Fix fasta formatter to correctly format sequence files

Signed-off-by: Vivek Rai <vivekraiiitkgp@gmail.com>
No rounded border for navbar and default bottom margin.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Allow dragging and dropping query file into query sequence textarea.

All of the code is courtesy Clayton Wheeler (@csw) and Ben Woodcroft (@wwood),
(see #98) with very minor modifications from myself:
1. No need to dynamically position dnd-target-marker.
2. We already had a button to clear query sequences. Integrate with that.

Because of the recent frontend overhaul (including BS3 upgrade) it was easiest
for me to cherry-pick code, rather than merge csw:dnd or wwood:dnd branches.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Change drag n drop behavior.

* Drop anywhere.
* Show drop error on dnd overlay.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Use relative URL in download button in the modal as well.

See: c87f1f0bfc01f7a82896d50ab00b91bd873d7b88.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Quote blastdbcmd -db arguments to allow multiple dbs

Some refactoring resulted in broken command, which was causing errors
when run against multiple databases. Fix this. See NCBI BLAST+ help
manual for reference.

Signed-off-by: Vivek Rai <vivekraiiitkgp@gmail.com>
Show database ids, not full path to database, if error retrieving sequences.

User / admin can get full path from `sequenceserver -l`.

Plus slight refactoring around sequence retrieval.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Graph controls now handled by jquery.t.js itself, Refactor

* The button click event listeners and the corresponding behavior are now
implemented in t.js itself, requring ss.js to call only one draw
function on the appropriate element.

* Graphic overview buttons are now shown/hidden instead of disabling.

* Refactor, and document the code slightly.

Signed-off-by: Vivek Rai <vivekraiiitkgp@gmail.com>
Link to directly download FASTA.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Switch to Bootstrap.Scrollspy.

Previously we were using a horribly inefficient scrollspy written by me. This
should improve responsiveness in general.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Let browser add ellipsis to entries in the index if id too long.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Remove some dead code.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Focus textbox on clear sequence.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
BLASTN hsp stats - use +/- instead of plus/minus.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Rubocop: lib/blast.rb, refactor

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