Match highlighted orthologue by gene and species

[twalsh-ebi]

Description

In conjunction with eg-web-common PR 143 and eg-web-metazoa PR 46, this PR would:

• pass an s1 parameter with the gene-tree links in an orthologue table, whose value is the URL of the species containing the given orthologue;
• add an s1 parameter to gene-tree views, which is expected to contain the species URL of the genome containing the gene specified by g1;
• use the species indicated by s1 to help unambiguously identify the gene specified by g1 for highlighting in a given gene-tree view; and
• repurpose the '_leaves' item of node features in the genetree GlyphSet to identify leaves by their concatenated genome_db_id and gene stable ID, making it possible for a highlighted orthologue to be identified even if in a collapsed branch of the gene tree.

Views affected

This is expected to affect gene-tree views in which an orthologue is highlighted, such as those linked from the ComparaOrthologs view.

Some example links have been added to the related JIRA issue.

Possible complications

Complications are not expected, as the s1 parameter has not (as far as I know) been used in a ComparaTree component, and the '_leaves' item of node features should be safe to repurpose as they are not (as far as I know) currently used.

Merge conflicts

None detected.

Related JIRA Issues (EBI developers only)

• ENSCOMPARASW-8505