Raw content of Bio::EnsEMBL::ExternalData::Expression::Library
<![CDATA[
#
# EnsEMBL module for Bio::EnsEMBL::ExternalData::Expression::Library
#
# Cared for by EnsEMBL (www.ensembl.org)
#
# Copyright GRL and EBI
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::EnsEMBL::ExternalData::Expression::Library
=head1 SYNOPSIS
my $dbname='expression';
my $lib_ad=Bio::EnsEMBL::ExternalData::Expression::LibraryAdaptor->new($obj);
$lib_ad->dbname($dbname);
my @libs=$lib_ad->fetch_by_SeqTag_Synonym("ENSG00000080561");
foreach my $lib (@libs){
print $lib->id,"\t",$lib->name,"\t",$lib->total_seqtags,"\n";
}
=head1 DESCRIPTION
Represents information on one Clone
=head1 CONTACT
Describe contact details here
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::EnsEMBL::ExternalData::Expression::Library;
use vars qw(@ISA);
use strict;
# Object preamble
use Bio::EnsEMBL::Root;
@ISA = qw(Bio::EnsEMBL::Root);
=head2 new
Title : new
Usage :
Function:
Example :
Returns : Library object
Args :
=cut
sub new {
my ($class,$adaptor,@args) = @_;
my $self = {};
bless $self,$class;
$self->adaptor($adaptor);
$self->_set_from_args(@args);
return $self;
}
=head2 fetch_SeqTag_by_dbID
Title : fetch_SeqTag_by_dbID
Usage : $obj->fetch_SeqTag_by_dbID
Function:
Example :
Returns : seqtag object
Args :
=cut
sub fetch_SeqTag_by_dbID {
my ($self,$id)=@_;
$self->throw ("need a seqtag id") unless $id;
return $self->adaptor->fetch_SeqTag_by_dbID($self->id,$id);
}
=head2 fetch_SeqTag_by_Name
Title : fetch_SeqTag_by_Name
Usage : $obj->fetch_SeqTag_by_Name
Function:
Example :
Returns : an array of seqtag objects
Args :
=cut
sub fetch_SeqTag_by_Name {
my ($self,$synonym)=@_;
$self->throw ("need a seqtag name") unless $synonym;
return $self->adaptor->fetch_SeqTag_by_Name($self->id,$synonym);
}
=head2 fetch_all_SeqTags
Title : fetch_all_SeqTags
Usage : $obj->fetch_all_SeqTags
Function:
Example :
Returns : array of seqtags objects
Args :
=cut
sub fetch_all_SeqTags {
my ($self)=shift;
return $self->adaptor->fetch_all_SeqTags($self->id);
}
=head2 fetch_all_SeqTags_above_frequency
Title : fetch_all_SeqTags_above_frequency
Usage : $obj->fetch_all_SeqTags_above_frequency
Function: returns seqtags with expression above given level
Example :
Returns : array of seqtags objects
Args :
=cut
sub fetch_all_SeqTags_above_frequency {
my ($self,$frequency)=@_;
return $self->adaptor->fetch_all_SeqTags_above_frequency($self->id,$frequency);
}
=head2 fetch_all_SeqTags_above_relative_frequency
Title : fetch_all_SeqTags_above_relative_frequency
Usage : $obj->fetch_all_SeqTags_above_realtive_frequency
Function: returns seqtags with expression above given level
Example :
Returns : array of seqtags objects
Args :
=cut
sub fetch_all_SeqTags_above_relative_frequency {
my ($self,$frequency,$multiplier)=@_;
return $self->adaptor->fetch_all_SeqTags_above_relative_frequency($self->id,$frequency,$multiplier);
}
=head2 fetch_all_SeqTags_below_relative_frequency
Title : fetch_all_SeqTags_below_relative_frequency
Usage : $obj->fetch_all_SeqTags_below_realtive_frequency
Function: returns seqtags with expression below given level
Example :
Returns : array of seqtags objects
Args :
=cut
sub fetch_all_SeqTags_below_relative_frequency {
my ($self,$frequency,$multiplier)=@_;
return $self->adaptor->fetch_all_SeqTags_below_relative_frequency($self->id,$frequency,$multiplier);
}
=head2 id
Title : id
Usage : $obj->id($newval)
Function:
Example :
Returns : value of id
Args : newvalue (optional)
=cut
sub id {
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'_library_id'} = $value;
}
return $obj->{'_library_id'};
}
=head2 source
Title : source
Usage : $obj->source($newval)
Function:
Example :
Returns : value of source
Args : newvalue (optional)
=cut
sub source {
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'_source'} = $value;
}
return $obj->{'_source'};
}
=head2 cgap_id
Title : cgap_id
Usage : $obj->cgap_id($newval)
Function:
Example :
Returns : value of cgap_id
Args : newvalue (optional)
=cut
sub cgap_id {
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'_cgap_id'} = $value;
}
return $obj->{'_cgap_id'};
}
=head2 dbest_id
Title : dbest_id
Usage : $obj->dbest_id($newval)
Function:
Example :
Returns : value of dbest_id
Args : newvalue (optional)
=cut
sub dbest_id {
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'_dbest_id'} = $value;
}
return $obj->{'_dbest_id'};
}
=head2 name
Title : name
Usage : $obj->name($newval)
Function:
Example :
Returns : value of name
Args : newvalue (optional)
=cut
sub name {
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'_name'} = $value;
}
return $obj->{'_name'};
}
=head2 tissue_type
Title : tissue_type
Usage : $obj->tissue_type($newval)
Function:
Example :
Returns : value of tissue_type
Args : newvalue (optional)
=cut
sub tissue_type {
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'_tissue_type'} = $value;
}
return $obj->{'_tissue_type'};
}
=head2 description
Title : description
Usage : $obj->description($newval)
Function:
Example :
Returns : value of tissue_type
Args : newvalue (optional)
=cut
sub description {
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'_description'} = $value;
}
return $obj->{'_description'};
}
=head2 total_seqtags
Title : total_seqtags
Usage : $obj->total_seqtags($newval)
Function:
Example :
Returns : value of tissue_type
Args : newvalue (optional)
=cut
sub total_seqtags {
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'_total_seqtags'} = $value;
}
return $obj->{'_total_seqtags'};
}
=head2 adaptor
Title : adaptor
Usage : $obj->adaptor($newval)
Function:
Example :
Returns : value of adaptor
Args : newvalue (optional)
=cut
sub adaptor {
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'adaptor'} = $value;
}
return $obj->{'adaptor'};
}
sub _set_from_args {
my ($self,@args)=@_;
my ($library_id,$source,$cgap_id,$dbest_id,$name,$tissue_type,$description,$total_seqtags)=@args;
$self->id($library_id);
$self->source($source);
$self->cgap_id($cgap_id);
$self->dbest_id($dbest_id);
$self->name($name);
$self->tissue_type($tissue_type);
$self->description($description);
$self->total_seqtags($total_seqtags);
}
]]>