Facilitate CACTUS_DB alignment views in all divisions

[twalsh-ebi]

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Description

In conjunction with other pull requests, this draft PR would facilitate display of CACTUS_DB alignments.

It would:

• alter default configuration of CACTUS_DB alignslice views to hide gene tracks when the size of the region being accessed exceeds a 'transcript' threshold (e.g. 25 kb), and hide contig tracks when the size of the region exceeds a greater 'sequence' threshold (e.g. 50 kb).
• display a 'scale-dependent track config' info box in image alignment views if any tracks are hidden;
• include as_track_threshold_data in packed files, providing easy access to the scale-dependent track threshold region sizes;
• display a warning box in text genomic alignment views if the user tries to access a per-subgenome alignment from the wrong subgenome, and if possible, recommend the appropriate per-subgenome alignment;
• configure GENCODE tracks according to the genome in the given alignslice row rather than the genome from which the view is being accessed; and
• update genomic alignment stats pages to handle per-subgenome CACTUS_DB alignment stats.

Views affected

Affected views include image and text alignment views, as well as genomic alignment stats views.

Possible complications

• TBD

Merge conflicts

None detected.

Related JIRA Issues (EBI developers only)

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