Ensembl/ensembl-webcode — pull request #98 by muffato (2014-09-03 09:20:50+00:00)
Title: Species groups for the colouring of gene-trees

This is the counterpart of #97 for the gene-tree view.
The Compara species groups were also used to define the colouring on the gene-tree view. With these commits, the view uses the web-site configuration (which I had to update: Ensembl/public-plugins#15)

In DEFAULTS.ini, I have reorganized the names of the groups, mainly to use the correct taxon names. I have added two variables: TAXON_GENETREE_BGCOLOUR and TAXON_GENETREE_FGCOLOUR to define the colours used for background / foreground colouring.
Then, in this PR, I've first updated the ConfigPacker to list all the groups a species belong to. Previously, a species had a SPECIES_GROUP variable that was the tightest group it was in. Now, there is a SPECIES_GROUP_HIERARCHY with all the groups (in the order of TAXON_ORDER) it belongs to. This is needed to draw nested boxes (see green and pink on http://enssand-01.internal.sanger.ac.uk:9073/Homo_sapiens/Gene/Compara_Tree?g=ENSG00000139618;r=13:32315474-32400266 )

NB: This means that I had to rebuild the packed files

The last commit is the switch itself:
- stop reading the Compara groups (ConfigPacker.pm)
- get the correct groups in the configuration page (ViewConfig/Gene/ComparaTree.pm)
- update the gene-tree component (Component/Gene/ComparaTree.pm)

The drop-down list on the main page still works: http://enssand-01.internal.sanger.ac.uk:9073/index.html

With this PR and the previous one, we don't need to store species groups in the Compara databases any more, they are configured only once, in DEFAULTS.INI