fixing parseBoolean bug

When comparing the rules generated by my recent changes to parseBoolean with the existing iND750 rules, I found 2 bugs: Markus' code generated rules with whitespace around & and | characters, and my code's regexes were too greedy, and missed ORFs with suffixes like -A.

So, my code was generating rules like this:

'(x(96)-A&x(282))|(x(97)&x(525))|(x(97)&x(593))'


instead of like this:
'(x(97) & x(282)) | (x(97) & x(525)) | (x(97) & x(593))'

This change fixes that, changes the way the rxnGeneMat is initialized to avoid a MATLAB memory warning, and does some reformatting to the existing code to clean it up.

commit 803b7fb6bb0c45e9e65110acd03f51e839597cc9
Author: Ben Heavner <bheavner@gmail.com>
Date:   Wed Jun 19 13:21:25 2013 -0700

    fixed parseBoolean bugs and reformatted code

commit b49936ccee97c838015d64de3c9ae035ccab8c1c
Author: Ben Heavner <bheavner@gmail.com>
Date:   Wed Jun 19 12:13:48 2013 -0700

    fixed -A bug

commit 15916a97f9613db586dec9c2925906ff8b3f4b89
Author: Ben Heavner <bheavner@gmail.com>
Date:   Wed Jun 19 10:22:52 2013 -0700

    fixed the & and | whitespace problem