Saturday, August 15, 2009

Hilmar's Goal Met...

...at least technically. I'll get to that in a second. Of the 432 objects in Bio++, I have the vast majority of them wrapped (I think all but 3), and 208 of them doc-tested. Hilmar asked me to have 80% of them wrapped, and 60% of those documented.

Managed to uncover some of the formats by doing some fair involved web hunts. Did Clustal and DCSE. Both of those inherit from a couple other objects, so I could do those too. Also did one of the static "Tools" objects. So yes, I met the quota without "cheating" by unit-testing ├╝bersmall Exceptions. (Found out that the Clustal format that Bio++ does is out-of-date, but these can change so fast that that's not totally unexpected. More serious is the off-by-one error that causes it to chop off the first amino acid in a protein.)

Finally figured out why I hadn't been able to post to the various Bio++ message boards, even though I've been getting all their messages. I subscribed with my gmail address, when I was trying to send with my cs.wisc.edu address. It's sorted out now. Actually, I was thinking of doing some coding for them this fall. I'll have some free time, and I think I'll be able to do more good for this project there, working on Bio++ code to make it more palatable for SWIG. At the very least, I'm hoping that I can get all the compilable code into the .cpp files, rather than the .h files. That would make a lot of things easier for SWIG.

So...I think now I've technically met the goals that Hilmar set for me to get a passing grade. However, the doctests are ugly. Basically, they show a ton of examples using the code, with barely any explanation. But I need to make sure that these documents are useful. So...this weekend I'm going to work on beautifying them, so that they might help someone actually use this tool.

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