s/settings.log/logger in  scan_blast_database_directory.

Residual change from SHA: 776c46ee.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Use ptools 1.2.6 which addresses Ruby 1.8.7 and 1.9.2 incompatibility.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Bring back jquery.scrollspy.js.

Which was accidentally removed in commit e072a26f, thus breaking highlighting
of focused search results.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Upgrade to Bootstrap 3, and a more modern, vanilla Bootstrap 3 UI.

Development of new features will gain from Bootstrap 3 upgrade. And the new UI
aligns better with SequenceServer's minimal, intuitive, and elegant philosophy.

No changes were made to the user work flow.

SequenceServer will no longer pop-up users to tweet us though. Instead, I
placed the Twitter button in the footer. And citation, which was previously
randomised together with marketing quotes, is also always visible in footer
now.

NOTES:
* Excluded Carousel and Glyphicons from Bootstrap build. Using FontAwesome 4
  instead of Glyphicons.
* Removed dependency on unmaintained jquery.activity.js. Using FontAwesome's
  spinner instead.
* Re-formatted search.erb.
* Include all JS just before closing 'body' tag, which improves page load time.
* Merged databases.erb into search.erb - easier to maintain.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Use monospace font in sequence textarea.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
BLAST to XML, parse XML to create Ruby objects, render HTML.

...

[ap: commit message]

Signed-off-by: Vivek Rai <vivekraiiitkgp@gmail.com>
Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>