comparison variant_effect_predictor/Bio/EnsEMBL/Funcgen/Array.pm @ 0:1f6dce3d34e0

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#
# Ensembl module for Bio::EnsEMBL::Funcgen::Array
#
# You may distribute this module under the same terms as Perl itself


=head1 LICENSE

  Copyright (c) 1999-2011 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]>.


=head1 NAME

Bio::EnsEMBL::Funcgen::Array - A module to represent a nucleotide microarray.

=head1 SYNOPSIS

use Bio::EnsEMBL::Funcgen::Array;

my $array = Bio::EnsEMBL::Funcgen::Array->new(
	    -NAME        => 'Array-1',
        -FORMAT      => 'Tiled',
        -SIZE        => '1',
     	-VENDOR      => 'Nimblegen',
        -DESCRIPTION => $desc,
        -TYPE        => 'OLIGO',
        -CLASS       => 'VENDOR_FORMAT'
);

my $db_adaptor = Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor->new(...);
my $array_adaptor = $db_adaptor->get_ArrayAdaptor();
my $array = $array_adaptor->fetch_by_name($array_name)

=head1 DESCRIPTION

An Array object represents a nucleotide (OLIGO, PCR etc.) microarray. The data
(currently the name, format, size, species, vendor and description) are stored
in the array table.

=cut


use strict;
use warnings;


package Bio::EnsEMBL::Funcgen::Array;


use Bio::EnsEMBL::Utils::Argument qw( rearrange );
use Bio::EnsEMBL::Utils::Exception qw( throw warning );
use Bio::EnsEMBL::Funcgen::Storable;

use vars qw(@ISA);# %VALID_TYPE);
@ISA = qw(Bio::EnsEMBL::Funcgen::Storable);


# Possible types for OligoArray objects
#This should match the vendor enum values?
#%VALID_TYPE = (
#	'AFFY'  => 1,
#	'OLIGO' => 1,
#);


=head2 new

  Arg [-NAME]        : string - the name of this array
  Arg [-VENDOR]      : string - the vendor of this array (AFFY, NIMBLEGEN etc)
  Arg [-TYPE]        : string - type of array e.g. OLIGO, PCR
  Arg [-FORMAT]      : string - the format of this array (TILED, TARGETTED, GENE etc)
  Arg [-DESCRIPTION] : strin - description of the array 

#array_chips is array of hashes or design_id and name, dbID will be populated on store, this should be a simple object!

  Example    : my $array = Bio::EnsEMBL::Funcgen::Array->new(
								  -NAME        => 'Array-1',
								  -FORMAT      => 'Tiled',
								  -SIZE        => '1',
								  -VENDOR      => 'Nimblegen',
                                  -TYPE        => 'OLIGO',
								  -DESCRIPTION => $desc,
                                  -CLASS       => 'VENDOR_FORMAT',#e.g. AFFY_UTR, ILLUMINA_WG
								 );
  Description: Creates a new Bio::EnsEMBL::Funcgen::Array object.
  Returntype : Bio::EnsEMBL::Funcgen::Array
  Exceptions : None ? should throw if mandatort params not set/valid
  Caller     : General
  Status     : At risk

=cut

sub new {
  my $caller = shift;

  my $class = ref($caller) || $caller;
  my $self = $class->SUPER::new(@_);
  
  my ($name, $format, $size,  $vendor, $type, $desc, $aclass)
    = rearrange( ['NAME', 'FORMAT', 'SIZE',  'VENDOR', 'TYPE', 'DESCRIPTION', 'CLASS'], @_ );
  
  #mandatory params?
  #name, format, vendor
  #enum on format?

  my @stack = caller();

  if($self->dbID() && $stack[0] ne "Bio::EnsEMBL::Funcgen::DBSQL::ArrayAdaptor"){
    throw("You must use the ArrayAdaptor($stack[0]) to generate Arrays with a dbID i.e. from the DB, as this module accomodates updating which may cause incorrect data if the object is not generated form the DB");
  } 


  throw("Must provide a vendor parameter") if ! $vendor;
  throw("Must provide a name parameter") if ! $name;
  #any others?

  
  $self->name($name);
  $self->format($format)    if defined $format;

  if(defined $format && $format eq 'EXPRESSION' && ! defined $class){
	throw('You must defined a class if you are importing and array with an EXPRESSION format');
  }

  $self->class(uc($aclass))     if defined $aclass;
  $self->size($size)        if defined $size;
  $self->vendor($vendor);
  $self->description($desc) if defined $desc;
  $self->type($type)        if defined $type;
  
  return $self;
}

=head2 get_all_Probes

  Args       : None
  Example    : my $probes = $array->get_all_Probes();
  Description: Returns all probes on an array. Needs a database connection.
  Returntype : Listref of Bio::EnsEMBL::Funcgen::Probe objects
  Exceptions : None
  Caller     : General
  Status     : At Risk

