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>
Updated to Bootstrap v3.2

Signed-off-by: Vivek Rai <vivekraiiitkgp@gmail.com>
BS3 upgrade.

TODO:
0. modal#spinner
1. modal#social
2. BLAST buttons
4. notification stutters
5. Results - highlighting focused query report is not working.
6. Use font-awesome. Remove jquery.activity.js.
7. Use min version of all files.
8. Insert JS at the end.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Initial experimental code

Backed up original blast.rb file and trying out experimental code in
new file. The code/changes are most likely to be changed drastically in
future commits. Please check further commits for stable code.

added result.erb

Changed result.erb

added l,k,h values to result.erb

Signed-off-by: Vivek Rai <vivekraiiitkgp@gmail.com>
Fixed not showing up of all hits
Added comments, removed old code

Signed-off-by: Vivek Rai <vivekraiiitkgp@gmail.com>
Improved result.erb, minor changes

Signed-off-by: Vivek Rai <vivekraiiitkgp@gmail.com>
Code for correct aligned display of sequences

Tried to used the grid system offered by Bootstrap model but it didn't
work out as expected. Instead I decided to go off working with the
tables. However, the main problem was splittig up the alignments into
multiple rows and displaying properly. This required a lot of
not-nice-looking code. Morever, taking care of Plus/Minus of the hseq
was another tricky case (which again added a even more code). However,
it is working as in the original version.

Signed-off-by: Vivek Rai <vivekraiiitkgp@gmail.com>
Handled case of no hits

The earlier implementation did not handle the cases where no hits were
obtained. This patch fixes the issue.

Signed-off-by: Vivek Rai <vivekraiiitkgp@gmail.com>
Added positives information, minor changes

Signed-off-by: Vivek Rai <vivekraiiitkgp@gmail.com>
Testing grid layout

<pre> tag was causing problems and has been done away with. The outcome
is on the lines of expectations but the midline information doesn't
aligns nicely with the query and hit sequence as it did earlier. That
remains to be fixed, along with splitting the individual hits.

Signed-off-by: Vivek Rai <vivekraiiitkgp@gmail.com>
Overhaul previous User Interface for SS with BSv3

This commit utilises the power of Bootstrap v3 to display enhanced
interactive interface for SequenceServer. The <pre> tags have been done
away with for the results and now use collapsible feature for
individual aligments like NCBI.

results.erb was messy and has been rewritten from scratch.

Signed-off-by: Vivek Rai <vivekraiiitkgp@gmail.com>
qseq, midline and hseq properly aligned now

Used monospace font family to properly align the midline with query
sequence and hit sequence.

Signed-off-by: Vivek Rai <vivekraiiitkgp@gmail.com>
Comments, removed old code, adding db information

Minor format changes too.

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