Add script interface options to do BiPlots
Merge branch 'master' of git://github.com/qiime/emperor into issue_12
Add basework basework for biplots module and tests
Add controller for biplot processing & test suite

This controller function will let you process the raw data i. e. otu
table and coordinates file and will let you retrieve the scores and N
most prevalent taxons.
Add use of preprocess_otu_table

Script is now capable of writting the biplots coordinates file.
Add function to format the data for the biplots
Change format to be clearer in HTML output
Add sort module and tests module to emperor

This module currently aids with the sorting that should take place
when operating otu tables from the script interface.

The all variable in the __init__.py file is now updated.
Fix bug in preprocess_otu_table

This bug caused the biplot information to be placed in the exact
coordinates where samples were positioned. This function now makes use
of emperor.sort to make sure that the sample identifiers match between
coordinates files and otu tables.

The script interface was updated accordingly since the filtering of the
otu table is now performed using the header in the coordinates data.
Add formatting function for the footer

A new function has been added to the format module, this function is
responsible for presenting the appropriate GUI elements on screen.
Add taxalabels div for biplots and update tests
Add taxa labels functionality for biplots

The following functions were added to the javascript file:
    - Callback to respond to the controller in the user interface
    to show or hide the labels with the taxonomic lineages.
    - Scaling of the biplots when they appear on screen
    - Presentation of the labels when for each frame

Minor updates took place in the emperor.css file to reflec the changes
in format.py and in emperor.js.
Add biplots script usage examples and test data

The main script now supports biplots and jackknifed plots.

Test data was added for the new examples that have been added to the
script interface.

This closes #12
Change processing structure in the interface

preprocess_otu_table is now capable of handling empty inputs for the otu
table related values. This will generate empty outputs. This change
allows the script interface to follow the same structure as
preprocess_mapping_file and preprocess_coodinates.

This change also now allows using a custom axis and biplots.
Fix comparison that was being done incorrectly
Change default output path from ./ to emperor

The -o option now has a default, previously it was not the case as it
would manually prepend ./ to every output.

Fixes #60
Merge branch 'master' of git://github.com/qiime/emperor into issue_12
Add visibility and color GUI elements for biplots

The color of the biplots on screen can now be changed to any color.
The biplots can now be turned-off.
Add note about coloring for biplots.
Remove unnecessary files

These files came from the E-vident repository migration. Shouldn't be
needed in Emperor itself.