Facilitate config of contributing gene trees

[twalsh-ebi]

Description

In conjunction with eg-web-metazoa PR 48, this pull request would facilitate handling of gene tree configuration.

This PR would:

• add method EnsEMBL::Web::Object::Gene::_resolve_clusterset_ids, which resolves the appropriate consensus and alternative clusterset_id values;
• update EnsEMBL::Web::Object::Gene::get_GeneTree to prioritise an explicit clusterset_id parameter over a consensus clusterset (e.g. "pig_breeds") where that clusterset_id represents an alternative clusterset appropriate to the given gene-tree view, facilitating display of contributing clustersets of a strain gene tree (e.g. "pig_breeds_raxml_parsimony");
• change EnsEMBL::Web::Object::Gene::get_GeneTree to use the consensus clusterset if a given gene or tree is not relevant to the current gene-tree view;
• adjust the EnsEMBL::Draw::GlyphSet::genetree::features method to use the ref_root_id of a gene tree in order to fetch the reference/consensus gene tree (instead of explicitly requesting the "default" gene tree);
• add method EnsEMBL::Web::ViewConfig::Gene::ComparaTree::_replace_default_clusterset_id_option, which can be used to replace the "default" clusterset_id option with an explicit default clusterset_id (e.g. strain consensus clusterset "murinae");
• update method EnsEMBL::Web::ViewConfig::Gene::ComparaTree::init_form_non_cacheable to facilitate configuration of the contributing clustersets of a strain gene tree, and to replace the default clusterset_id with the relevant strain consensus clusterset;
• ensure align_type and clusterset_id are passed as parameters for data export, while removing the (unused) Newick/NHX/Text clusterset_id dropdown from the gene-tree export config modal window;
• fix a link to the Ktreedist webpage.

Views affected

This PR would affect strain and default gene-tree views, as well as the gene-tree config modal window.

See related ticket ENSCOMPARASW-8520 for an example test case.

Possible complications

None expected, though the changes to handling of $clusterset_id in method EnsEMBL::Web::Object::Gene::get_GeneTree merit consideration.

Merge conflicts

None detected.

Related JIRA Issues (EBI developers only)

• ENSCOMPARASW-8520

[EbiArnie]

I approve