[jgap-users] Planning a chromosome and other questions

[Ryan R. V. <rv...@gm...>]

Hello.  I'm new to JGAP... it looks great so far.  I especially
appreciate the documentation.  The code is very well documented;
however, there are some cases where I could use a bit of a higher
level picture.

For example: mutation.  As I plan my chromosome, I'm not sure if I
should piggyback on the IntegerGene class or define my own.  The
problem is that I'm not really sure how values are represented
internally, or how they are mutated.

I'm trying to represent a machine with physical connections.  Hence I
plan to allocate one gene for each potential connection.  The gene
should indicate what type of connection, if any, is present (the
"type") and how it is configured (the "value").  I used to maintain a
simple GA in Perl that encoded these two featuers into one gene;
however, I think I want to get away from that.  It really seems that
these should be distinct genes, perhaps united as a supergene.  Does
this sound right?

Anyway, that's the motivation for my question.  I see from the
MinimizeMakeChange example that each coin is really just an
IntegerGene who's "meaning" is imposed in the fitness function, based
on the position of the gene.  Hence the gene itself is a kind of black
box to me.

For my chromosome, the gene index already maps to the the index of the
physical connection, so I still have type and configuration to
represent.  If I had to guess, I would say that I should devote two
IntegerGenes to each position.  The first has an integer range from
0-(num_types), where 0 represents a "repressed" or "dormant" gene.
The second is an integer, probably limited to 0-1000 that means
different things depending on the type.

Am I on the right track here?  Is it clear what I am trying to do?
I'd like to sanity check my notes before I spend too much time on
something silly.  Because I don't have a clear understanding of the
internal representation of values, and how mutation effects these
values, I'm not entirely confident in my approach.  Any help would be
appreciated.

Thanks again for a great project.

Ryan