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Summary

Bio::EnsEMBL::ExternalData::Expression::Library

Package variables

Included modules

Inherit

Bio::EnsEMBL::Root

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";
    }

Description

Represents information on one Clone

Methods

Methods description

 Title   : adaptor
 Usage   : $obj->adaptor($newval)
 Function: 
 Example : 
 Returns : value of adaptor
 Args    : newvalue (optional)

 Title   : cgap_id
 Usage   : $obj->cgap_id($newval)
 Function: 
 Example : 
 Returns : value of cgap_id
 Args    : newvalue (optional)

 Title   : dbest_id
 Usage   : $obj->dbest_id($newval)
 Function: 
 Example : 
 Returns : value of dbest_id
 Args    : newvalue (optional)

 Title   : description
 Usage   : $obj->description($newval)
 Function: 
 Example : 
 Returns : value of tissue_type
 Args    : newvalue (optional)

 Title   : fetch_SeqTag_by_Name
 Usage   : $obj->fetch_SeqTag_by_Name
 Function: 
 Example : 
 Returns : an array of seqtag objects
 Args    :

 Title   : fetch_SeqTag_by_dbID
 Usage   : $obj->fetch_SeqTag_by_dbID
 Function: 
 Example : 
 Returns : seqtag object
 Args    :

 Title   : fetch_all_SeqTags
 Usage   : $obj->fetch_all_SeqTags
 Function: 
 Example : 
 Returns : array of seqtags objects
 Args    :

 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    :

 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    :

 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    :

 Title   : id
 Usage   : $obj->id($newval)
 Function: 
 Example : 
 Returns : value of id
 Args    : newvalue (optional)

 Title   : name
 Usage   : $obj->name($newval)
 Function: 
 Example : 
 Returns : value of name
 Args    : newvalue (optional)

 Title   : new
 Usage   : 
 Function: 
 Example : 
 Returns : Library object
 Args    :

 Title   : source
 Usage   : $obj->source($newval)
 Function: 
 Example : 
 Returns : value of source
 Args    : newvalue (optional)

 Title   : tissue_type
 Usage   : $obj->tissue_type($newval)
 Function: 
 Example : 
 Returns : value of tissue_type
 Args    : newvalue (optional)

 Title   : total_seqtags
 Usage   : $obj->total_seqtags($newval)
 Function: 
 Example : 
 Returns : value of tissue_type
 Args    : newvalue (optional)

Methods code

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);

}

sub adaptor {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'adaptor'} = $value;
    }
    return $obj->{'adaptor'};

}

sub cgap_id {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_cgap_id'} = $value;
    }
    return $obj->{'_cgap_id'};

}

sub dbest_id {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_dbest_id'} = $value;
    }
    return $obj->{'_dbest_id'};

}

sub description {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_description'} = $value;
    }
    return $obj->{'_description'};

}

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);

}

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);

}

sub fetch_all_SeqTags {

    my ($self)=shift;

    return $self->adaptor->fetch_all_SeqTags($self->id);

}

sub fetch_all_SeqTags_above_frequency {

    my ($self,$frequency)=@_;

    return $self->adaptor->fetch_all_SeqTags_above_frequency($self->id,$frequency);

}

sub fetch_all_SeqTags_above_relative_frequency {

    my ($self,$frequency,$multiplier)=@_;


 return $self->adaptor->fetch_all_SeqTags_above_relative_frequency($self->id,$frequency,$multiplier);

}

sub fetch_all_SeqTags_below_relative_frequency {

    my ($self,$frequency,$multiplier)=@_;


 return $self->adaptor->fetch_all_SeqTags_below_relative_frequency($self->id,$frequency,$multiplier);

}

sub id {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_library_id'} = $value;
    }
    return $obj->{'_library_id'};

}

sub name {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_name'} = $value;
    }
    return $obj->{'_name'};

}

sub new {

    my ($class,$adaptor,@args) = @_;

    my $self = {};
    bless $self,$class;

    $self->adaptor($adaptor);
    $self->_set_from_args(@args);

    return $self;

}

sub source {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_source'} = $value;
    }
    return $obj->{'_source'};

}

sub tissue_type {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_tissue_type'} = $value;
    }
    return $obj->{'_tissue_type'};

}

sub total_seqtags {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_total_seqtags'} = $value;
    }
    return $obj->{'_total_seqtags'};

}

General documentation

Describe contact details here

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _