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Summary

Bio::EnsEMBL::Funcgen::DBSQL::ArrayChipAdaptor - A database adaptor for fetching and
storing Funcgen ArrayChip objects.

Package variables

Included modules

Inherit

Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor

Synopsis

my $ac_adaptor = $db->get_ArrayChipAdaptor();
my @achips = @{$ec_adaptor->fetch_all_by_Array($array)};

Description

The ArrayChipAdaptor is a database adaptor for storing and retrieving
Funcgen ArrayChip objects.

Methods

Methods description

  Args       : None
  Example    : None
  Description: PROTECTED implementation of superclass abstract method.
               Returns a list of columns to use for queries.
  Returntype : List of strings
  Exceptions : None
  Caller     : Internal
  Status     : Medium Risk

  Arg [1]    : DBI statement handle object
  Example    : None
  Description: PROTECTED implementation of superclass abstract method.
               Creates Array objects from an executed DBI statement
			   handle.
  Returntype : Listref of Bio::EnsEMBL::Funcgen::ArrayChip objects
  Exceptions : None
  Caller     : Internal
  Status     : At Risk

  Args       : None
  Example    : None
  Description: PROTECTED implementation of superclass abstract method.
               Returns the names and aliases of the tables to use for queries.
  Returntype : List of listrefs of strings
  Exceptions : None
  Caller     : Internal
  Status     : Medium Risk

  Arg [1]    : Bio::EnsEMBL::Funcgen::Array
  Example    : my @ccs = @{$ec_a->fetch_all_by_Array($array);
  Description: Returns all ArrayChips which belong to the given Array
  Returntype : Arrayref of Bio::EnsEMBL::Funcgen::ArrayChip objects
  Exceptions : Throws if ARg not valid and stored
  Caller     : General
  Status     : At Risk

  Arg [1]    : arrayref of - Bio::EnsEMBL::Funcgen::ExperimentalChips
  Example    : my @achips = @{$ec_a->fetch_all_by_ExperimentalChips($echips);
  Description: Gets a non-redundant list of the corresponding ArrayChips
  Returntype : Listref of Bio::EnsEMBL::Funcgen::ArrayChips
  Exceptions : Throws if no ExperimentalChips passed or if ExperimentalChips are not stored or valid
  Caller     : General
  Status     : at risk

  Arg [1]    : int - dbID of Array
  Example    : my @ccs = @{$ec_a->fetch_all_by_array_dbID($array->dbID());
  Description: Does what it says on the tin
  Returntype : Listref of Bio::EnsEMBL::Funcgen::ArrayChip
  Exceptions : None
  Caller     : General
  Status     : Medium Risk

  Arg [1]    : int - dbID of Array
  Arg [2]    : string - Design ID of ArrayChip
  Example    : my $ac = $ac_adaptpr->fetch_by_array_design_ids($array->dbID, $design_id);
  Description: Does what it says on the tin
  Returntype : Bio::EnsEMBL::Funcgen::ArrayChip
  Exceptions : Throws if args not met.
  Caller     : General
  Status     : Medium Risk

  Args       : None
  Example    : my @array_ids = @{$ec_a->list_dbIDs()};
  Description: Gets an array of internal IDs for all ArrayChip objects in the
               current database.
  Returntype : List of ints
  Exceptions : None
  Caller     : ?
  Status     : Medium Risk

  Args       : List of Bio::EnsEMBL::Funcgen::ArrayChip objects
  Example    : $arraychip_adaptor->store($ac1, $ac2, $ac3);
  Description: Stores given ArrayChip objects in the database. Should only be
               called once per ArrayChip because no checks are made for duplicates.
  Returntype : ARRAYREF
  Exceptions : warns if passed non-ArrayChip arg
  Caller     : General
  Status     : At Risk

Methods code

sub _columns {

  my $self = shift;
	
  return qw( ac.array_chip_id ac.design_id ac.array_id ac.name);

}

sub _objs_from_sth {

  my ($self, $sth) = @_;
  
  my (@result, $ac_id, $design_id, $array_id, $name);
  
