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Summary

Bio::EnsEMBL::Funcgen::DBSQL::ArrayAdaptor - A database adaptor for fetching and
storing Funcgen Array objects.

Package variables

Included modules

Inherit

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

Synopsis

my $oaa = $db->get_ArrayAdaptor();
my $array = $oaa->fetch_by_name('Array-1');
my @arrays = @{$oaa->fetch_all()};

Description

The ArrayAdaptor is a database adaptor for storing and retrieving
Funcgen Array 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     : At 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::Array 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     : At Risk

  Arg [1]    : Bio::EnsEMBL::Funcgen::Experiement
  Example    : my @arrays = @{$aa->fetch_all_by_Experiment($exp)};
  Description: Fetch all arrays associated with a given Experiment
               This is a convenience method to hide the 3 adaptor required 
               for this call.
  Returntype : Listref of Bio::EnsEMBL::Funcgen::Array objects
  Exceptions : none
  Caller     : General
  Status     : at risk

  Arg [1]    : string - class
  Example    : my $array = $oaa->fetch_all_by_class(''AFFY_ST');
  Description: Retrieves Array object from the database based class.
  Returntype : ARRAYREF of Bio::EnsEMBL::Funcgen::Array objects
  Exceptions : Throws if nor class passed
  Caller     : General
  Status     : At Risk

  Arg [1]    : List of strings - type(s) (e.g. OLIGO, PCR)
  Example    : my @arrays = @{$aa->fetch_all_by_type('OLIGO')};
  Description: Fetch all arrays of a particular type.
  Returntype : Listref of Bio::EnsEMBL::Funcgen::Array objects
  Exceptions : Throws if no type is provided
  Caller     : General
  Status     : at risk

  Arg [1]    : Bio::EnsEMBL::Funcgen::Array - array to fetch attributes for
  Example    : None
  Description: This function is solely intended to lazy load attributes into
               empty Array objects. You should not need to call this.
  Returntype : None
  Exceptions : None
  Caller     : Bio::EnsEMBL::Funcgen::Array getters
  Status     : Medium Risk

  Arg [1]    : int - dbID of array_chip
  Example    : my $array = $oaa->fetch_by_array_chip_dbID($ac_dbid);
  Description: Retrieves a named Array object from the database.
  Returntype : Bio::EnsEMBL::Funcgen::Array
  Exceptions : None
  Caller     : General
  Status     : At Risk

  Arg [1]    : string - name of an array
  Arg [2]    : string - class of array e.g. AFFY_UTR
  Example    : my $array = $oaa->fetch_by_name_class('HuGene_1_0_st_v1', 'AFFY_ST');
  Description: Retrieves Array object from the database based on name and class.
  Returntype : Bio::EnsEMBL::Funcgen::Array
  Exceptions : Throws is name and class not passed
  Caller     : General
  Status     : At Risk

  Arg [1]    : string - name of an array
  Arg [2]    : string - name of vendor e.g. NIMBLEGEN
  Example    : my $array = $oaa->fetch_by_name('Array-1');
  Description: Retrieves a named Array object from the database.
  Returntype : Bio::EnsEMBL::Funcgen::Array
  Exceptions : None
  Caller     : General
  Status     : At Risk

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

  Args       : List of Bio::EnsEMBL::Funcgen::Array objects
  Example    : $oaa->store($array1, $array2, $array3);
  Description: Stores given Array objects in the database. This
               method checks for arrays previously stored and updates 
               and new array_chips accordingly.
  Returntype : Listref of stored Array objects
  Exceptions : None
  Caller     : General
  Status     : At Risk

Methods code

sub _columns {

	my $self = shift;
	
	return qw( a.array_id a.name a.format a.vendor a.description a.type a.class);

}

sub _objs_from_sth {

  my ($self, $sth) = @_;
	
  my (@result, $array_id, $name, $format, $vendor, $description, $type, $class);
  
  $sth->bind_columns(\$array_id,\$ name,\$ format,\$ vendor,\$ description,\$ type,\$ class);
  
  while ( $sth->fetch() ) {

    my $array = Bio::EnsEMBL::Funcgen::Array->new
	  (
	   -dbID        => $array_id,
	   -adaptor     => $self,
	   -name        => $name,
	   -format      => $format,
	   -vendor      => $vendor,
	   -description => $description,
	   -type        => $type,
	   -class       => $class, 
	  );

    push @result, $array;
    
 
  }
  return\@ result;

}

sub _tables {

	my $self = shift;
	
	return ['array', 'a'];

