Mercurial > repos > willmclaren > ensembl_vep
diff variant_effect_predictor/Bio/EnsEMBL/Compara/MemberSet.pm @ 0:21066c0abaf5 draft
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| author | willmclaren |
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| date | Fri, 03 Aug 2012 10:04:48 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/variant_effect_predictor/Bio/EnsEMBL/Compara/MemberSet.pm Fri Aug 03 10:04:48 2012 -0400 @@ -0,0 +1,873 @@ +=head1 LICENSE + + Copyright (c) 1999-2012 The European Bioinformatics Institute and + Genome Research Limited. All rights reserved. + + This software is distributed under a modified Apache license. + For license details, please see + + http://www.ensembl.org/info/about/code_licence.html + +=head1 CONTACT + + Please email comments or questions to the public Ensembl + developers list at <dev@ensembl.org>. + + Questions may also be sent to the Ensembl help desk at + <helpdesk@ensembl.org>. + +=head1 AUTHORSHIP + +Ensembl Team. Individual contributions can be found in the CVS log. + +=cut + +=head1 NAME + +MemberSet - A superclass for pairwise or multiple relationships, base of +Bio::EnsEMBL::Compara::Family, Bio::EnsEMBL::Compara::Homology and +Bio::EnsEMBL::Compara::Domain. + +=head1 DESCRIPTION + +A superclass for pairwise and multiple relationships + +Currently the Member objects are used in the GeneTree structure +to represent the leaves of the trees. Each leaf contains an aligned +sequence, which is represented as an Member object. + +=head1 INHERITANCE TREE + + Bio::EnsEMBL::Compara::MemberSet + +=head1 METHODS + +=cut + +package Bio::EnsEMBL::Compara::MemberSet; + +use strict; +use Scalar::Util qw(weaken); +use Bio::EnsEMBL::Utils::Argument; +use Bio::EnsEMBL::Utils::Scalar qw(:all); +use Bio::EnsEMBL::Utils::Exception; +use Bio::EnsEMBL::Compara::Attribute; +use Bio::EnsEMBL::Compara::Member; + + +#################################### +# # +# Constructor, getters / setters # +# # +#################################### + + +=head2 new + + Arg [-DBID] : + int - internal ID for this object + Arg [-ADAPTOR]: + Bio::EnsEMBL::Compara::DBSQL::MemberSetAdaptor - the object adaptor + Arg [-STABLE_ID] : + string - the stable identifier of this object + Arg [-VERSION] : + int - the version of the stable identifier of this object + Arg [-METHOD_LINK_SPECIES_SET_ID] : + int - the internal ID for the MethodLinkSpeciesSet object + Arg [-DESCRIPTION]: + string - the description for the object + Example : $family = Bio::EnsEMBL::Compara::MemberSet->new(...); + Description: Creates a new MemberSet object + Returntype : Bio::EnsEMBL::Compara::MemberSet + Exceptions : none + Caller : subclass->new + Status : Stable + +=cut + +sub new { + my ($class, @args) = @_; + + my $self = bless {}, $class; + + if (scalar @args) { + #do this explicitly. + my ($dbid, $stable_id, $version, $method_link_species_set_id, $description, $adaptor) + = rearrange([qw(DBID STABLE_ID VERSION METHOD_LINK_SPECIES_SET_ID DESCRIPTION ADAPTOR)], @args); + + $dbid && $self->dbID($dbid); + $stable_id && $self->stable_id($stable_id); + $version && $self->version($version); + $description && $self->description($description); + $method_link_species_set_id && $self->method_link_species_set_id($method_link_species_set_id); + $adaptor && $self->adaptor($adaptor); + } + + return $self; +} + +=head2 new_fast + + Arg [1] : hash reference $hashref + Example : none + Description: This is an ultra fast constructor which requires knowledge of + the objects internals to be used. + Returntype : + Exceptions : none + Caller : + Status : Stable + +=cut + +sub new_fast { + my ($class, $hashref) = @_; + + return bless $hashref, $class; +} + +=head2 dbID + + Arg [1] : int $dbID (optional) + Example : + Description: Getter/setter for the internal ID of this relation + Returntype : int + Exceptions : none + Caller : general + Status : Stable + +=cut + +sub dbID { + my $self = shift; + $self->{'_dbID'} = shift if(@_); + return $self->{'_dbID'}; +} + +=head2 stable_id + + Arg [1] : string $stable_id (optional) + Example : + Description: Getter/setter for the stable ID of this relation + Returntype : string + Exceptions : none + Caller : general + Status : Stable + +=cut + +sub stable_id { + my $self = shift; + $self->{'_stable_id'} = shift if(@_); + return $self->{'_stable_id'}; +} + +=head2 version + + Arg [1] : string $version (optional) + Example : + Description: Getter/setter for the version number of the stable ID + Returntype : int + Exceptions : none + Caller : general + Status : Stable + +=cut + +sub version { + my $self = shift; + $self->{'_version'} = shift if(@_); + return $self->{'_version'}; +} + +=head2 description + + Arg [1] : string $description (optional) + Example : + Description: Getter/setter for the description corresponding to this relation + Returntype : string + Exceptions : none + Caller : general + Status : Stable + +=cut + +sub description { + my $self = shift; + $self->{'_description'} = shift if(@_); + return $self->{'_description'}; +} + +=head2 method_link_species_set + + Arg [1] : MethodLinkSpeciesSet object (optional) + Example : + Description: getter/setter method for the MethodLinkSpeciesSet for this relation. + Can lazy-load the method_link_species_set from the method_link_species_set_id + if that one is set and the adaptor is set. + Returntype : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet + Exceptions : throws if setting to an unsuitable object + Caller : general + Status : Stable + +=cut + +sub method_link_species_set { + my $self = shift; + + if(@_) { + my $mlss = shift; + assert_ref($mlss, 'Bio::EnsEMBL::Compara::MethodLinkSpeciesSet'); + $self->{'_method_link_species_set'} = $mlss; + $self->{'_method_link_species_set_id'} = $mlss->dbID; + + } elsif (defined $self->{'_method_link_species_set_id'}) { + #lazy load from method_link_species_set_id + if ((not defined $self->{'_method_link_species_set'}) + or ($self->{'_method_link_species_set'}->dbID ne $self->{'_method_link_species_set_id'})) { + my $mlssa = $self->adaptor->db->get_MethodLinkSpeciesSetAdaptor; + my $mlss = $mlssa->fetch_by_dbID($self->method_link_species_set_id); + $self->{'_method_link_species_set'} = $mlss; + } + } + + return $self->{'_method_link_species_set'}; +} + +=head2 method_link_species_set_id + + Arg [1] : integer (optional) + Example : + Description: getter/setter method for the internal ID of the MethodLinkSpeciesSet + for this relation. + Returntype : integer + Exceptions : none + Caller : general + Status : Stable + +=cut + +sub method_link_species_set_id { + my $self = shift; + + $self->{'_method_link_species_set_id'} = shift if (@_); + return $self->{'_method_link_species_set_id'}; +} + +=head2 method_link_type + + DEPRECATED. Use method_link_species_set()->method()->type() instead. This is not a setter any more. + +=cut + +sub method_link_type { # DEPRECATED + my $self = shift; + deprecate('Use method_link_species_set()->method()->type() instead. This is not a setter any more.'); + return $self->method_link_species_set->method->type() if defined $self->{'_method_link_species_set_id'}; +} + + +=head2 method_link_id + + DEPRECATED. Use method_link_species_set()->method()->dbID() instead. This is not a setter any more. + +=cut + +sub method_link_id { # DEPRECATED + my $self = shift; + deprecate('Use method_link_species_set()->method()->dbID() instead. This is not a setter any more.'); + return $self->method_link_species_set->method->dbID if defined $self->{'_method_link_species_set_id'}; +} + +=head2 adaptor + + Arg [1] : string $adaptor (optional) + corresponding to a perl module + Example : + Description: getter/setter method for the adaptor for this relation. Usually + this will be either GeneTreeAdaptor, FamilyAdaptor, or + HomologyAdaptor + Returntype : Bio::EnsEMBL::Compara::DBSQL::BaseAdaptor object + Exceptions : none + Caller : general + Status : Stable + +=cut + +sub adaptor { + my $self = shift; + $self->{'_adaptor'} = shift if(@_); + return $self->{'_adaptor'}; +} + + + +########################### +# # +# Member content # +# # +########################### + +=head2 member_class + + Description: Returns the