Spent some amount of time this evening working with Pjotr, trying to get my cmake files up to standards. A lot of this involved git--git still frustrates me, but I do learn.
Also worked with wrapping files in Java. I'm unsure if Java will really work. As near as I can tell, SWIG's performance in Java is quite different from the way it does scripting languages. And one of the things that's causing a lot of problems is multiple inheritence. SWIG starts screaming bloody murder whenever I try to wrap some object that inherits from multiple other objects. It works by just not inheriting from more than one parent object--other parents are just ignored. Multiple inheritence is used a lot in Bio++. Hence, the Java environment will be lacking several methods, and also not able to perform some basic assignment operations. Is it even worth having it available in Java, if the library will be severely crippled?
I think tomorrow I'm going to try Perl. Hopefully, that'll be highly similar to the Python I've already done.
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