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 _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