type of member used in the set + Returntype : String: Bio::EnsEMBL::Compara::Member + Caller : general + Status : Stable + +=cut + +sub member_class { + return 'Bio::EnsEMBL::Compara::Member'; +} + + +=head2 deep_copy + + Description: Returns a copy of $self. All the members are themselves copied + Returntype : Bio::EnsEMBL::Compara::MemberSet + Caller : general + Status : Stable + +=cut + +sub deep_copy { + my $self = shift; + my $copy = {}; + bless $copy, ref($self); + + foreach my $attr (qw(_dbID _adaptor _version _stable_id _description _method_link_species_set_id)) { + $copy->{$attr} = $self->{$attr}; + } + + foreach my $member (@{$self->get_all_Members}) { + $copy->add_Member($member->copy()); + } + + return $copy; +} + + +=head2 add_Member + + Arg [1] : Member + Example : + Description: Add a new Member to this set + Returntype : none + Exceptions : Throws if input objects don't check + Caller : general + Status : Stable + +=cut + +sub add_Member { + my ($self, $member) = @_; + + assert_ref($member, $self->member_class); + my $source_name = $member->source_name(); + my $taxon_id = $member->taxon_id(); + my $genome_db_id = $member->genome_db_id(); + #print "adding $source_name: ", $member->dbID, "\n"; + + if (defined $self->{'_this_one_first'} && $self->{'_this_one_first'} eq $member->stable_id) { + unshift @{$self->{'_member_array'}}, $member ; + unshift @{$self->{'_members_by_source'}{$source_name}}, $member; + unshift @{$self->{'_members_by_source_taxon'}{"${source_name}_${taxon_id}"}}, $member; + if(defined $genome_db_id) { + unshift @{$self->{_members_by_source_genome_db}{"${source_name}_${genome_db_id}"}}, $member; + unshift @{$self->{_members_by_genome_db}{$genome_db_id}}, $member; + } + } else { + push @{$self->{'_member_array'}}, $member ; + push @{$self->{'_members_by_source'}{$source_name}}, $member; + push @{$self->{'_members_by_source_taxon'}{"${source_name}_${taxon_id}"}}, $member; + if(defined $genome_db_id) { + push @{$self->{_members_by_source_genome_db}{"${source_name}_${genome_db_id}"}}, $member; + push @{$self->{_members_by_genome_db}{$genome_db_id}}, $member; + } + } + + $member->{'set'} = $self; + weaken($member->{'set'}); +} + +sub add_Member_Attribute { # DEPRECATED + my ($self, $member_attribute) = @_; + my ($member, $attr) = @{$member_attribute}; + + my $am = Bio::EnsEMBL::Compara::Member::copy($member); + bless $am, $self->member_class; + foreach my $key (keys %Bio::EnsEMBL::Compara::Attribute::ok_field) { + $am->$key($attr->$key) if defined $attr->key; + } + $self->add_Member($am); +} + + +sub _tranform_array_to_Member_Attributes { + my ($self, $array) = @_; + my @all_ma; + foreach my $member (@$array) { + my $attribute = new Bio::EnsEMBL::Compara::Attribute; + foreach my $key (keys %Bio::EnsEMBL::Compara::Attribute::ok_field) { + $attribute->$key($member->can($key) ? $member->$key : undef); + } + push @all_ma, [$member, $attribute]; + } + return \@all_ma; +} + + +=head2 get_all_Members + + Arg [1] : None + Example : + Description: + Returntype : array reference of Bio::EnsEMBL::Compara::Member + Exceptions : + Caller : + +=cut + +sub get_all_Members { + my ($self) = @_; + + unless (defined $self->{'_member_array'}) { + + my $am_adaptor = $self->adaptor->db->get_MemberAdaptor(); + my $members = $am_adaptor->fetch_all_by_MemberSet($self); + + $self->{'_member_array'} = []; + $self->{'_members_by_source'} = {}; + $self->{'_members_by_source_taxon'} = {}; + $self->{'_members_by_source_genome_db'} = {}; + $self->{'_members_by_genome_db'} = {}; + foreach my $member (@{$members}) { + $self->add_Member($member); + } + } + return $self->{'_member_array'}; +} + + + +=head2 get_all_GeneMember + + Arg [1] : None + Example : + Description: + Returntype : array reference of Bio::EnsEMBL::Compara::Member + Exceptions : + Caller : public + +=cut + +sub get_all_GeneMembers { + my ($self) = @_; + + my $members = []; + foreach my $aligned_member (@{$self->get_all_Members}) { + push @$members, $aligned_member->gene_member if defined $aligned_member->gene_member; + } + + return $members; +} +=head2 gene_list + + Example : my $pair = $homology->gene_list + Description: return the pair of members for the homology + Returntype : array ref of (2) Bio::EnsEMBL::Compara::Member objects + Caller : general + +=cut + + +sub gene_list { # DEPRECATED + my $self = shift; + return $self->get_all_GeneMembers +} + + +sub get_all_Member_Attribute { # DEPRECATED + my $self = shift; + return $self->_tranform_array_to_Member_Attributes($self->get_all_Members); +} + + +################################# +# # +# Members per category # +# # +################################# + +=head2 get_Member_by_source + + Arg [1] : string $source_name + e.g. "ENSEMBLPEP" + Example : + Description: + Returntype : array reference of Bio::EnsEMBL::Compara::Member + Exceptions : + Caller : public + +=cut + +sub get_Member_by_source { + my ($self, $source_name) = @_; + throw("Should give defined source_name as arguments\n") unless (defined $source_name); + my ($scope, $key) = ('_members_by_source', $source_name); + return $self->_get_Member($scope, $key); +} + +=head2 get_Member_by_source_taxon + + Arg [1] : string $source_name + Arg [2] : int $taxon_id + Example : $domain->get_Member_by_source_taxon('ENSEMBLPEP',9606) + Description: + Returntype : array reference of Bio::EnsEMBL::Compara::Member + Exceptions : + Caller : public + +=cut + +sub get_Member_by_source_taxon { + my ($self, $source_name, $taxon_id) = @_; + throw("Should give defined source_name and taxon_id as arguments\n") unless (defined $source_name && defined $taxon_id); + my ($scope, $key) = ('_members_by_source_taxon', "${source_name}_${taxon_id}"); + return $self->_get_Member($scope, $key); +} + +=head2 get_Member_by_GenomeDB + + Arg [1] : Bio::EnsEMBL::Compara::GenomeDB $genome_db + Example : $domain->get_Member_by_GenomeDB($genome_db) + Description: Returns all [Member] entries linked to this GenomeDB. + This will only return EnsEMBL based entries since UniProtKB + entries are not linked to a GenomeDB. + Returntype : array reference of Bio::EnsEMBL::Compara::Member + Exceptions : If input is undefined & genome db is not of expected type + Caller : public + +=cut + +sub get_Member_by_GenomeDB { + my ($self, $genome_db) = @_; + throw("Should give defined genome_db as an argument\n") unless defined $genome_db; + assert_ref($genome_db, 'Bio::EnsEMBL::Compara::GenomeDB'); + my ($scope, $key) = ('_members_by_genome_db', $genome_db->dbID()); + return $self->_get_Member($scope, $key); +} + +=head2 get_Member_by_source_GenomeDB + + Arg [1] : string $source_name + Arg [2] : Bio::EnsEMBL::Compara::GenomeDB $genome_db + Example : $domain->get_Member_by_source_taxon('ENSEMBLPEP', $genome_db) + Description: Returns all [Member] entries linked to this GenomeDB + and the given source_name. This will only return EnsEMBL based + entries since UniProtKB entries are not linked to a GenomeDB. + Returntype : array reference of Bio::EnsEMBL::Compara::Member + Exceptions : If input is undefined & genome db is not of expected type + Caller : public + +=cut + +sub get_Member_by_source_GenomeDB { + my ($self, $source_name, $genome_db) = @_; + throw("Should give defined source_name & genome_db as arguments\n") unless defined $source_name && $genome_db; + assert_ref($genome_db, 'Bio::EnsEMBL::Compara::GenomeDB'); + my ($scope, $key) = ('_members_by_source_genome_db', "${source_name}_".$genome_db->dbID()); + return $self->_get_Member($scope, $key); +} + +=head2 _get_Member + + Arg [1] : string $scope + Arg [2] : string $key + Example : $domain->_get_Member('_members_by_source', 'ENSEMBLPEP') + Description: Used as the generic reference point for all + get_Memeber_by* methods. The method searches the given + scope & if the values cannot be found will initalize that value + to an empty array reference. + Returntype : array reference of Bio::EnsEMBL::Compara::Member + Exceptions : None. + Caller : internal + +=cut + +sub _get_Member { + my ($self, $scope, $key) = @_; + $self->get_all_Members(); + $self->{$scope}->{$key} = [] unless defined $self->{$scope}->{$key}; + return $self->{$scope}->{$key}; +} + + +=head2 