Affine gaps now accept a affine gap at the start of the alignment.

Bdel[i][j-1] is not the same than Bdel[i-1][j]

We should never reach these values.
It's good that the tests are passing with this commit.

B, Bins and Bdel were never initialized outside the first row and column.
Even if this not really useful, this might be safer and help to find bugs.

Mikaël Salson authored Mar 03, 2016 and Mathieu Giraud committed Mar 11, 2016

First and last letter are always aligned together, even if that doesn't make sense.

Moved CDR3 checkbox out of devel-mode

This was one of the discrepancies found by @mikael-s who discovered that while fixing browser unit tests

There were some discrepancies that made the situation ambiguous.
Now we clearly state that positions must start at 1.

The code is updated accordingly.

Positions start at 0, not 1

setAttribute, and not addAttribute, and further typo

The current colors were selected in d97cfefa in May 2014 and never changed.

This highly debatable commit sets new colors and new rendering for V/D/J segments,
with homogenous colors with the V/D/J segments highlighted when querying IMGT-VQUEST.
The goal is both to improve the contrast between the segments
and to be not too intrusive for the eye.

This reverts commit 240b40ae.
Commit broke several javascript tests

No need for the qualifier, it is already in the label.
And the whole string was too long for the new interface

Information from seg is displayed (nt sequences extracted using start
and stop). Some info can be omitted if needed

Several methods are defined to acces the seg fields.
Hence the getCDR3length is useless now as the same can be achieved by
calling getSegLength('cdr3').

When major clones are hidden (filtered out) the bars may be quite small
making the differences hard to view. Now the scale of the bar plot is
scaled depending on the active clones.

Color depending on the productivity of the sequence
(found in the seg.junction.productive field)

The cdr3 field in seg is not anymore a string field but is similar to the
other fields in seg. And we use the start and stop field to know
the length of the CDR3 in nt.