  $sth->bind_columns(\$ac_id,\$ design_id,\$ array_id,\$ name);
  
  while ( $sth->fetch() ) {
    my $array = Bio::EnsEMBL::Funcgen::ArrayChip->new(
						      -dbID      => $ac_id,
						      -design_id => $design_id,
						      -array_id  => $array_id,
						      -name      => $name,
						      -adaptor   => $self,
						     );
    
    push @result, $array;
    
  }
  return\@ result;

}

sub _tables {

	my $self = shift;
	
	return ['array_chip', 'ac'];

}

sub fetch_all_by_Array {

  my ($self, $array) = @_;
  
  if(! (ref($array) && $array->isa->('Bio::EnsEMBL::Funcgen::Array') && $array->dbID())){
	throw("Must pass a valid stored Bio::EnsEMBL::Funcgen::Array");
  }
  
  return $self->fetch_all_by_array_id($array->dbID);

}

sub fetch_all_by_ExperimentalChips {

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

  my %ac_ids;

  foreach my $echip(@$echips){

	if(! ($echip->isa('Bio::EnsEMBL::Funcgen::ExperimentalChip') && $echip->dbID())){
	  throw('Must provide an arrayref of valid stored Bio::EnsEMBL::Funcgen::ExperimentalChips');
	}
	
	$ac_ids{$echip->array_chip_id} = 1;
	
  }
	
  if(! keys(%ac_ids)){
	throw('Must provide an arrayref of valid stored Bio::EnsEMBL::Funcgen::ExperimentalChips');
  }
  
  return $self->generic_fetch('ac.array_chip_id IN ('.join(', ', keys(%ac_ids)).')');

}

sub fetch_all_by_array_id {

    my $self = shift;
    my $array_id = shift;

    throw("Must specify an array dbID") if(! $array_id);

    my $constraint = "ac.array_id='$array_id'";

    return $self->generic_fetch($constraint);

}

sub fetch_by_array_design_ids {

    my ($self, $array_id, $design_id) = @_;

	if( ! ($array_id && $design_id)){
	  throw('You must pass an Array dbID and a ArrayChip design ID');
	}

    my $constraint = "ac.array_id='$array_id' and ac.design_id='$design_id'";

    my ($ac) = @{$self->generic_fetch($constraint)};
    #unique key means this always has just one element

    return $ac;
}





#fetch by Array_array_chip_name??
#would need this if we're going to check for previously imported ArrayChips, as there's no guarantee that the design_name will be populated.

}

sub list_dbIDs {

    my ($self) = @_;	
    return $self->_list_dbIDs('array_chip');
}



1;

}

sub store {

  my $self = shift;
  my @args = @_;
  
  #my ($stored_ac);

  #Should we implement a throw here is the caller is not Array?
  #make private _store?

  
  my $sth = $self->prepare("
			INSERT INTO array_chip
			(design_id, array_id, name)
			VALUES (?, ?, ?)"
			  );
  
    
  
  foreach my $ac (@args) {
    if ( ! $ac->isa('Bio::EnsEMBL::Funcgen::ArrayChip') ) {
      warning('Can only store ExperimentalChip objects, skipping $ec');
      next;
    }
    
    throw("ArrayChip must have an array_id to be stored") if ! $ac->array_id();

    #check for array_id here? this is done by not null in sql
    

    #check for previously stored array_chips is done in Array via add_ArrayChip
    
    
    
    if (!( $ac->dbID() && $ac->adaptor() == $self )){

      my $s_ac = $self->fetch_by_array_design_ids($ac->array_id(), $ac->design_id());

      if(! $s_ac){
	
	$sth->bind_param(1, $ac->design_id(), SQL_VARCHAR);
	$sth->bind_param(2, $ac->array_id(),  SQL_INTEGER);
	$sth->bind_param(3, $ac->name(),      SQL_VARCHAR);	
	$sth->execute();

	my $dbID = $sth->{'mysql_insertid'};
	$ac->dbID($dbID);
	$ac->adaptor($self);	
	
      }else{
	  $ac = $s_ac;
	  #	my @states = @{$self->db->fetch_all_states('experimental_chip', $ec->dbID())};
	  #	warn("Using previously stored ExperimentalChip (".$ec->unique_id().") with states\t@states\n");
	}
    }
  }
  return\@ args;

}

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