Wednesday, August 12, 2009

Only 160

Six objects today. Not a good day.

Spent a couple of hours hacking around with VectorTools. This ended up not being a good idea. Well...yeah, I got a lot of it tested. And it is an important class. But it turns out that sections of the thing give SWIG indigestion when it tries to compile the wrapper files. This seems to be a really solid reason to put your code in the .cpp files, not the .h files. If these bits of code were already compiled, tucked away in their object files, I wouldn't be having these problems. Instead, it's in the header, where it gets entangled with SWIG, and SWIG starts having problems with certain templates.

And then I spent a fair amount of time today working with VectorSiteContainer. The main constructor to that requires a vector as one of its arguments. I tried for a very long time to get SWIG to wrap such an object, with no luck. The closest I could get was a vector, which isn't good enough. Every time I tried to add that "const" in there, the SWIG-generated wrapper file wouldn't compile. Finally, very late at night, I threw a request for help to the swig mailing list (and also CC'ed to the phyloinformatics people), but I don't expect a response soon.

Update--message came in, as I was writing that last paragraph. It turns out that this is a known bug in SWIG. Which means that it's not going to be fixed this week, which means that there are 27 classes in seq that I won't be able to test.  So...I'm going to have to move on to phyl and popgen.

On other piece of info, though. According to Bio++ docs, there are 432 objects. Multiplying this by 0.48 yields a little less than 208, so that's my goal. That means that I now have 48 to go.

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