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revision 1.66, Mon Aug 18 20:25:42 2008 UTC revision 1.67, Wed Aug 20 17:06:47 2008 UTC
# Line 319  Line 319 
319  =cut  =cut
320    
321  sub get_objects {  sub get_objects {
322      my ($self,$fid,$fig,$scope) = @_;      my ($self,$fid,$fig,$parameters,$scope) = @_;
323    
324      my $objects = [];      my $objects = [];
325      my @matched_datasets=();      my @matched_datasets=();
# Line 337  Line 337 
337          $domain_classes{'PFAM'} = 1;          $domain_classes{'PFAM'} = 1;
338          get_identical_proteins($fid,\@matched_datasets,$fig);          get_identical_proteins($fid,\@matched_datasets,$fig);
339          get_attribute_based_domain_observations($fid,\%domain_classes,\@matched_datasets,\@attributes,$fig);          get_attribute_based_domain_observations($fid,\%domain_classes,\@matched_datasets,\@attributes,$fig);
340          get_sims_observations($fid,\@matched_datasets,$fig);          get_sims_observations($fid,\@matched_datasets,$fig,$parameters);
341          get_functional_coupling($fid,\@matched_datasets,$fig);          get_functional_coupling($fid,\@matched_datasets,$fig);
342          get_attribute_based_location_observations($fid,\@matched_datasets,\@attributes,$fig);          get_attribute_based_location_observations($fid,\@matched_datasets,\@attributes,$fig);
343          get_pdb_observations($fid,\@matched_datasets,\@attributes,$fig);          get_pdb_observations($fid,\@matched_datasets,\@attributes,$fig);
# Line 711  Line 711 
711      my ($fid,$datasets_ref,$fig,$parameters) = (@_);      my ($fid,$datasets_ref,$fig,$parameters) = (@_);
712    
713      my ($max_sims, $max_expand, $max_eval, $sim_order, $db_filter, $sim_filters);      my ($max_sims, $max_expand, $max_eval, $sim_order, $db_filter, $sim_filters);
714      if ($parameters->{flag}){      if ( (defined $parameters->{flag}) && ($parameters->{flag})){
715        $max_sims = $parameters->{max_sims};        $max_sims = $parameters->{max_sims};
716        $max_expand = $parameters->{max_expand};        $max_expand = $parameters->{max_expand};
717        $max_eval = $parameters->{max_eval};        $max_eval = $parameters->{max_eval};
# Line 720  Line 720 
720        #$sim_order = $parameters->{sim_order};        #$sim_order = $parameters->{sim_order};
721        $group_by_genome = 1 if (defined ($parameters->{group_genome}));        $group_by_genome = 1 if (defined ($parameters->{group_genome}));
722      }      }
723        elsif ( (defined $parameters->{sims_db}) && ($parameters->{sims_db} eq 'all')){
724          $max_sims = 50;
725          $max_expand = 5;
726          $max_eval = 1e-5;
727          $db_filter = "all";
728          $sim_filters->{ sort_by } = 'id';
729        }
730      else{      else{
731        $max_sims = 50;        $max_sims = 50;
732        $max_expand = 5;        $max_expand = 5;

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