Analysis saving is smelly

[diane]

Analysis saving uses system calls to make a directory and splatter a bunch of files in it. This makes loading an analysis a bit odd as you need to load a directory, and you get a bunch of errors on standard out.

It'd be nice if everything was saved into a single file? or at least used a more multiplatform way for creating directories.

[diane]

Loading is pretty bad too. I have no idea why Mussa keeps track of the information needed to load a sequence in several parallel arrays, instead of just loading the sequence when presented with enough information?

[diane]

Ok I started writing something using the boost serialization library. But then realized that requires fairly significant changes.

I already have the single shared_ptr<string> but converting annots and motifs to use a nested tree of sequences and subsequences is a fairly large change.

So I'm going to punt on this until we have one release out.

Though might still be worth it to write everything into a zip file.