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Commit 81d933c1 authored by Magali Ruffier's avatar Magali Ruffier
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added more methods:

- get_assembly_name
- get_assembly_date
- get_genebuild_start_date
- get_genebuild_method
- get_genebuild_initial_release_date
- get_genebuild_last_geneset_update

bug fixes for methods:
- get_toplevel
- get_karyotype
- get_coord_systems
parent bf81a6e6
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......@@ -128,8 +128,7 @@ sub get_version {
}
if (!defined $self->{'version'}) {
my $csa = $self->db()->get_adaptor('CoordSystem');
my @cs = @{ $csa->fetch_all() };
$self->{'version'} = $cs[0]->version();
$self->{'version'} = $csa->get_default_version;
}
return $self->{'version'};
}
......@@ -158,6 +157,157 @@ sub get_accession {
return $self->{'accession'};
}
=head2 get_assembly_name
Arg [1] : (optional) assembly name
Example : $assembly_name = $genome->get_assembly_name();
Description: Getter/setter for the name of the assembly currently used
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub get_assembly_name {
my ($self, $assembly_name) = @_;
if (defined $assembly_name) {
$self->{'assembly_name'} = $assembly_name;
}
if (!defined $self->{'assembly_name'}) {
$self->{'assembly_name'} = $self->_meta_container->single_value_by_key('assembly.name');
}
return $self->{'assembly_name'};
}
=head2 get_assembly_date
Arg [1] : (optional) assembly date
Example : $assembly_date = $genome->get_assembly_date();
Description: Getter/setter for the date of the assembly currently used
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub get_assembly_date {
my ($self, $assembly_date) = @_;
if (defined $assembly_date) {
$self->{'assembly_date'} = $assembly_date;
}
if (!defined $self->{'assembly_date'}) {
$self->{'assembly_date'} = $self->_meta_container->single_value_by_key('assembly.date');
}
return $self->{'assembly_date'};
}
=head2 get_genebuild_start_date
Arg [1] : (optional) genebuild start date
Example : $genebuild_start_date = $genome->get_genebuild_start_date();
Description: Getter/setter for the start date of the genebuild currently used
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub get_genebuild_start_date {
my ($self, $genebuild_start_date) = @_;
if (defined $genebuild_start_date) {
$self->{'genebuild_start_date'} = $genebuild_start_date;
}
if (!defined $self->{'genebuild_start_date'}) {
$self->{'genebuild_start_date'} = $self->_meta_container->single_value_by_key('genebuild.start_date');
}
return $self->{'genebuild_start_date'};
}
=head2 get_genebuild_method
Arg [1] : (optional) genebuild start date
Example : $genebuild_method = $genome->get_genebuild_method();
Description: Getter/setter for the method of the genebuild currently used
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub get_genebuild_method {
my ($self, $genebuild_method) = @_;
if (defined $genebuild_method) {
$self->{'genebuild_method'} = $genebuild_method;
}
if (!defined $self->{'genebuild_method'}) {
$self->{'genebuild_method'} = $self->_meta_container->single_value_by_key('genebuild.method');
}
return $self->{'genebuild_method'};
}
=head2 get_genebuild_initial_release_date
Arg [1] : (optional) genebuild initial release date
Example : $genebuild_initial_release_date = $genome->get_initial_release_date();
Description: Getter/setter for the initial release date of the genebuild currently used
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub get_genebuild_initial_release_date {
my ($self, $genebuild_initial_release_date) = @_;
if (defined $genebuild_initial_release_date) {
$self->{'genebuild_initial_release_date'} = $genebuild_initial_release_date;
}
if (!defined $self->{'genebuild_initial_release_date'}) {
$self->{'genebuild_initial_release_date'} = $self->_meta_container->single_value_by_key('genebuild.initial_release_date');
}
return $self->{'genebuild_initial_release_date'};
}
=head2 get_genebuild_last_geneset_update
Arg [1] : (optional) genebuild last geneset update
Example : $genebuild_last_geneset_update = $genome->get_last_geneset_update();
Description: Getter/setter for the last geneset update of the genebuild currently used
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub get_genebuild_last_geneset_update {
my ($self, $genebuild_last_geneset_update) = @_;
if (defined $genebuild_last_geneset_update) {
$self->{'genebuild_last_geneset_update'} = $genebuild_last_geneset_update;
}
if (!defined $self->{'genebuild_last_geneset_update'}) {
$self->{'genebuild_last_geneset_update'} = $self->_meta_container->single_value_by_key('genebuild.last_geneset_update');
}
return $self->{'genebuild_last_geneset_update'};
}
=head2 _get_length
Arg [1] : none
......@@ -188,7 +338,6 @@ sub _get_length {
Arg [1] : (optional) golden path length
Example : $ref_length = $genome->get_ref_length();
Description: Getter/setter for the golden path of the assembly currently used
Returntype : integer
Exceptions : none
Caller : general
......@@ -246,11 +395,9 @@ sub get_total_length {
=cut
sub get_toplevel {
my $self = @_;
if (!defined $self->{'toplevel'}) {
my $sa = $self->db()->get_adaptor('Slice');
$self->{'toplevel'} = $sa->fetch_all('toplevel');
}
my ($self) = @_;
my $sa = $self->db->get_adaptor('Slice');
$self->{'toplevel'} = $sa->fetch_all('toplevel');
return $self->{'toplevel'};
}
......@@ -269,11 +416,9 @@ sub get_toplevel {
=cut
sub get_karyotype {
my $self = @_;
if (!defined $self->{'karyotype'}) {
my $sa = $self->db()->get_adaptor('Slice');
$self->{'karyotype'} = $sa->fetch_all_karyotype;
}
my ($self) = @_;
my $sa = $self->db->get_adaptor('Slice');
$self->{'karyotype'} = $sa->fetch_all_karyotype;
return $self->{'karyotype'};
}
......@@ -291,11 +436,13 @@ sub get_karyotype {
=cut
sub get_coord_systems {
my $self = @_;
if (!defined $self->{'coord_systems'}) {
my $version = $self->version();
my $csa = $self->db->get_adaptor('CoordSystem');
my ($self, $all) = @_;
my $csa = $self->db->get_adaptor('CoordSystem');
if (!$all) {
my $version = $self->get_version();
$self->{'coord_systems'} = $csa->fetch_all_by_version($version);
} else {
$self->{'coord_systems'} = $csa->fetch_all();
}
return $self->{'coord_systems'};
}
......
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