Fix setORF bugs.

* setORF was slicing out incorrect CDNA sequence.
* always read in triplets. If no stop codon found, extend reading frame to the
  end of the CDNA.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Reverting to non canonical translation start / stop site being 3bp long.

Or JB doesn't display them properly.

(ref: ae627246)

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
setORF: set CDS in triplets of 3 even if stop codon not found.

Previous behaviour was to extend CDS to the end of transcript.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
setCDS, setTranslationStart & setTranslationStop fixes.

Plus refactoring and new functions here and there.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Change documentation comment style for a few functions.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Adds CI with Drone and Docker

Signed-off-by: Bruno Vieira <mail@bmpvieira.com>
Add db:init to default rake task.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Update docker's build.sh to match latest changes.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Resizing exon to it's neighbour should merge. This was broken. Fixed it.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Decouple setLongestORF from actual calculation and updating the views.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Refactor setLongestORF & setORF.

They both make use of getCDNA now instead of calculating CDNA themselves. Both
shared common functionality of translating coordinates on refSeq to coordinates
on mRNA. Extracted them out into a separate function.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
More methods for coordinate translation and get more info off a transcript.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
getProtein - account for phase of CDS features.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
drop feature on transcript in edit track now works

as if both were dragged at the same time, i.e., merge them taking opposite strandedness into account.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
update 'which strand' modal a bit

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Link to Github from home page.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Show browser not supported message only if the user is on hidden login page.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Do no update reading frame when transcript is split.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
setORF: if no stop codon found extend reading frame to all the way to the end.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
getStopCodon: return last 3 in-frame chars from CDS

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