Bio::EnsEMBL::Funcgen::DBSQL
CellTypeAdaptor
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Summary
Bio::EnsEMBL::Funcgen::DBSQL::CellTypeAdaptor - A database adaptor for fetching and
storing Funcgen CellType objects.
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
my $ct_adaptor = $db->get_CellTypeAdaptor();
my $cell_type = $ct_adaptor->fetch_by_name("U2OS");
#my @cell_types = $st_adaptor->fetch_all_by_type("TISSUE");
Description
The CellTypeAdaptor is a database adaptor for storing and retrieving
Funcgen CellType 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 Channel objects from an executed DBI statement
handle.
Returntype : Listref of Bio::EnsEMBL::Funcgen::CellType 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] : string - name of CellType
Arg [1] : optional string - class of CellType
Example : my $ct = $ct_adaptor->fetch_by_name('U2OS');
Description: Retrieves CellType objects by name.
Returntype : Bio::EnsEMBL::Funcgen::CellType object
Exceptions : Throws no name given
Caller : General
Status : At risk |
Args : None
Example : my @ct_ids = @{$ct_a->list_dbIDs()};
Description: Gets an array of internal IDs for all CellType objects in the
current database.
Returntype : List of ints
Exceptions : None
Caller : ?
Status : At risk |
Args : List of Bio::EnsEMBL::Funcgen::CellType objects
Example : $chan_a->store($c1, $c2, $c3);
Description: Stores CellType objects in the database.
Returntype : None
Exceptions : None
Caller : General
Status : At Risk |
Methods code
sub _columns
{ my $self = shift;
return qw( ct.cell_type_id ct.name ct.display_label ct.description);
} | sub _objs_from_sth
{ my ($self, $sth) = @_;
my (@result, $ct_id, $name, $dlabel, $desc);
$sth->bind_columns(\$ct_id,\$ name,\$ dlabel,\$ desc);
while ( $sth->fetch() ) {
my $ctype = Bio::EnsEMBL::Funcgen::CellType->new(
-dbID => $ct_id,
-NAME => $name,
-DISPLAY_LABEL => $dlabel,
-DESCRIPTION => $desc,
-ADAPTOR => $self,
);
push @result, $ctype;
}
return\@ result;} | sub _tables
{ my $self = shift;
return (
['cell_type', 'ct'],
); } | sub fetch_by_name
{ my ($self, $name) = @_;
throw("Must specify a CellType name") if(! $name);
my $constraint = "ct.name ='$name'";
my @ctype = @{$self->generic_fetch($constraint)};
return $ctype[0];} | sub list_dbIDs
{ my ($self) = @_;
return $self->_list_dbIDs('cell_type');
}
1;} | sub store
{ my $self = shift;
my @args = @_;
my $sth = $self->prepare("
INSERT INTO cell_type
(name, display_label, description)
VALUES (?, ?, ?)");
foreach my $ct (@args) {
if ( ! $ct->isa('Bio::EnsEMBL::Funcgen::CellType') ) {
warning('Can only store CellType objects, skipping $ct');
next;
}
if ( $ct->dbID() && $ct->adaptor() == $self ){
warn("Skipping previously stored CellType dbID:".$ct->dbID().")");
next;
}
$sth->bind_param(1, $ct->name(), SQL_VARCHAR);
$sth->bind_param(2, $ct->display_label(), SQL_VARCHAR);
$sth->bind_param(3, $ct->description(), SQL_VARCHAR);
$sth->execute();
$ct->dbID($sth->{'mysql_insertid'});
$ct->adaptor($self);
}
return\@ args;} | General documentation
This module was created by Nathan Johnson.
This module is part of the Ensembl project:
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