=cut

sub get_all_Probes {
	my $self = shift;

	if ( $self->dbID() && $self->adaptor() ) {
		my $opa = $self->adaptor()->db()->get_ProbeAdaptor();
		my $probes = $opa->fetch_all_by_Array($self);
		return $probes;
	} else {
		warning('Need database connection to retrieve Probes');
		return [];
	}
}

=head2 get_all_Probe_dbIDs

  Args       : None
  Example    : my @dbids = @{$array->get_all_Probe_dbIDs};
  Description: Returns an array ref of all the Probe database IDs for this array
  Returntype : arrayref of ints
  Exceptions : None
  Caller     : General
  Status     : At Risk

=cut

sub get_all_Probe_dbIDs {
  my $self = shift;

  if(!  $self->{probe_dbids}){
	#check for adaptor here?
	
	if(! $self->adaptor){
	  throw('Must have set an adaptor to get_all_Probe_dbIDs');
	}
	
	$self->{probe_dbids} = $self->adaptor->fetch_Probe_dbIDs_by_Array($self);
  }

  return  $self->{probe_dbids};
}




#Nath new get methods

=head2 get_all_ProbeSets

  Args       : None
  Example    : my $probesets = $array->get_all_ProbeSets();
  Description: Returns all probesets on an array. Needs a database connection.
  Returntype : Listref of Bio::EnsEMBL::Funcgen::ProbeSets objects
  Exceptions : None
  Caller     : General
  Status     : Medium Risk

=cut

sub get_all_ProbeSets {
	my $self = shift;

	if ( $self->dbID() && $self->adaptor() ) {
		my $opsa = $self->adaptor()->db()->get_ProbeSetAdaptor();
		my $probesets = $opsa->fetch_all_by_Array($self);
		return $probesets;
	} else {
		warning('Need database connection to retrieve ProbeSets');
		return [];
	}
}


#All the array_chip methods will be migrated to ArrayChip.pm

=head2 get_array_chip_ids

  Example    : my @ac_ids = @{$array->get_array_chip_ids()};
  Description: Returns all array_chip_ids for this array.
  Returntype : Listref of array_chip ids
  Exceptions : Throws if none retrieved
  Caller     : General
  Status     : At Risk

=cut

sub get_array_chip_ids {
  my $self = shift;

  my @ac_ids;


  $self->get_ArrayChips();

  #should we get_ArrayChips is we have none cached?
  #this may cause problem


  foreach my $achip(values %{$self->{'array_chips'}}){
    push @ac_ids, $achip->dbID();
  }

  if(! @ac_ids){
    throw("No array_chip_ids available"); # should this be warn?
  }
  
  return \@ac_ids;
}

=head2 get_design_ids

  Example    : my @design_ids = @{$array->get_design_ids()};
  Description: Returns a the design_ids for each array_chip contained within this array
  Returntype : list
  Exceptions : None
  Caller     : General
  Status     : Medium Risk

=cut



sub get_design_ids{
  my $self = shift;
  return [keys %{$self->{'array_chips'}}];
}
    


=head2 name

  Arg [1]    : (optional) string - the name of this array
  Example    : my $name = $array->name();
  Description: Getter, setter of the name attribute for Array
               objects.
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : Medium Risk

=cut

sub name{
  my $self = shift;
  
  $self->{'name'} = shift if @_;
  
  #do we need this?
  #if ( !exists $self->{'name'} && $self->dbID() && $self->adaptor() ) {
  #  $self->adaptor->fetch_attributes($self);
  #}
  
  return $self->{'name'};
}


=head2 type

  Arg [1]    : (optional) string - the type of this array
  Example    : $array->type('OLIGO');
  Description: Getter, setter of the type attribute for Array
               objects.
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : Medium Risk

=cut

sub type{
  my $self = shift;
  
  $self->{'type'} = shift if @_;
    
  return $self->{'type'};
}


=head2 format

  Arg [1]    : (optional) string - the format of the array
  Example    : my $format = $array->format();
  Description: Getter, setter of format attribute for
               Array objects e.g. Tiled, Targetted etc...
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : Medium Risk

=cut

sub format {
  my $self = shift;
  
  $self->{'format'} = shift if @_;
  
  #do we need this?
  #if ( !exists $self->{'format'} && $self->dbID() && $self->adaptor() ) {
  #  $self->adaptor->fetch_attributes($self);
  #}
  
  return $self->{'format'};
}

=head2 class

  Arg [1]    : (optional) string - the class of the array
  Example    : my $class = $array->class('AFFY_UTR');
  Description: Getter, setter of class attribute for
               Array objects e.g. AFFY_UTR, AFFY_ST
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : Medium Risk

=cut

sub class {
  my $self = shift;
  
  $self->{'class'} = shift if @_;
  
  return $self->{'class'};
}


=head2 size

  Arg [1]    : (optional) int - the number of ? in the array
  Example    : my $size = $array->size();
  Description: Getter of size attribute for Array objects. This
               simply counts the constituent ArrayChips
  Returntype : int
  Exceptions : None
  Caller     : General
  Status     : Medium Risk

