Load underlying slices iff needed for alignslice view

[twalsh-ebi]

Description

On line 390 of ensembl-webcode/modules/EnsEMBL/Web/Object.pm ...

ensembl-webcode/modules/EnsEMBL/Web/Object.pm

Line 390 in 370648c

my $underlying_slices = !$args->{image}; # Don't get underlying slices for alignment images - they are only needed for text sequence views, and the process is slow.

...in method EnsEMBL::Web::Object::get_slices, the 'image' parameter is used to control whether underlying_slices of a Compara AlignSlice::Slice are loaded for a formatted slice.

The loaded underlying_slices value is used in various places in text alignment views. However, in genomic alignment image (alignslice) views, it appears to be used only to control visibility of ancestral sequences, in line 417 of ensembl-webcode/modules/EnsEMBL/Web/Object.pm:

ensembl-webcode/modules/EnsEMBL/Web/Object.pm

Line 417 in 370648c

my $ga_node = $formatted_slices[-1]->{underlying_slices}->[0]->{_node_in_tree};

This PR would set the get_slices 'image' parameter to 0 for genomic alignment image views lacking an ancestral sequence (i.e. not of class GenomicAlignTree.ancestral_alignment). In tests done so far on the 91 Mammals EPO-Extended alignment, this has reduced loading times by ~10% on average.

Views affected

This change would affect image (alignslice) views of all non-ancestral genomic alignments, including EPO-Extended, Cactus and LastZ alignments.

Further details on testing are available in the related Jira ticket.

Possible complications

This is not expected to adversely affect any views. The change is restricted to non-ancestral image alignments, where the underlying_slices value is not currently needed.

Merge conflicts

None detected.

Related JIRA Issues (EBI developers only)

• ENSCOMPARASW-8396