index.html, js/model.js: make the 'sequences (when short)' the new default for visualizing N regions

Aurélien Béliard authored Jan 10, 2017 and Mathieu Giraud committed Jan 10, 2017

See #1765

The browser is quite large and can sometimes take some time to download
and start up.
Therfore the "patients" menu entry could sometimes take a long time to
be displayed if at all.
Adding this indicator will let the user know when everything has
finished loading and whether or not a server is configured with the
browser more clearly.

Added indicator when ajax query is in progress

Extracted the uploads recap from the top container in order to change
the z-index to a higher value than the db_div

Whole top container is no longer disabled, only browser menus

Adjusted the top menu layout. Patient name now has a dropdown menu to
open said patient page and save analysis.
Patient list and previously viewed results are unchanged

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

HERBERT Ryan authored Jan 27, 2016 and Vidjil Team committed Mar 08, 2016

open patients in the menu now opens the patients list rather than reloading the last page served by the database

Reintroduce cluster by locus.
Partially revert 70bd7ef6.

Vidjil Team authored Dec 17, 2015 and Mathieu Giraud committed Dec 17, 2015

The "V" / "J" designations can bring some confusion with incomplete recombinations such as DJ or Dd2-Dd3.
However, we prefer to keep these designations for the majority of cases.
These "V/5'" / "J/3'" are thus some compromise.

This was not really meaningful when displaying several locus on the grid,
and less functional than the 'germline' box in the info panel

This is more generic than what was previously in the development menu.
Applied to 'highlight menu' in js/segmenter.js.