Minor refactoring and bug fixes.

* ensure getCDS returns spliced sequence.
* CDS returned by getCDS had an extra bp.
* functions that require sequence to work with now take refSeq feature object
  instead of raw sequence.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Adds specifics DOM classes to bases. Colours M green and * red

Signed-off-by: Bruno Vieira <mail@bmpvieira.com>
Allows to still see colour bars in ORFs when zoomed out too much to see bases

Signed-off-by: Bruno Vieira <mail@bmpvieira.com>
Slightly refactor codon colour code from Bruno.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Use 12px for displaying nucleotides and amino acid.

This seems to avoid space b/w coloured acid elements (start / stop codon) and
sequence div.

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