Bio::EnsEMBL::Funcgen ExperimentalSet
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvsRaw content
Summary
Bio::EnsEMBL::ExperimentalSet - A module to represent ExperimentalSet object.
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Funcgen::ExperimentalSubset
Bio::EnsEMBL::Funcgen::Set
Bio::EnsEMBL::Utils::Argument qw ( rearrange )
Bio::EnsEMBL::Utils::Exception qw ( throw warning deprecate )
Inherit
Bio::EnsEMBL::Funcgen::Set
Synopsis
use Bio::EnsEMBL::Funcgen::ExpeimentalSet;
my $data_set = Bio::EnsEMBL::Funcgen::ExperimentalSet->new(
-DBID => $dbID,
-ADAPTOR => $self,
-EXPERIMENT => $exp,
-FEATURE_TYPE => $ftype,
-CELL_TYPE => $ctype,
-FORMAT => 'READ_FORMAT',
-VENDOR => 'SOLEXA',
-NAME => 'ExpSet1',
);
Description
An ExperimentalSet object provides a generic container for any non-array based feature import,
allowing tracking of file import via the status table and integration into Data and FeatureSets to
provide traceability to the source experiment from a given FeatureSet.
Methods
add_new_subsetDescriptionCode
formatDescriptionCode
get_ExperimentDescriptionCode
get_subset_by_nameDescriptionCode
get_subset_namesDescriptionCode
get_subsetsDescriptionCode
newDescriptionCode
vendorDescriptionCode
Methods description
add_new_subsetcode    nextTop
  Arg [1]    : string - sub set name e.g. the file name (not path as we're restricted to 30 chars)
  Example    : $expset->add_new_subset($ss_name, $exp_subset);
  Description: Adds experimental_subset
  Returntype : none
  Exceptions : Throws if set is already present
               Throws if ExperimentalSubset is not valid or stored
  Caller     : General
  Status     : At Risk
formatcodeprevnextTop
  Arg[1]     : string - format i.e. product type/format
  Example    : my $eset->format('DATASET1');
  Description: Getter/Setter for the format attribute of this ExperimentalSet.
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : At Risk
get_ExperimentcodeprevnextTop
  Example    : my $exp = $exp_set->get_Experiment();
  Description: Getter for the Experiment of this DataSet.
  Returntype : Bio::EnsEMBL::Fuuncgen::Experiment
  Exceptions : None
  Caller     : General
  Status     : At Risk
get_subset_by_namecodeprevnextTop
  Example    : my $subsets = $exp_set->get_subset_by_name('subset1');
  Description: Getter for the subset of a given name for this ExperimentalSet.
  Returntype : Bio::EnsEMBL::Funcgen::ExpeirmentalSubset
  Exceptions : None
  Caller     : General
  Status     : At Risk
get_subset_namescodeprevnextTop
  Example    : my @subset_names = @{$exp_set->get_subset_names()};
  Description: Getter for the subset names for this ExperimentalSet.
  Returntype : Arrayref
  Exceptions : None
  Caller     : General
  Status     : At Risk
get_subsetscodeprevnextTop
  Example    : my @subsets = @{$exp_set->get_subsets()};
  Description: Getter for the subsets for this ExperimentalSet.
  Returntype : Arrayref
  Exceptions : None
  Caller     : General
  Status     : At Risk
newcodeprevnextTop
  Example    : my $eset = Bio::EnsEMBL::Funcgen::ExperimentalSet->new(
                                                                     -EXPERIMENT   => $exp,
                                                                     -FEATURE_TYPE => $ftype,
                                                                     -CELL_TYPE    => $ctype,
                                                                     -FORMAT       => 'READ_FORMAT',
                                                                     -VENDOR       => 'SOLEXA',
                                                                     -NAME         => 'ExpSet1',
                                                                     -ANALYSIS     => $anal,
                                                                     );

  Do we want to define subsets likes this or are we more likely to add them one by one?

