diff variant_effect_predictor/Bio/EnsEMBL/Compara/Method.pm @ 0:21066c0abaf5 draft

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author willmclaren
date Fri, 03 Aug 2012 10:04:48 -0400
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+++ b/variant_effect_predictor/Bio/EnsEMBL/Compara/Method.pm	Fri Aug 03 10:04:48 2012 -0400
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+=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>.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::Compara::Method
+
+=head1 SYNOPSIS
+
+    my $my_method       = Bio::EnsEMBL::Compara::Method->new( -type => 'FAMILY', -class => 'Family.family' );
+
+    $method_adaptor->store( $my_method );
+
+    my $dbID = $my_method->dbID();
+
+=head1 DESCRIPTION
+
+Method is a data object that roughly represents the type of pipeline run and the corresponding type of data generated.
+
+=head1 METHODS
+
+=cut
+
+
+package Bio::EnsEMBL::Compara::Method;
+
+use strict;
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+
+use base ('Bio::EnsEMBL::Storable');        # inherit dbID(), adaptor() and new() methods
+
+
+=head2 new
+
+  Arg [..]   : Takes a set of named arguments
+  Example    : my $my_method = Bio::EnsEMBL::Compara::Method->new(
+                                -dbID            => $dbID,
+                                -type            => 'SYNTENY',
+                                -class           => 'SyntenyRegion.synteny',
+                                -adaptor         => $method_adaptor );
+  Description: Creates a new Method object
+  Returntype : Bio::EnsEMBL::Compara::Method
+
+=cut
+
+
+sub new {
+    my $caller = shift @_;
+    my $class = ref($caller) || $caller;
+
+    my $self = $class->SUPER::new(@_);
+
+    my ($type, $mclass) =
+        rearrange([qw(TYPE CLASS)], @_);
+
+    $self->type($type)        if (defined ($type));
+    $self->class($mclass)     if (defined ($mclass));
+
+    return $self;
+}
+
+
+=head2 type
+
+  Arg [1]    : (opt.) string type
+  Example    : my $type = $method->type();
+  Example    : $method->type('BLASTZ_NET');
+  Description: Getter/Setter for the type of this method
+  Returntype : string type
+
+=cut
+
+sub type {
+    my $self = shift;
+
+    $self->{'_type'} = shift if(@_);
+
+    return $self->{'_type'};
+}
+
+
+=head2 class
+
+  Arg [1]    : (opt.) string class
+  Example    : my $class = $method->class();
+  Example    : $method->class('GenomicAlignBlock.pairwise_alignment');
+  Description: Getter/Setter for the class of this method
+  Returntype : string class
+
+=cut
+
+sub class {
+    my $self = shift;
+
+    $self->{'_class'} = shift if(@_);
+
+    return $self->{'_class'};
+}
+
+
+=head2 toString
+
+  Args       : (none)
+  Example    : print $method->toString()."\n";
+  Description: returns a stringified representation of the method
+  Returntype : string
+
+=cut
+
+sub toString {
+    my $self = shift;
+
+    return ref($self).": dbID=".($self->dbID || '?').", type='".$self->type."', class='".$self->class."'";
+}
+
+1;
+