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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =cut
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20
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21 =head1 NAME
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22
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23 Bio::EnsEMBL::Compara::Method
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24
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25 =head1 SYNOPSIS
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26
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27 my $my_method = Bio::EnsEMBL::Compara::Method->new( -type => 'FAMILY', -class => 'Family.family' );
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28
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29 $method_adaptor->store( $my_method );
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30
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31 my $dbID = $my_method->dbID();
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32
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33 =head1 DESCRIPTION
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34
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35 Method is a data object that roughly represents the type of pipeline run and the corresponding type of data generated.
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36
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37 =head1 METHODS
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38
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39 =cut
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40
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41
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42 package Bio::EnsEMBL::Compara::Method;
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43
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44 use strict;
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45 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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46
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47 use base ('Bio::EnsEMBL::Storable'); # inherit dbID(), adaptor() and new() methods
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48
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49
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50 =head2 new
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51
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52 Arg [..] : Takes a set of named arguments
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53 Example : my $my_method = Bio::EnsEMBL::Compara::Method->new(
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54 -dbID => $dbID,
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55 -type => 'SYNTENY',
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56 -class => 'SyntenyRegion.synteny',
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57 -adaptor => $method_adaptor );
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58 Description: Creates a new Method object
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59 Returntype : Bio::EnsEMBL::Compara::Method
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60
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61 =cut
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62
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63
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64 sub new {
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65 my $caller = shift @_;
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66 my $class = ref($caller) || $caller;
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67
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68 my $self = $class->SUPER::new(@_);
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69
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70 my ($type, $mclass) =
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71 rearrange([qw(TYPE CLASS)], @_);
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72
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73 $self->type($type) if (defined ($type));
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74 $self->class($mclass) if (defined ($mclass));
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75
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76 return $self;
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77 }
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78
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79
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80 =head2 type
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81
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82 Arg [1] : (opt.) string type
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83 Example : my $type = $method->type();
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84 Example : $method->type('BLASTZ_NET');
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85 Description: Getter/Setter for the type of this method
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86 Returntype : string type
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87
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88 =cut
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89
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90 sub type {
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91 my $self = shift;
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92
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93 $self->{'_type'} = shift if(@_);
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94
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95 return $self->{'_type'};
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96 }
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97
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98
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99 =head2 class
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100
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101 Arg [1] : (opt.) string class
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102 Example : my $class = $method->class();
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103 Example : $method->class('GenomicAlignBlock.pairwise_alignment');
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104 Description: Getter/Setter for the class of this method
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105 Returntype : string class
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106
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107 =cut
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108
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109 sub class {
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110 my $self = shift;
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111
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112 $self->{'_class'} = shift if(@_);
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113
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114 return $self->{'_class'};
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115 }
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116
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117
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118 =head2 toString
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119
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120 Args : (none)
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121 Example : print $method->toString()."\n";
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122 Description: returns a stringified representation of the method
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123 Returntype : string
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124
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125 =cut
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126
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127 sub toString {
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128 my $self = shift;
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129
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130 return ref($self).": dbID=".($self->dbID || '?').", type='".$self->type."', class='".$self->class."'";
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131 }
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132
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133 1;
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134
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