Bio::EnsEMBL::DBSQL
OligoArrayAdaptor
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Summary
Bio::EnsEMBL::DBSQL::OligoArrayAdaptor - A database adaptor for fetching and
storing OligoArray objects.
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
my $oaa = $db->get_OligoArrayAdaptor();
my $array = $oaa->fetch_by_name('Array-1');
my @arrays = @{ $oaa->fetch_all() };
Description
The OligoArrayAdaptor is a database adaptor for storing and retrieving
OligoArray objects.
Methods
Methods description
Args : None
Example : None
Description: PROTECTED implementation of superclass abstract method.
Returns a list of columns to use for queries.
Returntype : List of strings
Exceptions : None
Caller : Internal
Status : Medium Risk |
Arg [1] : DBI statement handle object
Example : None
Description: PROTECTED implementation of superclass abstract method.
Creates OligoArray objects from an executed DBI statement
handle.
Returntype : Listref of Bio::EnsEMBL::OligoArray objects
Exceptions : None
Caller : Internal
Status : Medium Risk |
Args : None
Example : None
Description: PROTECTED implementation of superclass abstract method.
Returns the names and aliases of the tables to use for queries.
Returntype : List of listrefs of strings
Exceptions : None
Caller : Internal
Status : Medium Risk |
Arg [1] : List of strings - type(s) (e.g. AFFY or OLIGO)
Example : my @arrays = @{$oaa->fetch_all_by_type('OLIGO')};
Description: Fetch all arrays of a particular type.
Returntype : Listref of Bio::EnsEMBL::OligoArray objects
Exceptions : Throws if no type is provided
Caller : General
Status : Medium Risk |
Arg [1] : Bio::EnsEMBL::OligoArray - array to fetch attributes for
Example : None
Description: This function is solely intended to lazy load attributes into
empty OligoArray objects. You should not need to call this.
Returntype : None
Exceptions : None
Caller : Bio::EnsEMBL::OligoArray getters
Status : Medium Risk |
Arg [1] : string - name of an array
Example : my $array = $oaa->fetch_by_name('Array-1');
Description: Retrieves a named OligoArray object from the database.
Returntype : Bio::EnsEMBL::OligoArray
Exceptions : None
Caller : General
Status : Medium Risk |
Args : None
Example : my @array_ids = @{$oaa->list_dbIDs()};
Description: Gets an array of internal IDs for all OligoArray objects in the
current database.
Returntype : List of ints
Exceptions : None
Caller : ?
Status : Medium Risk |
Args : List of Bio::EnsEMBL::OligoArray objects
Example : $oaa->store($array1, $array2, $array3);
Description: Stores given OligoArray objects in the database. Should only be
called once per array because no checks are made for duplicates.
Sets dbID and adaptor on the objects that it stores.
Returntype : None
Exceptions : None
Caller : General
Status : Medium Risk |
Methods code
sub _columns
{ my $self = shift;
return qw( oa.oligo_array_id oa.parent_array_id oa.probe_setsize oa.name oa.type ); } | sub _objs_from_sth
{ my ($self, $sth) = @_;
my (@result, $array_id, $parent_id, $setsize, $name, $type);
$sth->bind_columns(\$ array_id,\$ parent_id,\$ setsize,\$ name,\$ type );
while ( $sth->fetch() ) {
my $array = Bio::EnsEMBL::OligoArray->new(
-dbID => $array_id,
-adaptor => $self,
-name => $name,
-setsize => $setsize,
-type => $type,
);
push @result, $array;
if ($parent_id) {
my $parent_array = Bio::EnsEMBL::OligoArray->new(
-dbID => $parent_id,
-adaptor => $self,
);
$array->superset($parent_array);
}
}
return\@ result;} | sub _tables
{ my $self = shift;
return ['oligo_array', 'oa']; } | sub fetch_all_by_type
{ my ($self, @types) = @_;
throw('Need type as parameter') if !@types;
my $constraint;
if (scalar @types == 1) {
$constraint = qq( oa.type = ? );
$self->bind_param_generic_fetch($types[0],SQL_VARCHAR);
} else {
$constraint = join q(','), @types;
$constraint = qq( oa.type IN ('$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_name
{ my $self = shift;
my $name = shift;
$self->bind_param_generic_fetch($name,SQL_VARCHAR);
my $result = $self->generic_fetch("oa.name = ?");
if (scalar @$result > 1) {
warning("Array $name is not unique in the database, but only one result has been returned");
}
return $result->[0];} | sub list_dbIDs
{ my ($self) = @_;
return $self->_list_dbIDs('oligo_array');
}
1;} | sub store
{ my $self = shift;
my @args = @_;
foreach my $array (@args) {
if ( !$array->isa('Bio::EnsEMBL::OligoArray') ) {
warning('Can only store OligoArray objects');
next;
}
next if ( $array->dbID() && $array->adaptor() == $self );
my $superset = $array->superset();
if ( defined $superset && !$superset->dbID() ) {
$self->store($superset);
}
my $sth = $self->prepare("
INSERT INTO oligo_array
(name, probe_setsize, type, parent_array_id)
VALUES (?, ?, ?, ?)
");
$sth->bind_param(1, $array->name(), SQL_VARCHAR);
$sth->bind_param(2, $array->setsize(), SQL_INTEGER);
$sth->bind_param(3, $array->type(), SQL_VARCHAR);
if (defined $superset) {
$sth->bind_param(4, $superset->dbID(), SQL_INTEGER);
} else {
$sth->bind_param(4, undef);
}
$sth->execute();
my $dbID = $sth->{'mysql_insertid'};
$array->dbID($dbID);
$array->adaptor($self);
}} | General documentation
Copyright (c) 1999-2009 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
/info/about/code_licence.html