
create classes that implement certain interfaces of BioJava.

BioJava looks very objectified. However, for performance reasons I had
to use byte arrays for sequences in STRAP.  Otherwise I tried
to follow the basic rules of modern programming.  As BioJava it
defines many interfaces. E.g. all different alignment procedures are
implementations of the interface SequenceAligner.

I would like to know what additional functionality STRAP could gain by
BioJava.

I would highly appreciate your opinion of this matter.

Many thanks

Christoph