diff variant_effect_predictor/Bio/EnsEMBL/Variation/Study.pm @ 0:1f6dce3d34e0

Uploaded

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+++ b/variant_effect_predictor/Bio/EnsEMBL/Variation/Study.pm	Thu Apr 11 02:01:53 2013 -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 <[e-mail]>.
+
+ Questions may also be sent to the Ensembl help desk at
+ <[e-mail]>.
+
+=cut
+
+# Ensembl module for Bio::EnsEMBL::Variation::Study
+#
+# Copyright (c) 2011 Ensembl
+#
+
+
+=head1 NAME
+
+Bio::EnsEMBL::Variation::Study - Ensembl representation of a study.
+
+=head1 SYNOPSIS
+
+    # Study
+		$study = Bio::EnsEMBL::Variation::Study->new
+       (-name => 'EGAS00000000001',
+        -external_reference   => 'pubmed/17554300',
+				-url => 'http://www.ebi.ac.uk/ega/page.php?page=study&study=EGAS00000000001&cat=www.wtccc.studies.xml.ega&subcat=BD'
+				);
+    ...
+
+
+=head1 DESCRIPTION
+
+This is a class representing a study from the ensembl-variation database.
+
+=head1 METHODS
+
+=cut
+
+use strict;
+use warnings;
+
+package Bio::EnsEMBL::Variation::Study;
+
+use Bio::EnsEMBL::Storable;
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+use Bio::EnsEMBL::Utils::Argument  qw(rearrange);
+
+our @ISA = ('Bio::EnsEMBL::Storable');
+
+
+=head2 new
+
+  Arg [-dbID] :
+    see superclass constructor
+  Arg [-ADAPTOR] :
+    see superclass constructor
+  Arg [-NAME] :
+    name of the study 
+  Arg [-DESCRIPTION] :
+    study description
+	Arg [-URL] :
+    string - url of the database/file where the data are stored
+	Arg [-EXTERNAL_REFERENCE] :
+    string - the pubmed/ids or project/study names
+	Arg [-TYPE] :
+    string - type of the study (e.g. GWAS)
+	Arg [-SOURCE] :
+    string - name of the source
+	Arg [-ASSOCIATE] :
+    array ref - list of the study objects associated with the current study
+			
+  Example    :
+		
+    $study = Bio::EnsEMBL::Variation::Study->new
+       (-name => 'EGAS00000000001',
+        -external_reference   => 'pubmed/17554300',
+				-url => 'http://www.ebi.ac.uk/ega/page.php?page=study&study=EGAS00000000001&cat=www.wtccc.studies.xml.ega&subcat=BD'
+				);
+
+  Description: Constructor. Instantiates a new Study object.
+  Returntype : Bio::EnsEMBL::Variation::Study
+  Exceptions : none
+  Caller     : general
+  Status     : At Risk
+
+=cut
+
+sub new {
+  my $caller = shift;
+  my $class = ref($caller) || $caller;
+
+  my $self = $class->SUPER::new(@_);
+	my ($dbID,$adaptor,$study_name,$study_description,$study_url,$external_reference,
+	    $study_type,$source_name,$associate) = 
+			rearrange([qw(dbID ADAPTOR NAME DESCRIPTION URL EXTERNAL_REFERENCE TYPE SOURCE ASSOCIATE)], @_);
+
+  $self = {
+			'dbID' => $dbID,
+			'adaptor' => $adaptor,
+  		'name' => $study_name,
+			'description' => $study_description,
+			'url' => $study_url,
+			'external_reference' => $external_reference,
+			'type' => $study_type,
+			'source' => $source_name,
+			'associate' => $associate
+	};
+	
+	return bless $self, $class;
+}
+
+
+=head2 name
+
+  Arg [1]    : string $newval (optional)
+               The new value to set the name attribute to
+  Example    : $name = $obj->name()
+  Description: Getter/Setter for the name attribute
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : At Risk
+
+=cut
+
+sub name{
+  my $self = shift;
+  return $self->{'name'} = shift if(@_);
+  return $self->{'name'};
+}
+
+
+=head2 description
+
+  Arg [1]    : string $newval (optional)
+               The new value to set the description attribute to
+  Example    : $name = $obj->description()
+  Description: Getter/Setter for the description attribute
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : At Risk
+
+=cut
+
+sub description{
+  my $self = shift;
+  return $self->{'description'} = shift if(@_);
+  return $self->{'description'};
+}
+
+
+=head2 url
+
+  Arg [1]    : string $newval (optional)
+               The new value to set the url attribute to
+  Example    : $name = $obj->url()
+  Description: Getter/Setter for the url attribute
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : At Risk
+
+=cut
+
+sub url{
+  my $self = shift;
+  return $self->{'url'} = shift if(@_);
+  return $self->{'url'};
+}
+
+
+=head2 external_reference
+
+  Arg [1]    : string $newval (optional)
+               The new value to set the external_reference attribute to
+  Example    : $name = $obj->external_reference()
+  Description: Getter/Setter for the external_reference attribute
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : At Risk
+
+=cut
+
+sub external_reference{
+  my $self = shift;
+  return $self->{'external_reference'} = shift if(@_);
+  return $self->{'external_reference'};
+}
+
+
+=head2 type
+
+  Arg [1]    : string $newval (optional)
+               The new value to set the type attribute to
+  Example    : $name = $obj->type()
+  Description: Getter/Setter for the type attribute
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : At Risk
+
+=cut
+
+sub type{
+  my $self = shift;
+  return $self->{'type'} = shift if(@_);
+  return $self->{'type'};
+}
+
+
+=head2 source
+
+  Arg [1]    : string $newval (optional)
+               The new value to set the source attribute to
+  Example    : $name = $obj->source()
+  Description: Getter/Setter for the source attribute
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : At Risk
+
+=cut
+
+sub source{
+  my $self = shift;
+  return $self->{'source'} = shift if(@_);
+  return $self->{'source'};
+}
+
+
+=head2 associated_studies
+  Example    : $name = $obj->associate_studies()
+  Description: Getter/Setter for the associated_studies attribute
+  Returntype : reference to list of Bio::EnsEMBL::Variation::Study
+  Exceptions : none
+  Caller     : general
+  Status     : At Risk
+
+=cut
+
+sub associated_studies{
+  my $self = shift;
+	
+	my $results;
+	
+  if (defined($self->{'associate'}) && defined($self->{'adaptor'})) {
+		my $studya = $self->{'adaptor'}->db()->get_StudyAdaptor();
+		return $studya->fetch_all_by_dbID_list($self->{'associate'});
+	}
+	else {
+  	return [];
+	}
+}