Add ability to process input data for comparisons

preprocess_coords_data adds a new functionality to deal with the case
where the input is a set of coordinate files and the intended use is for
a comparison plot. This function now also return the number of of the
mapping file that will be needed.

preprocess_mapping file adds the ability to clone the data in the
mapping file as many times as requested by passing a new parameter; this
in turn will add a suffix to each replication.

Test suite was also updated for the util.py module
Add basework for comparison plots

A new option has been added to specify whether or not the required end
result needs to be a comparison plot. The help for the input option now
reflects this new option.

Some changes were also made to fit the latest changes that ocurred in
util.py.
Channge footer formatting

The footer formatting function, no longer adds the ellipsoids controls
into the GUI for a comparison plot.
Add format_comparison_bars_to_js to format module

format_comparison_bars_to_js is a function that takes care of the
formatting of coordinates data into javascript objects to create the
connecting lines between compared plots.
Fix error in formatting

Javascript keys were not being created as strings
Add option to format in edges visibility

An edges selector can now formatted into the end result
Add drawEdges function an toggleEdgesVisibility

These functions deal with the new g_comparisonPositons global variable,
in case there are comparisons, it draws them and responds to the
callback on whether or not to draw them with a selector.
Add script usage example for plot comparison

And added the option to reflect the addition in the footer.

Fixes #103
Add script usage example for plot comparison
Add note about plot comparisons in ChangeLog.md
This should address issues 48 and 120
Addressing comments
Merge pull request #124 from meganap/master

Checking in Parallel Plots functionality
Fixing arrow legacy error
Fixing conflicts
Merge pull request #125 from antgonza/issue_48

This should address issues 48 and 120
Fix bug with summarize_coords

This problem would cause a bug with summarize_coords, should now be
fixed.
Add checks for input directories

This new checks allow the script interface to check whether it should
ignore or not a file that's passed in.
Merge branch 'master' of git://github.com/qiime/emperor into issue_103

Conflicts:
	ChangeLog.md
	emperor/format.py
	emperor/support_files/emperor/js/emperor.js
	emperor/util.py
Remove console.log statement from emperor.js