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Commit 132666f5 authored by Web Admin's avatar Web Admin
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Added calls for assembly name/version to slice via DBAdaptor

parent 7beea4ad
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......@@ -815,24 +815,99 @@ sub assembly_type{
if($value) {
$obj->{'assembly'} = $value;
}
if (! defined $obj->{'assembly'}) {
my $ass;
eval {
$ass = $obj->dnadb->get_MetaContainer()->get_default_assembly();
};
if ( $@ ) {
$obj->throw("*** get_MetaContainer->get_default_assembly failed:\n$@\n"
."assembly type must be set with assembly_type() first");
} elsif (! $ass) {
$obj->throw("No default assembly defined in ".$obj->dnadb->dbname. " - must set with assembly_type() first");
}
$obj->{'assembly'} = $ass;
}
return $obj->{'assembly'};
if (! defined $obj->{'assembly'}) {
my $ass;
eval {
$ass = $obj->dnadb->get_MetaContainer()->get_default_assembly();
};
if ( $@ ) {
$obj->throw("*** get_MetaContainer->get_default_assembly failed:\n$@\n"
."assembly type must be set with assembly_type() first");
} elsif (! $ass) {
$obj->throw("No default assembly defined in ".$obj->dnadb->dbname. " - must set with assembly_type() first");
}
$obj->{'assembly'} = $ass;
}
return $obj->{'assembly'};
}
=head2 assembly_name
Arg [1] : (optional) string $value
the new assembly name value
Example : $db_adaptor->assembly_name($newval);
Description: Getter / Setter for the name of assembly used by
this database. If the value is not set then the
default value is obtained from the MetaContainer
Returntype : string
Exceptions : warn if there is no defined assembly name, and the default
assembly name cannot be obtained from the MetaContainer
Caller : ?
=cut
sub assembly_name {
my ($obj,$value) = @_;
if($value) {
$obj->{'assembly_name'} = $value;
}
if (! defined $obj->{'assembly_name'}) {
my $ass;
eval {
$ass = $obj->dnadb->get_MetaContainer()->get_default_assembly_name();
};
if ( $@ ) {
warn("*** get_MetaContainer->get_default_assembly_name failed ***\n$@\n");
} elsif (! $ass) {
warn("No default assembly name defined in ".$obj->dnadb->dbname. "!");
}
$obj->{'assembly_name'} = $ass;
}
return $obj->{'assembly_name'};
}
=head2 assembly_version
Arg [1] : (optional) string $value
the new assembly version value
Example : $db_adaptor->assembly_version($newval);
Description: Getter / Setter for the version of assembly used by
this database. If the value is not set then the
default value is obtained from the MetaContainer
Returntype : string
Exceptions : warn if there is no defined assembly version, and the default
assembly version cannot be obtained from the MetaContainer
Caller : ?
=cut
sub assembly_version {
my ($obj,$value) = @_;
if($value) {
$obj->{'assembly_version'} = $value;
}
if (! defined $obj->{'assembly_version'}) {
my $ass;
eval {
$ass = $obj->dnadb->get_MetaContainer()->get_default_assembly_version();
};
if ( $@ ) {
warn("*** get_MetaContainer->get_default_assembly_version failed ***\n$@\n");
} elsif (! $ass) {
warn("No default assembly version defined in ".$obj->dnadb->dbname. "!");
}
$obj->{'assembly_version'} = $ass;
}
return $obj->{'assembly_version'};
}
=head2 dnadb
Title : dnadb
......
......@@ -863,7 +863,7 @@ sub strand{
=cut
sub assembly_type{
sub assembly_type {
my ($self,$value) = @_;
if( defined $value) {
$self->{'assembly_type'} = $value;
......@@ -874,6 +874,52 @@ sub assembly_type{
=head2 assembly_name
Arg [1] : string $value
Example : $slice->assembly_name();
Description: Gets/Sets the assembly name that this slice is constructed
from. This is generally set by the slice adaptor and probably
shouldnt be set outside of this context.
Returntype : string
Exceptions : none
Caller : general
=cut
sub assembly_name {
my ($self,$value) = @_;
if( defined $value) {
$self->adaptor->db->assembly_name($value);
}
return $self->adaptor->db->assembly_name();
}
=head2 assembly_version
Arg [1] : string $value
Example : $slice->assembly_version();
Description: Gets/Sets the assembly version that this slice is constructed
from. This is generally set by the slice adaptor and probably
shouldnt be set outside of this context.
Returntype : string
Exceptions : none
Caller : general
=cut
sub assembly_version {
my ($self,$value) = @_;
if( defined $value) {
$self->adaptor->db->assembly_version($value);
}
return $self->adaptor->db->assembly_version();
}
=head2 get_all_KaryotypeBands
Arg [1] : none
......
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