Initial commit
deleted some unnecessary files
Changed vase to work with the VASE Data Object
enabled custom xml files in browser
changed residue numbering so it starts from 1 instead of 0; added toggle buttons for the table headers
BUGFIX: handle missing cache dir

fixed a nullpointer exception that only appeared when the cache
directory name was invalid.
locale fix for svg transforms

makes sure that the output locale for svg transform attributes is always
english. Otherwise, the application has problems properly displaying the
plots when running on computers with a different language.
Reduced complexity for sequence highlighting.

The sequences in the alignment are still highlighted, but by an
algorithm that is expected to have a better performance.
locale fix for data table

This locale fix makes sure the numerical data is displayed in english
locale. Otherwise the application might have trouble running on machines
with a different language.
implemented the mouseOver functionality

Hovering the mouse over the column headers in the alignment shows table
values, for which mouseover has been set to 'true'.
BUGFIX: prevents zero stepsizes
now taking residue names from pdb files, not from the stockholm file anymore
Adjustment to produce rounded stepsize numbers
starting to integrate bootstrap
Only layout issues remaining
There's no more white space between the lines in the alignment. Column hashtags can now be used for toggling.
moved 'clear selection' link to the right, since it's different from the other buttons
fixed an issue with the jmol window, not being able to toggle
Fix column alignment in alignment table
Selected column highlight now a contiguous block