}

sub fetch_all_by_Experiment {

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

  my %array_ids;
	
  my $echips = $self->db->get_ExperimentalChipAdaptor->fetch_all_by_Experiment($exp);

  foreach my $achip(@{$self->db->get_ArrayChipAdaptor->fetch_all_by_ExperimentalChips($echips)}){
	$array_ids{$achip->array_id()} = 1;
  }

  return $self->generic_fetch('a.array_id IN ('.join(', ', keys %array_ids).')');

}

sub fetch_all_by_class {

    my ($self, $class) = @_;
    
    throw("Must provide and array class e.g.'AFFY_ST'") if (! defined $class);

    return $self->generic_fetch("a.class='".uc($class)."'");

}

sub fetch_all_by_type {

  my ($self, @types) = @_;
	
  throw('Need type as parameter') if ! @types;
	
  my $constraint;
  if (scalar @types == 1) {
    $constraint = qq( a.type = '$types[0]' );
  } else {
    $constraint = join q(','), @types;
    $constraint = qq( a.type IN ('$constraint') );
  }

  return $self->generic_fetch($constraint);

}

sub fetch_attributes {

    my $self = shift;
    my $array = shift;

    my $tmp_array = $self->fetch_by_dbID( $array->dbID() );
    %$array = %$tmp_array;

}

sub fetch_by_array_chip_dbID {

    my $self = shift;
    my $ac_dbid = shift;
	my $sth = $self->prepare("
		SELECT a.array_id
		FROM array a, array_chip ac
		WHERE a.array_id = ac.array_id
		AND ac.array_chip_id = $ac_dbid
	");


	$sth->execute();
	my ($array_id) = $sth->fetchrow();

	return $self->fetch_by_dbID($array_id);

}

sub fetch_by_name_class {

    my ($self, $name, $class) = @_;
    
    throw("Must provide and array and class e.g.'HuGene_1_0_st_v1', 'AFFY_ST'") if (! ($name && $class));


    my ($result) = @{$self->generic_fetch("a.name = '$name' and a.class='".uc($class)."'")};	
    return $result;

}

sub fetch_by_name_vendor {

    my ($self, $name, $vendor) = @_;
    
    throw("Must provide and array and vendor name") if (! ($name && $vendor));

    #unique key means this only returns one element
    my ($result) = @{$self->generic_fetch("a.name = '$name' and a.vendor='".uc($vendor)."'")};	
    return $result;

}

sub list_dbIDs {

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


#New Funcgen methods
#fetch_all_by_group?
#fetch_by_channel_id?
#fetch_by_chip_id?
#fetch_by_probe_id
#fetch_by_probe_set_id


1;

}

sub store {

  my $self = shift;
  my @args = @_;
  
  my ($sarray);
  
  my $sth = $self->prepare("
			INSERT INTO array
			(name, format, vendor, description, type, class)
			VALUES (?, ?, ?, ?, ?, ?)");
  
    
  foreach my $array (@args) {
    if ( !$array->isa('Bio::EnsEMBL::Funcgen::Array') ) {
      warning('Can only store Array objects, skipping $array');
      next;
    }
    
    if (!( $array->dbID() && $array->adaptor() == $self )){
      #try and fetch array here and set to array if valid
      $sarray = $self->fetch_by_name_vendor($array->name(), $array->vendor());#this should be name_vendor?
      
      if( ! $sarray){
		#sanity check here
		throw("Array name must not be longer than 30 characters") if (length($array->name) > 40);
		$sth->bind_param(1, $array->name(),         SQL_VARCHAR);
		$sth->bind_param(2, $array->format(),       SQL_VARCHAR);
		$sth->bind_param(3, $array->vendor(),       SQL_VARCHAR);
		$sth->bind_param(4, $array->description(),  SQL_VARCHAR);
		$sth->bind_param(5, $array->type(),         SQL_VARCHAR);
		$sth->bind_param(6, $array->class(),        SQL_VARCHAR);
		
		
		$sth->execute();
		my $dbID = $sth->{'mysql_insertid'};
		$array->dbID($dbID);
		$array->adaptor($self);
      }
      else{
		#warn("Array already stored, using previously stored array\n");# validating array_chips\n");
		$array = $sarray;
      }
    }
  }
    
  return\@ args;

}

General documentation

This module was created by Nathan Johnson, but is almost entirely based on the
ArrayAdaptor modules written by Ian Sealy and Arne Stabenau.
This module is part of the Ensembl project: /

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