get_Member_Attribute_by_source + + Arg [1] : string $source_name + e.g. "ENSEMBLPEP" + Example : + Description: + Returntype : array reference of Bio::EnsEMBL::Compara::Member and attribute + Exceptions : + Caller : public + +=cut + +sub get_Member_Attribute_by_source { # DEPRECATED + my ($self, $source_name) = @_; + throw("Should give defined source_name as arguments\n") unless (defined $source_name); + my ($attribute_scope, $key) = ('_members_by_source', $source_name); + return $self->_get_Member_Attribute($attribute_scope, $key); +} + +=head2 get_Member_Attribute_by_source_taxon + + Arg [1] : string $source_name + Arg [2] : int $taxon_id + Example : $domain->get_Member_by_source_taxon('ENSEMBLPEP',9606) + Description: + Returntype : array reference of Bio::EnsEMBL::Compara::Member + Exceptions : + Caller : public + +=cut + +sub get_Member_Attribute_by_source_taxon { # DEPRECATED + my ($self, $source_name, $taxon_id) = @_; + throw("Should give defined source_name and taxon_id as arguments\n") unless (defined $source_name && defined $taxon_id); + my ($attribute_scope, $key) = ('_members_by_source_taxon', "${source_name}_${taxon_id}"); + return $self->_get_Member_Attribute($attribute_scope, $key); +} + +=head2 get_Member_Attribute_by_GenomeDB + + Arg [1] : Bio::EnsEMBL::Compara::GenomeDB $genome_db + Example : $domain->get_Member_Attribute_by_GenomeDB($genome_db) + Description: Returns all [Member_Attribute] entries linked to this GenomeDB. + This will only return EnsEMBL based entries since UniProtKB + entries are not linked to a GenomeDB. + Returntype : array reference of Bio::EnsEMBL::Compara::Member + Exceptions : If input is undefined & genome db is not of expected type + Caller : public + +=cut + +sub get_Member_Attribute_by_GenomeDB { # DEPRECATED + my ($self, $genome_db) = @_; + throw("Should give defined genome_db as an argument\n") unless defined $genome_db; + assert_ref($genome_db, 'Bio::EnsEMBL::Compara::GenomeDB'); + my ($attribute_scope, $key) = ('_members_by_genome_db', $genome_db->dbID()); + return $self->_get_Member_Attribute($attribute_scope, $key); +} + +=head2 get_Member_Attribute_by_source_GenomeDB + + Arg [1] : string $source_name + Arg [2] : Bio::EnsEMBL::Compara::GenomeDB $genome_db + Example : $domain->get_Member_by_source_taxon('ENSEMBLPEP', $genome_db) + Description: Returns all [Member_Attribute] entries linked to this GenomeDB + and the given source_name. This will only return EnsEMBL based + entries since UniProtKB entries are not linked to a GenomeDB. + Returntype : array reference of Bio::EnsEMBL::Compara::Member + Exceptions : If input is undefined & genome db is not of expected type + Caller : public + +=cut + +sub get_Member_Attribute_by_source_GenomeDB { # DEPRECATED + my ($self, $source_name, $genome_db) = @_; + throw("Should give defined source_name & genome_db as arguments\n") unless defined $source_name && $genome_db; + assert_ref($genome_db, 'Bio::EnsEMBL::Compara::GenomeDB'); + my ($attribute_scope, $key) = ('_members_by_source_genome_db', "${source_name}_".$genome_db->dbID()); + return $self->_get_Member_Attribute($attribute_scope, $key); +} + +=head2 _get_Member_Attribute + + Arg [1] : string $attribute_scope + Arg [2] : string $key + Example : $domain->_get_Member_Attribute('_members_by_source', 'ENSEMBLPEP') + Description: Used as the generic reference point for all + get_Memeber_Attribute_by* methods. The method searches the given + scope & if the values cannot be found will initalize that value + to an empty array reference. + Returntype : array reference of Bio::EnsEMBL::Compara::Member + Exceptions : None. + Caller : internal + +=cut + +sub _get_Member_Attribute { # DEPRECATED + my ($self, $attribute_scope, $key) = @_; + $self->get_all_Member_Attribute(); + $self->{$attribute_scope}->{$key} = [] unless defined $self->{$attribute_scope}->{$key}; + return $self->_tranform_array_to_Member_Attributes($self->{$attribute_scope}->{$key}); +} + + + + + +=head2 Member_count_by_source + + Arg [1] : string $source_name + e.g. "ENSEMBLPEP" + Example : $domain->Member_count_by_source('ENSEMBLPEP'); + Description: + Returntype : int + Exceptions : + Caller : public + +=cut + +sub Member_count_by_source { + my ($self, $source_name) = @_; + + throw("Should give a defined source_name as argument\n") unless (defined $source_name); + + return scalar @{$self->get_Member_by_source($source_name)}; +} + +=head2 Member_count_by_source_taxon + + Arg [1] : string $source_name + Arg [2] : int $taxon_id + Example : Member_count_by_source_taxon('ENSEMBLPEP',9606); + Description: + Returntype : int + Exceptions : + Caller : public + +=cut + +sub Member_count_by_source_taxon { + my ($self, $source_name, $taxon_id) = @_; + + throw("Should give defined source_name and taxon_id as arguments\n") unless (defined $source_name && defined $taxon_id); + + return scalar @{$self->get_Member_by_source_taxon($source_name,$taxon_id)}; +} + +=head2 Member_count_by_GenomeDB + + Arg [1] : Bio::EnsEMBL::Compara::GenomeDB $genome_db + Example : Member_count_by_GenomeDB($genome_db); + Description: Convenience wrapper for member counts by a GenomeDB + Returntype : int + Exceptions : Thrown by subrountines this call. See get_Member + equivalent + Caller : public + +=cut + +sub Member_count_by_GenomeDB { + my ($self, $genome_db) = @_; + return scalar @{$self->get_Member_by_GenomeDB($genome_db)}; +} + +=head2 Member_count_by_source_GenomeDB + + Arg [1] : string $source_name + Arg [2] : Bio::EnsEMBL::Compara::GenomeDB $genome_db + Example : Member_count_by_source_GenomeDB('ENSEMBLPEP', $genome_db); + Description: Convenience wrapper for member counts by a GenomeDB + Returntype : int + Exceptions : Thrown by subrountines this call. See get_Member + equivalent + Caller : public + +=cut + + +sub Member_count_by_source_GenomeDB { + my ($self, $source_name, $genome_db) = @_; + return scalar @{$self->get_Member_by_source_GenomeDB($source_name, $genome_db)}; +} + + +=head2 get_all_taxa_by_member_source_name + + Arg [1] : string $source_name + e.g. "ENSEMBLPEP" + Example : + Description: Returns the distinct taxons found in this family across + the specified source. If you do not specify a source then + the code will return all taxons in this family. + Returntype : array reference of distinct Bio::EnsEMBL::Compara::NCBITaxon + objects found in this family + Exceptions : + Caller : public + +=cut + +sub get_all_taxa_by_member_source_name { + my ($self, $source_name) = @_; + + my $ncbi_ta = $self->adaptor->db->get_NCBITaxonAdaptor(); + my @taxa; + $self->get_all_Members; + foreach my $key (keys %{$self->{_members_by_source_taxon}}) { + my @parts = split('_', $key); + if ($parts[0] eq $source_name) { + push @taxa, $ncbi_ta->fetch_node_by_taxon_id($parts[1]); + } + } + return \@taxa; +} + +=head2 get_all_GenomeDBs_by_member_source_name + + Arg [1] : string $source_name + e.g. "ENSEMBLPEP" + Example : + Description: Returns the distinct GenomeDBs found in this family. Please note + that if you specify a source other than an EnsEMBL based one + the chances of getting back GenomeDBs are very low. + Returntype : array reference of distinct Bio::EnsEMBL::Compara::GenomeDB + objects found in this family + Exceptions : + Caller : public + +=cut + +sub get_all_GenomeDBs_by_member_source_name { + my ($self, $source_name) = @_; + + my $gdb_a = $self->adaptor->db->get_GenomeDBAdaptor(); + my @gdbs; + $self->get_all_Members; + foreach my $key (keys %{$self->{_members_by_source_genome_db}}) { + my @parts = split('_', $key); + if ($parts[0] eq $source_name) { + push @gdbs, $gdb_a->fetch_by_dbID($parts[1]); + } + } + return \@gdbs; +} + +=head2 has_species_by_name + + Arg [1] : string $species_name + Example : my $ret = $homology->has_species_by_name("Homo sapiens"); + Description: return TRUE or FALSE whether one of the members in the homology is from the given species + Returntype : 1 or 0 + Exceptions : + Caller : + +=cut + + +sub has_species_by_name { + my $self = shift; + my $species_name = shift; + + foreach my $member (@{$self->get_all_Members}) { + return 1 if defined $member->genome_db and ($member->genome_db->name eq $species_name); + } + return 0; +} + + +1;