Ensembl/ensembl-webcode — pull request #67 by muffato (2014-07-08 14:01:00+00:00)
Title: Genomic align tree display

Hi Web,

Here is an extension of the tree view for genomic alignments. Kathryn has finished that after leaving the EBI, and "handed it over" to us in April. The code was originally based on e75, and I've rebased it to master. GIT was able to follow the renamed files, and I've made a few changes to accommodate the recent refactoring (like calling $self->object->XXX instead of $sef->XXX)

I also had to fix a few things about the warning messages that are generated on that page (first 5 commits). Especially:
- The message to indicate missing species should be an information, not a warning (and not fatal)
- check_for_missing_species() is already called in check_for_align_problems(), so we don't need to call another time (that would duplicate its messages)

For the display itself (6th commit), there is a new draw_tree() method in modules/EnsEMBL/Web/Component/Compara_Alignments.pm and some conditional code in modules/EnsEMBL/Draw/GlyphSet/genetree(_legend).pm
We haven't enabled ZMenus for those trees (we don't know what to put there, anyway)

Examples (you can select which MSA to display):
http://enssand-01.internal.sanger.ac.uk:9073/Homo_sapiens/Location/Compara_Alignments?align=654;db=core;r=17:64202765-64207764
http://enssand-01.internal.sanger.ac.uk:9073/Homo_sapiens/Location/Compara_Alignments?align=660;db=core;r=17:14818999-14819998

Matthieu