Add option to use a master pcoa for comparisons

Comparison plots can now be passed a master pcoa file where all the
coordinate edges are originated at.
Edges can now be centered at a master pcoa file

The formatter for edges can now be centered at a set of principal
coordinates.

The test suite was updated accordingly.
Reposition elements in view tab

All checkboxes are now aligned and the color selectors for the edges are
now aligned with the other color selectors.
Add awareness for multiple comparison plots

The script is now aware of the naming conventions used in QIIME for
multiple procrustes comparisons where one file is the center of the
plot.
Support changes for better coordinate comparisons

The following changes have been added:
    - The system can now re-color the edges when visualizing a plot
      comparison.
    - The system can now select a master set of coordinates, this set
      of coordinates is where all the other coordinates originate.
    - Scaling by the percent explained now works for vectors and edges
      in the case of a plot comparison.
    - A bunch of typos have been removed.
    - A bug was fixed where axes would always re-color back to white
      when the coordinates were scaled by the percents explained.
    - A semantic bug was corrected where the checkbox to enable the
      edges visibility was negated.
    - Biplots are now removed from the plot when they are hidden not
      turned to 0 in opacity.
    - Axes are no longer transparent, which in part helps for #151.

Fixes #121, fixes #144 and fixes #143.
Add notes to ChangeLog
Add extra ordering step for plot comparisons

When the plot comparison is one with multiple procrustes transformations
the code now guesses the master file and forces it to be the first in
the list of samples when displayed in the interface.

This was already the case but with the added lines this is _going_ to be
the case always.

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Remove typos and empty lines.
Merge branch 'master' of git://github.com/qiime/emperor into issue_121_and_144

Conflicts:
	ChangeLog.md
	emperor/format.py
	scripts/make_emperor.py
	tests/test_format.py
Add utility function to sort filenames

The filenames used for comparison plots as defined by QIIME 1.7.0-dev in
transform_coordinate_matrices.py.

Add unit tests for the module.
Fix bug with comparison plots

Specifying the reference set of coordinates was previously taking the
effect of making a random set of coordinates the reference instead of
the one passed from the CLI. This has been corrected.

Change the way filenames were being sorted for comparison plots, these
are now sorted based on the suffix they have if they are in a
QIIME-compliant format.

Thanks @nbokulich for pointing thes out!
Add extra pattern to regular expresion

Regular expresion matches only extensions at the end of the line; a new
test was added to check for this.
Merge pull request #152 from ElDeveloper/issue_121_and_144

Changes for comparison plots