=cut

sub size {
  my $self = shift;

  return scalar(keys %{$self->{'array_chips'}});
}


=head2 vendor

  Arg [1]    : (optional) string - the name of the array vendor
  Example    : my $vendor = $array->vendor();
  Description: Getter, setter of vendor attribute for
               Array objects.
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : Medium Risk

=cut

sub vendor {
  my $self = shift;
  $self->{'vendor'} = shift if @_;
  
  #do we need this?
  #if ( !exists $self->{'vendor'} && $self->dbID() && $self->adaptor() ) {
  #  $self->adaptor->fetch_attributes($self);
  #}

  return $self->{'vendor'};
}

=head2 description

  Arg [1]    : (optional) string - the description of the array
  Example    : my $size = $array->description();
  Description: Getter, setter of description attribute for
               Array objects. 
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : Medium Risk

=cut

sub description {
  my $self = shift;
  $self->{'description'} = shift if @_;
  
  #do we need this?
  #if ( !exists $self->{'description'} && $self->dbID() && $self->adaptor() ) {
  #  $self->adaptor->fetch_attributes($self);
  #}

  return $self->{'description'};
}

=head2 probe_count

  Example    : my $num_probes = $array->probe_count();
  Description: Return number of probes on array
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : At Risk

=cut

sub probe_count {
  my ($self)  = @_;
  #Do we want a distinct flag here?

  if(! defined $self->{'probe_count'}){
	$self->{'probe_count'} = $self->adaptor->fetch_probe_count_by_Array($self);
  }
  
  return $self->{'probe_count'};
}



=head2 get_ArrayChips

  Example    : my @achips = @{$array->get_ArrayChips()};
  Description: Getter, setter and lazy loader of array_chip hashes
  Returntype : Arrays of ArrayChip objects
  Exceptions : Throws exception if none found for array_id
  Caller     : General
  Status     : High Risk - migrate to ArrayChip.pm

=cut

sub get_ArrayChips {
  my $self = shift;
 
  #lazy loaded as we won't want this for light DB
  #should do meta check and want here

  if ( ! exists $self->{'array_chips'}){

    if( $self->dbID() && $self->adaptor() ) {
      #$self->adaptor->fetch_attributes($self);
      #need to do this differently as we're accessing a different table
      $self->{'array_chips'} = {};

      foreach my $achip(@{$self->adaptor->db->get_ArrayChipAdaptor->fetch_all_by_array_id($self->dbID())}){
	$self->{'array_chips'}{$achip->design_id} = $achip;
	#%{$self->{'array_chips'}} = %{$self->adaptor->db->get_ArrayAdaptor->_fetch_array_chips_by_array_dbID($self->dbID())};
      }
    }
    else{
      throw("Need array dbID and DB connection to retrieve array_chips");
    }
  }

  return [ values %{$self->{'array_chips'}} ];
}

=head2 get_ArrayChip_by_design_id

  Arg [1]    : (mandatory) int - design_id
  Example    : my %ac = %{$array->get_ArrayChip_by_design_id('1234')};
  Description: Getter for array_chip hashes
  Returntype : Hashref
  Exceptions : Throws exception if no design_id defined, warns if not part of array
  Caller     : General
  Status     : At risk

=cut

sub get_ArrayChip_by_design_id{
  my ($self, $design_id) = @_;


  #warn "This needs to get the array chip if not defined?? but we're using it to test whether is has been stored same problem as probe_design?";

  my ($achip);
  throw("Must supply a valid array chip design_id") if (! defined $design_id);

  if(defined $self->{'array_chips'}{$design_id}){
    $achip = $self->{'array_chips'}{$design_id};
  }else{
    #No we use this to check whether it has been stored with the array
    #warn("should this throw? Array does not contain ArrayChip:$design_id\n"); 
  }

  return $achip;
}

=head2 add_ArrayChip

  Arg [1]    : mandatory - Bio::EnsEMBL::Funcgen::ArrayChip
  Example    : $array->add_ArrayChip($array_chip);
  Description: Setter for array chips
  Returntype : None
  Exceptions : Throws if arg not a Bio::EnsEMBL::Funcgen::ArrayChip, or Array not stored
  Caller     : General
  Status     : Ar risk

=cut

#This uses previosuly stored array_chips withotu warning
#Need to implement fetch_store method?

sub add_ArrayChip{
  my ($self, $array_chip) = @_;

  throw("You must supply a stored Bio::EnsEMBL::Funcgen::ArrayChip") if(! ($array_chip && 
									   $array_chip->isa("Bio::EnsEMBL::Funcgen::ArrayChip") && 
									   $array_chip->dbID()));
  
  if ($self->dbID() && $self->adaptor()){
    $self->get_ArrayChips() if (! $self->{'array_chips'});

    if(exists $self->{'array_chips'}{$array_chip->design_id}){
      $array_chip = $self->{'array_chips'}{$array_chip->design_id};
      #warn("Array chip for ".$array_chip->design_id()." already exists, using previous stored array chip\n");
    }else{
      $self->{'array_chips'}{$array_chip->design_id} = $array_chip;
    }

  }else{
    throw("Array must be stored before adding an array_chip");
  }

  return;
}


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