Bio::EnsEMBL::ExternalData::Mole::DBSQL
GeneNameAdaptor
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Included modules
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Synopsis
No synopsis!
Description
No description!
Methods
_columns | No description | Code |
_objs_from_sth | No description | Code |
_tables | No description | Code |
fetch_all_by_dbID_list | No description | Code |
fetch_by_Entry | No description | Code |
fetch_by_dbID | No description | Code |
fetch_by_entry_id | No description | Code |
fetch_by_name | No description | Code |
fetch_by_name_type | No description | Code |
Methods description
None available.
Methods code
sub _columns
{ my $self = shift;
return ( 'g.genename_id', 'g.entry_id',
'g.name', 'g.name_type'); } |
sub _objs_from_sth
{ my ($self, $sth) = @_;
my @out;
my ( $genename_id, $entry_id, $name, $name_type );
$sth->bind_columns(\$ genename_id,\$ entry_id,\$ name,\$ name_type );
while($sth->fetch()) {
push @out, Bio::EnsEMBL::ExternalData::Mole::GeneName->new(
-dbID => $genename_id,
-entry_id => $entry_id,
-adaptor => $self,
-name => $name,
-name_type => $name_type,
);
}
return\@ out;
}
1; } |
sub _tables
{ my $self = shift;
return (['genename' , 'g']); } |
sub fetch_all_by_dbID_list
{ my ($self,$id_list_ref) = @_;
if(!defined($id_list_ref) || ref($id_list_ref) ne 'ARRAY') {
croak("kill object id list reference argument is required");
}
return [] if(!@$id_list_ref);
my @out;
my @tabs = $self->_tables;
my ($name, $syn) = @{$tabs[0]};
my $max_size = 200;
my @id_list = @$id_list_ref;
while(@id_list) {
my @ids;
if(@id_list > $max_size) {
@ids = splice(@id_list, 0, $max_size);
} else {
@ids = splice(@id_list, 0);
}
my $id_str;
if(@ids > 1) {
$id_str = " IN (" . join(',', @ids). ")";
} else {
$id_str = " = " . $ids[0];
}
my $constraint = "${syn}.${name}_id $id_str";
push @out, @{$self->generic_fetch($constraint)};
}
return\@ out; } |
sub fetch_by_Entry
{ my $self = shift;
my $entry = shift;
my $sth = $self->prepare(
"SELECT g.genename_id ".
"FROM genename g ".
"WHERE g.entry_id = ?");
$sth->bind_param(1, $entry->dbID, SQL_INTEGER);
$sth->execute();
my $gname_id = $sth->fetchrow();
$sth->finish();
my $genename_object = $self->fetch_by_dbID($gname_id);
return $genename_object; } |
sub fetch_by_dbID
{ my $self = shift;
my $id = shift;
my $constraint = "g.genename_id = '$id'";
my ($genename_obj) = @{ $self->generic_fetch($constraint) };
return $genename_obj; } |
sub fetch_by_entry_id
{ my ($self, $entry_id) = @_;
my $constraint = "g.entry_id = '$entry_id'";
my ($genename_obj) = @{ $self->generic_fetch($constraint) };
return $genename_obj; } |
sub fetch_by_name
{ my $self = shift;
my $name = shift;
$sth = $self->prepare(
"SELECT entry_id ".
"FROM genename ".
"WHERE name = '$name' ");
$sth->execute();
my @array = @{$sth->fetchall_arrayref()};
my @entry_ids = map {$_->[0]} @array;
my $entries = $self->fetch_all_by_dbID_list(\@entry_ids);
return $entries; } |
fetch_by_name_type | description | prev | next | Top |
sub fetch_by_name_type
{ my $self = shift;
my $name_type = shift;
$sth = $self->prepare(
"SELECT entry_id ".
"FROM genename_type ".
"WHERE name_type = '$name_type' ");
$sth->execute();
my @array = @{$sth->fetchall_arrayref()};
my @entry_ids = map {$_->[0]} @array;
my $entries = $self->fetch_all_by_dbID_list(\@entry_ids);
return $entries; } |
General documentation
No general documentation available.