  Description: Constructor for ExperimentalSet objects.
  Returntype : Bio::EnsEMBL::Funcgen::ExperimentalSet
  Exceptions : Throws if no Experiment defined
               Throws if CellType or FeatureType are not valid or stored
  Caller     : General
  Status     : At risk
vendorcodeprevnextTop
  Arg[1]     : string - vendor 
  Example    : my $eset->vendor('SOLEXA');
  Description: Getter/Setter for the vendor attribute of this DataSet.
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : At Risk
Methods code
add_new_subsetdescriptionprevnextTop
sub add_new_subset {
  my ($self, $ss_name, $exp_sset) = @_;
	
  if($self->get_subset_by_name($ss_name)){
	throw("Subset $ss_name is already present in this ExperimentalSet, maybe you need to alter the filename?");
  }

  if(defined $exp_sset){

	if(!(ref($exp_sset) && $exp_sset->isa('Bio::EnsEMBL::Funcgen::ExperimentalSubset') && $exp_sset->dbID())){
	  throw('ExperimentalSubsets must be valid and stored');
	}
  }
  else{
	
	$exp_sset = Bio::EnsEMBL::Funcgen::ExperimentalSubset->new(
															   -name => $ss_name,
															   -experimental_set => $self,
															  );
  }

  $self->{'subsets'}{$ss_name} = $exp_sset;

  return $self->{'subsets'}{$ss_name};
}
formatdescriptionprevnextTop
sub format {
  my $self = shift;
     	
  $self->{'format'} = shift if @_;
  
  return $self->{'format'};
}

1;
}
get_ExperimentdescriptionprevnextTop
sub get_Experiment {
  my $self = shift;

  return $self->{'experiment'};
}
get_subset_by_namedescriptionprevnextTop
sub get_subset_by_name {
  my ($self, $name) = @_;

  return (exists $self->{'subsets'}{$name}) ? $self->{'subsets'}{$name} : undef;
}
get_subset_namesdescriptionprevnextTop
sub get_subset_names {
  my ($self) = shift;

  return [ keys %{$self->{'subsets'}} ];
}
get_subsetsdescriptionprevnextTop
sub get_subsets {
  my ($self)  = shift;

  return [ values %{$self->{'subsets'}} ];
}
newdescriptionprevnextTop
sub new {
  my $caller = shift;
	
  my $class = ref($caller) || $caller;
	
  my $self = $class->SUPER::new(@_);
	
  #do we need to add $fg_ids to this?  Currently maintaining one feature_group focus.(combi exps?)
  my ($exp, $format, $vendor)
    = rearrange(['EXPERIMENT', 'FORMAT', 'VENDOR'], @_);
    
  if (! (ref $exp && $exp->isa('Bio::EnsEMBL::Funcgen::Experiment') && $exp->dbID())){
	throw('Must specify a valid stored Bio::EnsEMBL::Funcgen::Experiment');
  }

  
  #These are set in Set, just validate here
  throw ('Must provide a FeatureType') if(! defined $self->feature_type);
  throw ('Must provide a CellType') if(! defined $self->cell_type);



  if(! defined $self->analysis){
	#default analysis hack for v47
	#Set directly to avoid dbID boolean check
	$self->{'analysis'} = Bio::EnsEMBL::Analysis->new(-logic_name => 'external',
													  -id       => 0,#??someone needs to rewrite analysis
													 );
  }

  $self->format($format) if defined $format;
  $self->vendor($vendor) if defined $vendor;
  $self->{'experiment'} = $exp;
  $self->{'subsets'} = {};
  
  return $self;
}
vendordescriptionprevnextTop
sub vendor {
  my $self = shift;
     	
  $self->{'vendor'} = shift if @_;

  return $self->{'vendor'};
}
General documentation
AUTHORTop
This module was created by Nathan Johnson.
This module is part of the Ensembl project: /
CONTACTTop
Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk