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1 package Bio::EnsEMBL::Compara::SpeciesSet;
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2
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3 use strict;
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4
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5 use Bio::EnsEMBL::Utils::Exception qw(warning deprecate throw);
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6 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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7
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8 # FIXME: add throw not implemented for those not tag related?
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9 use base ( 'Bio::EnsEMBL::Storable', # inherit dbID(), adaptor() and new() methods
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10 'Bio::EnsEMBL::Compara::Taggable' # inherit everything related to tagability
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11 );
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12
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13
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14 =head2 new
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15
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16 Arg [..] : Takes a set of named arguments
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17 Example : my $my_species_set = Bio::EnsEMBL::Compara::SpeciesSet->new(
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18 -dbID => $species_set_id,
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19 -genome_dbs => [$gdb1, $gdb2, $gdb3 ],
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20 -adaptor => $species_set_adaptor );
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21 Description: Creates a new SpeciesSet object
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22 Returntype : Bio::EnsEMBL::Compara::SpeciesSet
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23
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24 =cut
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25
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26 sub new {
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27 my $caller = shift @_;
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28 my $class = ref($caller) || $caller;
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29
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30 my $self = $class->SUPER::new(@_); # deal with Storable stuff
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31
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32 my ($genome_dbs) = rearrange([qw(GENOME_DBS)], @_);
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33
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34 $self->genome_dbs($genome_dbs) if (defined ($genome_dbs));
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35
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36 return $self;
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37 }
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38
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39
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40 =head2 genome_dbs
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41
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42 Arg [1] : (opt.) list of genome_db objects
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43 Example : my $genome_dbs = $species_set->genome_dbs();
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44 Example : $species_set->genome_dbs( [$gdb1, $gdb2, $gdb3] );
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45 Description: Getter/Setter for the genome_dbs of this object in the database
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46 Returntype : arrayref genome_dbs
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47 Exceptions : none
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48 Caller : general
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49
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50 =cut
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51
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52 sub genome_dbs {
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53 my ($self, $arg) = @_;
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54
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55 if (defined $arg) {
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56 ## Check content
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57 my $genome_dbs = {};
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58 foreach my $gdb (@$arg) {
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59 throw("undefined value used as a Bio::EnsEMBL::Compara::GenomeDB\n")
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60 if (!defined($gdb));
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61 throw("$gdb must be a Bio::EnsEMBL::Compara::GenomeDB\n")
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62 unless UNIVERSAL::isa($gdb, "Bio::EnsEMBL::Compara::GenomeDB");
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63
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64 unless (defined $genome_dbs->{$gdb->dbID}) {
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65 $genome_dbs->{$gdb->dbID} = $gdb;
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66 } else {
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67 warn("GenomeDB (".$gdb->name."; dbID=".$gdb->dbID .
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68 ") appears twice in this Bio::EnsEMBL::Compara::SpeciesSet\n");
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69 }
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70 }
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71 $self->{'genome_dbs'} = [ values %{$genome_dbs} ] ;
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72 }
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73 return $self->{'genome_dbs'};
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74 }
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75
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76
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77 =head2 toString
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78
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79 Args : (none)
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80 Example : print $species_set->toString()."\n";
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81 Description: returns a stringified representation of the species_set
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82 Returntype : string
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83
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84 =cut
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85
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86 sub toString {
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87 my $self = shift;
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88
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89 my $name = $self->get_tagvalue('name');
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90 return ref($self).": dbID=".($self->dbID || '?').", name='".($name || '?')."', genome_dbs=[".join(', ', map { $_->name.'('.($_->dbID || '?').')'} @{ $self->genome_dbs })."]";
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91 }
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92
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93
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94
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95 1;
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96
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