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Follows what is done for D in e6ffb915, and what was already done for V/J in -c segment.
Even if it may be counter-intuitive, the results of segmentation thus actually depends on the number of reads:
'-e 1' should mean that we expect one false positive segmentation in the output.
Even if some e-values slightly change, this commit does not affect the results of the tests.

We should investigate what happens when a FineSegmenter fails here.
Moreover, is it sane to have the same '-e' paramater for fixing both e-values of Kmer and FineSegmenter?
Or should we rather have another paramater?

endsWith method in the String class is from a recent ECMAScript standard
and is therefore not well supported.

Instead we provide a endsWith function that will make the same job.

This is not the case so far and should be corrected before next release.

Now not only the 5' and 3' parts of the genes are underlined

The value may not be defined when the sequence doesn't
have insertions.

When having insertions, positions correspond to the *corrected* sequence
rather than the original one.

HERBERT Ryan authored Sep 22, 2016 and Mathieu Giraud committed Oct 05, 2016

Many tests in this suite were dependant on data from testRunner and
therefore on the order of the execution of each testcase. This commit
encapsulates the test data in order to ensure the order of execution has
no effect on the result of these tests

HERBERT Ryan authored Oct 04, 2016 and Mathieu Giraud committed Oct 05, 2016

Fixed an issue where entering an invalid or unavailable patient or run
name would cause a server error and give little to no useful information
to the user.

HERBERT Ryan authored Oct 04, 2016 and Mathieu Giraud committed Oct 05, 2016

Altered some condition statements to improve clarity of code

Sequences sent to external website have now an unique identifier.
The clone index is prepended to the getName() (with a # as a separator).

This ensure that no sequence will share a same FASTA header, which could
cause some softwares to complain. Also, when analysing the results, we will
easily know which result belongs to which clone.

The clone index is put at the start rather than the end because
IMGT/V-QUEST cuts the header when it is too long.

At this point identity is a string, which cannot be NaN.
Therefore we start by converting the value to a float and
then we test whether is it NaN or not.

However the value may not be defined (when there are no indels),
in which case it is empty. In such a case we fallback to the
identity % without indels.

-tagselector appear closer to the user mouse
-tagSelector mousehover doesn't shrink the segmenter

-form generator (select samples/systems)
-form validator
-save/restore state mechanism

auto-resize/center

-fix missing args
-fix fake log function to match the signature of the real log function

HERBERT Ryan authored Aug 08, 2016 and Vidjil Team committed Oct 01, 2016

Fixed a bug in the hotfix where I used a python method of checking the
presence of a string in an array.

Ambiguous terms should be surrounded by parentheses

-2 : unexpected recombinations
-3: compute CDR3

We may want to launch the locus tests only without launching the whole test suite.

Never commit in a hurry!

The previous commit (see 8496cbb0) indicated a suffix for the backup files
(necessary with POSIX sed). Then we were overwriting the tap files with the
bak ones. This was totally stupid as we were overwriting the correct files
with the old ones…

This is now fixed we just delete the backup files as we don't really need them
(we just specify the option to ensure the compatibility between POSIX and GNU
sed).

GNU sed and POSIX sed have slightly different behaviors.  Those behaviors are
incompatible if we don't specify a “backup” suffix with -i. So we specify such
a suffix and then we move all the files so that they overwrite the original
files.
Moreover in this case, the -e option is necessary for FreeBSD's sed.