Integrate Rubocop to rake for HTML report generation.

Signed-off-by: Vivek Rai <vivekraiiitkgp@gmail.com>
Minor changes to Report, Query, and Hit classes.

* Report#parameters is now Report#params and returns a Hash.
* Query#meta is now Query#title.
* Hit#def is now Hit#title.

The last two changes aims for consistency with Sequence class, which derives
terminology from blastdbcmd's outfmt option.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Don't test on Ruby 1.9.2 on Travis.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Build index of seq_ids for each database

Each Database object now contains a set of seq_ids contained within it.
This allows us to determine whether a Database contains a particular
sequence id or not.

e.g., Database.include?(accession) => true/false

Another use of this feature is that it provides reverse lookup i.e.,
find which database contains this particular sequence. However, in many
cases a single sequence id can be present in multiple databases at a
time. We return all of the values and not just the first value.

e.g., Sequence.which_blastdb(accession) => [<Database object>, ..]

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