Facilitate config of contributing gene trees

Author: twalsh-ebi

modules/EnsEMBL/Draw/GlyphSet/genetree.pm

@@ -839,7 +839,22 @@ sub features {
 
       if ($show_exons) {
         my $ref_genetree = $tree->tree;
-        $ref_genetree = $ref_genetree->alternative_trees->{default} if $ref_genetree->ref_root_id;
+
+        if ($ref_genetree->ref_root_id) {
+
+          # If $ref_genetree is a contributing tree, we need to fetch the
+          # corresponding reference tree in order to get exon boundary data.
+          my @matching_ref_genetrees = grep {
+            !$_->ref_root_id && $_->root_id == $ref_genetree->ref_root_id
+          } values %{$ref_genetree->alternative_trees};
+
+          # Gene trees are uniquely identified by their root_id, so there can be at
+          # most one gene tree with a root_id matching $ref_genetree->ref_root_id
+          if (scalar(@matching_ref_genetrees) > 0) {
+            $ref_genetree = $matching_ref_genetrees[0];
+          }
+        }
+
         unless ($ref_genetree->{_exon_boundaries_hash}) {
           my $gtos_adaptor = $tree->adaptor->db->get_GeneTreeObjectStoreAdaptor;
           my $json_string = $gtos_adaptor->fetch_by_GeneTree_and_label($ref_genetree, 'exon_boundaries');

modules/EnsEMBL/Web/Command/DataExport/Output.pm

@@ -157,7 +157,7 @@ sub process {
     $url_params->{'__clear'}        = 1;
     ## Pass parameters needed for Back button to work
     my @core_params = keys %{$hub->core_object('parameters')};
-    push @core_params, qw(export_action data_type data_action component align g1 node strain hom_id);
+    push @core_params, qw(export_action data_type data_action component align align_type clusterset_id g1 hom_id node strain);
     push @core_params, $self->config_params; 
     foreach (@core_params) {
       my @values = $component->param($_);

modules/EnsEMBL/Web/Component/DataExport/GeneTree.pm

@@ -41,7 +41,7 @@ sub content {
   my $view_config  = $self->view_config;
 
   my $settings = $view_config->form_fields('export');
-  $settings->{'Hidden'} = [qw(align align_type node strain)];
+  $settings->{'Hidden'} = [qw(align align_type clusterset_id node strain)];
 
   ## Add export-specific settings
   my $fields_by_format;
@@ -87,9 +87,9 @@ sub content {
 
     ## Options per format
     $fields_by_format = [{'Tree formats' => {
-                                    'Newick'    => [qw(newick_mode clusterset_id)],
-                                    'NHX'       => [qw(nhx_mode clusterset_id)],
-                                    'Text'      => [qw(scale clusterset_id)],
+                                    'Newick'    => [qw(newick_mode)],
+                                    'NHX'       => [qw(nhx_mode)],
+                                    'Text'      => [qw(scale)],
                                     'OrthoXML'  => [],
                                     'PhyloXML'  => $self->phyloxml_fields, 
                             }}];

modules/EnsEMBL/Web/Object/Gene.pm

@@ -941,14 +941,23 @@ sub get_GeneTree {
   my $compara_db  = shift || 'compara';
   my $whole_tree  = shift;
   my $strain_tree = shift;
-  my $clusterset_id = $strain_tree || $self->hub->param('clusterset_id') || 'default';
+  my $clusterset_id = $self->hub->param('clusterset_id') || $strain_tree || 'default';
+
   my $cache_key  = sprintf('_protein_tree_%s_%s_%s', $compara_db, $clusterset_id, $strain_tree);
 
   if (!$self->{$cache_key}) {  
     my $args = {'stable_id' => $self->stable_id, 'cdb' => $compara_db};
     my $member  = $self->get_compara_Member($args)  || return;
     my $adaptor = $member->adaptor->db->get_adaptor('GeneTree') || return;
-    my $tree    = $adaptor->fetch_all_by_Member($member, -clusterset_id => $clusterset_id)->[0];
+    my $tree    = $adaptor->fetch_default_for_Member($member, $clusterset_id);
+
+    if (!$tree || defined $tree->ref_root_id) {
+      my $consensus_tree = $adaptor->fetch_default_for_Member($member, $strain_tree);
+      if (!$tree || $tree->ref_root_id != $consensus_tree->root_id) {
+        $tree = $consensus_tree;
+      }
+    }
+
     unless ($tree) {
         $tree = $adaptor->fetch_default_for_Member($member);
     }

modules/EnsEMBL/Web/ViewConfig/Gene/ComparaTree.pm

@@ -155,19 +155,27 @@ sub init_form_non_cacheable {
   my $form  = $self->SUPER::init_form_non_cacheable(@_);
   my %other_clustersets;
 
+  my $page_action = $hub->referer->{'ENSEMBL_ACTION'};
+  my $consensus_clusterset_id = $hub->param('strain') || $page_action =~ /^Strain_/
+                              ? $hub->species_defs->get_config($hub->species, 'RELATED_TAXON')
+                              : 'default'
+                              ;
+
   if($hub->param('g')) {
     my $database           = $hub->database($cdb);
     my $genome_db          = $database->get_GenomeDBAdaptor->fetch_by_name_assembly($hub->species_defs->SPECIES_PRODUCTION_NAME);
 
     my $member             = $database->get_GeneMemberAdaptor->fetch_by_stable_id_GenomeDB($hub->core_params->{'g'}, $genome_db);
     my $adaptor            = $database->get_GeneTreeAdaptor;
-    my $gene_tree          = $adaptor->fetch_default_for_Member($member);
+    my $gene_tree          = $adaptor->fetch_default_for_Member($member, $consensus_clusterset_id);
+    $consensus_clusterset_id = $gene_tree->clusterset_id if $gene_tree->clusterset_id ne $consensus_clusterset_id;
     %other_clustersets     = map { $_->clusterset_id => 1 } @{$adaptor->fetch_all_linked_trees($gene_tree)};
 
-    delete $other_clustersets{'default'};
+    delete $other_clustersets{$consensus_clusterset_id};
   }
 
   if (my $dropdown = $form->get_elements_by_name('clusterset_id')->[0]) {
+    $self->_replace_default_clusterset_id_option($dropdown, $consensus_clusterset_id) if $consensus_clusterset_id ne 'default';
     $dropdown->add_option({ 'value' => $_, 'caption' => $_ }) for sort keys %other_clustersets;
   }
 
@@ -179,4 +187,13 @@ sub _groups {
   return (@{ $_[0]->species_defs->TAXON_ORDER });
 }
 
+sub _replace_default_clusterset_id_option {
+  my ($self, $cset_id_dropdown, $clusterset_id) = @_;
+
+  my $default_option = $cset_id_dropdown->get_elements_by_attribute({'value' => 'default'})->[0];
+  my $cset_id_option = $cset_id_dropdown->dom->create_element('option', {'value' => $clusterset_id, 'inner_HTML' => 'Final (merged) tree'});
+  $default_option->after($cset_id_option);
+  $cset_id_dropdown->remove_option('default');
+}
+
 1;