Added heatmap plotting method to Alignment (and tests).

Fixes #765

Based on @gregcaporaso's scikit-bio cookbook recipe:

http://nbviewer.ipython.org/github/biocore/scikit-bio-cookbook/blob/master/Alignment%20viewing%20and%20filtering.ipynb
Since `sequence_order` can be a subset of the sequences, move this below `sequence_order` and have it store the length of `sequence_order`.