Lots of changes - I need to commit more often.

- Sequences are now stored in a Hypothesis container, which doesn't contain the align algorithm itself. SequenceContainer should probably be renamed some time.
- removed SequenceContainer::make() and the Phases enum.
- fixed a bug in get_topranking where some Sequences would be skipped.
- added dtor and assignment operator for Sequence.
- added ostream << overload for Pair (Sequence too, but that segfaults sometimes).
- added some doxygen comments.