Tweak handling of incomplete pairwise alignment stats

[twalsh-ebi]

Description

This PR would tweak handling of incomplete pairwise alignment stats by:

• Moving the assignment of a default LastZ scoring matrix from the fetch_pairwise_input method of EnsEMBL::Web::Document::HTML::Compara::MLSS to its render_pairwise method. Without this change, the conditional statement checking for alignment parameters on line 202 of modules/EnsEMBL/Web/Document/HTML/Compara/MLSS.pm never evaluates to false for LastZ. Consequently the message, "No configuration parameters are available.", is not shown even when no parameters have been stored for a LastZ alignment, because assignment of the default scoring matrix beforehand ensures keys %$blastz_parameters is nonempty.
  

  ensembl-webcode/modules/EnsEMBL/Web/Document/HTML/Compara/MLSS.pm

  Line 202 in b5c4e5f

  if (keys %$blastz_parameters || keys %$tblat_parameters) {

• Filtering the parameter @order array to keep only those parameter settings available for display.
• Showing an empty string for unavailable chunking parameters.

Views affected

This would affect pairwise whole-genome alignment stats pages.

Example pairwise alignment stats pages:

• T. aestivum self-alignment LastZ stats on sandbox and staging : note the "Configuration parameters" section.
• T. dicoccoides self-alignment LastZ stats on sandbox and staging : note the "Configuration parameters" and "Chunking parameters" sections.
• Arabidopsis thaliana vs Actinidia chinensis LastZ stats on sandbox and staging : note the entries for "HSP threshold (K)" and "Masking count (M)".
• Human self-alignment LastZ stats on sandbox and staging : note the undefined "Group set size".

Possible complications

Changing method EnsEMBL::Web::Document::HTML::Compara::MLSS::fetch_pairwise_input so that it does not assign a default scoring matrix could change the behaviour of this method if it is called outside this module.

However, I haven't been able to find any use of this method outside the Compara::MLSS module.

Merge conflicts

None detected.

Related JIRA Issues (EBI developers only)

• ENSCOMPARASW-8395