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Update Compara track description links #1110

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merged 1 commit into from
Sep 16, 2025
Merged

Update Compara track description links #1110

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12 changes: 6 additions & 6 deletions modules/EnsEMBL/Web/ImageConfigExtension/Tracks.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -946,7 +946,7 @@ sub add_synteny {
species => $species_2,
species_hr => $species_readable,
caption => $caption,
description => qq{<a href="/info/genome/compara/analyses.html#synteny" class="cp-external">Synteny regions</a> between $self_label and $label},
description => qq{<a href="/info/genome/compara/synteny.html" class="cp-external">Synteny regions</a> between $self_label and $label},
colours => $colours,
display => 'off',
renderers => [qw(off Off normal On)],
Expand All @@ -970,12 +970,12 @@ sub add_alignments {
my ($static, $wga_page);
my $division = $species_defs->EG_DIVISION;
if ($division) {
$wga_page = $static = 'whole_genome_alignment.html';
$static = 'whole_genome_alignment.html';
}
else {
$static = 'analyses.html';
$wga_page = $static.'#conservation';
}
$wga_page = 'multiple_genome_alignments.html';

foreach my $row (values %{$hashref->{'ALIGNMENTS'}}) {
next unless $row->{'species'}{$prod_name};
Expand Down Expand Up @@ -1007,7 +1007,7 @@ sub add_alignments {
$description = 'Pairwise alignments';
}

$description = qq{<a href="$static" class="cp-external">$description</a> between $self_label and $other_label};
$description = qq{<a href="/info/genome/compara/$static" class="cp-external">$description</a> between $self_label and $other_label};
$description .= " $1" if $row->{'name'} =~ /\((on.+)\)/;

$alignments->{$menu_key}{$row->{'id'}} = {
Expand Down Expand Up @@ -1043,13 +1043,12 @@ sub add_alignments {
if ($row->{'conservation_score'}) {
my ($program) = $hashref->{'CONSERVATION_SCORES'}{$row->{'conservation_score'}}{'type'} =~ /(.+)_CONSERVATION_SCORE/;

$options{'description'} = sprintf '<a href="/info/genome/compara/%s">%s conservation scores</a> based on the %s', $wga_page, $program, $row->{'name'};

$alignments->{'conservation'}{"$row->{'id'}_scores"} = {
%options,
conservation_score => $row->{'conservation_score'},
name => "Conservation score for $row->{'name'}",
caption => "$n_species way $program scores",
description => sprintf('<a href="/info/genome/compara/conservation_and_constrained.html">%s conservation scores</a> based on the %s', $program, $row->{'name'}),
order => sprintf('%12d::%s::%s', 1e12-$n_species*10, $row->{'type'}, $row->{'name'}),
display => 'off',
renderers => [ 'off', 'Off', 'tiling', 'Tiling array' ],
Expand All @@ -1060,6 +1059,7 @@ sub add_alignments {
constrained_element => $row->{'constrained_element'},
name => "Constrained elements for $row->{'name'}",
caption => "$n_species way $program elements",
description => sprintf('<a href="/info/genome/compara/conservation_and_constrained.html">%s constrained elements</a> based on the %s', $program, $row->{'name'}),
order => sprintf('%12d::%s::%s', 1e12-$n_species*10+1, $row->{'type'}, $row->{'name'}),
display => 'off',
renderers => [ 'off', 'Off', 'compact', 'On' ],
Expand Down