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Summary

Bio::EnsEMBL::Funcgen::Set - A module to represent a base Set object.

Package variables

Included modules

Inherit

Bio::EnsEMBL::Funcgen::Storable

Synopsis

use Bio::EnsEMBL::Funcgen::Set;
@INC = qw (Bio::EnsEMBL::Funcgen::Set)
sub new {
my $caller = shift;

my $class = ref($caller) || $caller;

my $self = $class->SUPER::new(@_);

  
}

Description

A base Set object which provides access common methods available across all Funcgen Set classes.

Methods

Methods description

  Example    : my $anal_name = $set->analysis->logic_name();
  Description: Getter for the analysis attribute for this Set.
  Returntype : Bio::EnsEMBL::Analysis
  Exceptions : None
  Caller     : General
  Status     : At Risk

  Example    : my $dset_ctype_name = $dset->cell_type->name();
  Description: Getter for the cell_type for this DataSet.
  Returntype : Bio::EnsEMBL::Funcgen::CellType
  Exceptions : throws if arg not valid
  Caller     : General
  Status     : At Risk

  Example    : print $set->display_label();
  Description: Getter for the display_label attribute for this Set.
               This is more appropriate for teh predicted_features of the set.
               Use the individual display_labels for each raw result set.
  Returntype : str
  Exceptions : None
  Caller     : General
  Status     : At Risk

  Example    : my $dset_ftype_name = $dset->feature_type->name();
  Description: Getter for the feature_type for this DataSet.
  Returntype : Bio::EnsEMBL::Funcgen::FeatureType
  Exceptions : Throws if arg not valid
  Caller     : General
  Status     : At Risk

  Example    : my $set->name('SET1');
  Description: Getter/Setter for the name of this Set.
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : At Risk

  Example    : my $self = $class->SUPER::new(@_);
  Description: Constructor for Set objects.
  Returntype : Bio::EnsEMBL::Funcgen::Set
  Exceptions : None
  Caller     : General
  Status     : At risk

  Example    : my $set_type = $set->set_type;
  Description: Getter for the Set type for this Set.
  Returntype : string e.g. result, feature, data or experimental
  Exceptions : None
  Caller     : General
  Status     : At Risk

Methods code

sub analysis {

  my $self = shift;

  if(@_){
	throw('Must pass a valid stored Analysis') if (! (ref($_[0]) eq 'Bio::EnsEMBL::Analysis'
													  && $_[0]->dbID()));
	$self->{'analysis'} = shift;
  }
  
 
  return $self->{'analysis'};

}

sub cell_type {

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

  if(defined $ctype){

	if(! (ref($ctype) eq 'Bio::EnsEMBL::Funcgen::CellType'
		  && $ctype->dbID())){ 
	  throw('Must pass a valid stored Bio::EnsEMBL::Funcgen::CellType');
	}
	$self->{'cell_type'} = $ctype;
  }

  return $self->{'cell_type'};

}

sub display_label {

  my $self = shift;

 
  #Add display label in table?
  #Can we aborc ResultSet method into this?

  if(! $self->{'display_label'}){

	#if($self->product_FeatureSet->feature_type->class() eq 'Regulatory Feature'){
	#  $self->{'display_label'} = 'Regulatory Features';
	#}
	#else{

	  $self->{'display_label'} = $self->feature_type->name()." -";
	  $self->{'display_label'} .= " ".($self->cell_type->display_label() || 
									   $self->cell_type->description()   ||
									   $self->cell_type()->name());
	  $self->{'display_label'} .= " Enriched Sites";
	#}
  }
 
  return $self->{'display_label'};

}

sub feature_type {

  my ($self, $ftype) = @_;
   
  if(defined $ftype){

	if(! (ref($ftype) eq 'Bio::EnsEMBL::Funcgen::FeatureType'
		  && $ftype->dbID())){ 
	  throw('Must pass a valid stored Bio::EnsEMBL::Funcgen::FeatureType');
	}
	$self->{'feature_type'} = $ftype;
  }

  		  
  return $self->{'feature_type'};

}

sub name {

  my $self = shift;

  return $self->{'name'};

}

sub new {

  my $caller = shift;
	
  my $class = ref($caller) || $caller;
	
  my $self = $class->SUPER::new(@_);
	
  #do we need to add $fg_ids to this?  Currently maintaining one feature_group focus.(combi exps?)
  my ($name, $anal, $ftype, $ctype)
    = rearrange(['NAME', 'ANALYSIS', 'FEATURE_TYPE', 'CELL_TYPE'], @_);
  
  throw('Need to specify a name') if ! defined $name;

  if(defined $anal){#Move this to child Sets, and just set anal here
	$self->analysis($anal);
  }elsif($self->set_type ne 'experimental'){
	throw('Must pass a valid -analysis parameter for a '.ref($self));
  }

  $self->{'name'} = $name;
  $self->cell_type($ctype) if $ctype;
  $self->feature_type($ftype) if $ftype;

  #Set type here but don't validate, as this can be done selectively in the Child Sets, do this for analysis too?
  
  return $self;

}

sub set_type {

  my $self = shift;
 
  my $type;
  my @namespace = split/\:\:/, ref($self);
  ($type = lc($namespace[$#namespace])) =~ s/set//;

  return $type;
}

1;

}

General documentation

This module was created by Nathan Johnson.
This module is part of the Ensembl project: /

Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk