[Biojava-l] Creating my own classes

Nathan S. Haigh n.haigh at sheffield.ac.uk
Thu Apr 27 15:12:34 UTC 2006

I’m trying to learn/think about OO programming as I’m learning Java and port
a Perl app into Java – could you tell me if this sounds reasonable for
writing some of my own classes!?

My application essentially defines sets of positions from an alignment - I
call them CHARSETs as they are analogous to CHARSETs in the Nexus file
format. I believe in Biojava the Locations object/interface (sorry, not
familiar enough with correct terminology yet) is essentially the same sort
of thing. In my app, the user can use several approaches to define a CHARSET
e.g. a CHARSET containing just invariable sites, or a CHARSET containing
sites above a given % identity.

My question is this, if I were to create a class called Charset, and I
create several subclasses called e.g. Invariable etc is this reasonable? Or
should the class Charset contain many methods for creating a different type

In my app, a CHARSET needs to be associated with a particular alignment, and
settings used to define the CHARSET, so my Charset class have variables such
as an Alignment object, Locations objects etc. I’d like to write a method
that returns a subalignment based on the CHARSETs associated alignment
object and Locations object but I’m not sure how to do this.

Thanks for any help/comments/corrections/critiques

Dr. Nathan S. Haigh
Bioinformatics PostDoctoral Research Associate
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