updated docs prior to release

[CHANGED] some formatting changes for consistency.
[CHANGED] integrated coevolution and motif module doc
          examples, contributed by Greg and Jeremy.

Docs passing, with the usual precision failures from working
on small data sets.
removed deprecated code earmarked for 1.2
updated __version__ project wide to 1.2
[ADDED/UPDATED]
    cogent.app.util:

    ParameterEnumerator object renamed to ParameterCombinations
    ParameterIterBase added, ParameterCombinations now subclasses
    ParameterCombinations now relies on cogent.util.transform.cartesian_product
    cmdline_generator added
[FIXED]
    cd_hit wasn't importing remove from os

[ADDED]
    TreeNode.iterativeNewick() returns a Newick-style representation of the
    tree from the node at which the method is called. This is an iterative
    implementation and is safe for use on very large trees.
[ADDED]
    .rest file for using the ParameterCombinations object and generating 
    command lines
tweaks to Daniel's app controller usage example

[NEW] linked in to main doc and updated the index.html
added usage example for querying NCBI

[NEW] new use case, added into index.html
[CHANGED] ChangeLog updated to final for 1.2 release
[MODDED]
    TreeNode._getDistances is now iterative. This is a modified version of the
    iterative code used for tipToTipDistances.
Added check for first open paren in tree -- allows us to skip arb comments.

Should really do this in a better way but this works for now.
updated __versionn__ to 1.3.0.dev

[CHANGED] also, check on cogent version number now only looks at integers
          after splitting on '.'
updated copyright to include 2009
mods to substitution models in support of Lindsay et al paper and sundry

[NEW] Introduced a new substitution model family. This family has the same
      form as that originally described by Muse and Gaut (Mol Biol Evol, 11,
      715-24). These models were applied in the article by Lindsay et al.
      (2008, Biol Direct, 3, 52). Model state defaults to the tuple weighted
      matrix (eg. the Goldman and Yang codon models). Selecting the nucleotide
      weighted matrix is done using the mprob_model argument. Tested in a new
      class in test_likelihood_function.py
[NEW] likelihood functions now have a getStatistics method. This returns
      cogent Table objects. Optional arguments are with_motif_probs and
      with_titles where the latter refers to the Table.Title attribute being
      set.
[CHANGED] parameter_controller.setParamRule now converts param_name to string.
[CHANGED] test_likelihood_function tests now use the cogent unittest framework
[CHANGED] Removed obsolete fpconst module, numpy provides equivalent
          functions. (from P Maxwell)
[CHANGED] Default to mean of (rather than median of) old parameter values. In
          the rare situation that the user sets a parameter to be global when
          it already has local values (eg: LF.setParamRule('x',
          is_independent=False) a default value is needed. The mean makes more
          sense, particularly for array inputs such as mprobs, and even more
          so now that (with numpy) arrays are no longer sortable so the median
          calculation gives an error. (from P Maxwell)
[CHANGED] Removed the nasty state-keeping matrix_exponentiation
          ExponentiatorFactory hack. See substitution_calculation.ExpDefn for
          the new approach to dynamically swapping between expm algorithms.
          (from P Maxwell)
[CHANGED] Matrix exponentiation fixes:
             - Don't count on not getting complex eigenvalues, even if the
               model is reversible.
             - Fix the check that we never return complex psubs.
             - Ensure the inverted eigenvector matrix is always contiguous
               since the pyrex code to check and convert it works with Numeric
               but not numpy.
          (from P Maxwell)

Note: The new substitution model family mods were done in collaboration with
Von Bing Yap and Peter Maxwell.
Updated MEME parser.  MEME changes format of motif lines when number of motifs is >100.  Parser now handles this case.
more motif formatters
Added rna_struct formatter and rna_plot parser. Added formatters in format/motif and updated format/stockholm

alignment: fixed bug in the sample methods and xsample (randint had the wrong max argument)

replaced distance_transform.py with substantially augmented version created by Justin
[FIXED]
    _getDistances relied on defaultdict breaking 2.4 backwards compatibility.
    This has been fixed.
Fixed warning about ACL so it no longer occurs with 2.5 versions, only 2.6.