started working on new method of distance matrix class get_adjacent_distances

this will be useful for plotting change in distance between adjacent timepoints, for example in a timeseries or following a spatial gradient. this isn't working right now, but need to run for a bit, so want to commit what i currently have. need to figure out indexing into distance matrices.
first working version of get_adjacent_distances

decided not to implement this with qiime.util.DistanceMatrix as we're not really using that in many places, and it seems kind of clunky.
added strict mode and additional documentation
addressing comments from @jrrideout. thanks!
moved get_adjacent_distances to qiime.group
few minor clean-ups

also, previous commit changes the interface to match other distance extraction functions.
modified interface

now additionally returns the pair of sample ids corresponding to each distance. after working with this code to generate some plots that i'm interested in, i'm finding that i need this information as well.
improved code associated with the last commit to make it less clunky
addressed comments from @jrrideout.
Merge pull request #665 from gregcaporaso/extract-adjacent-distances

Extract adjacent distances from distance matrix
getResults now uses the BIOM table API more effectively
Merge pull request #667 from wasade/issue666

getResults now uses the BIOM table API more effectively.

This solves this issue but the performance from SparseMat is still slightly better. Our tests indicate that this is due to cython so we expect that the new (future) implementation of CSMat/cython should address this.
Modified pick_otus.py and usearch.py to allow modulation of reverse strand matching for usearch.  Also made final sequence assignment to match percent identity of clustering.
Changed comment in code, changed default to False inside of usearch_qf function.
Merge pull request #671 from walterst/pick_otus_usearch_rev

Modified pick_otus.py and usearch.py to allow modulation of reverse stra...
Checking in fixed changes for TopiaryExplorer 1.0
Merge pull request #675 from meganap/master

Fixed changes for TE 1.0