Bio::EnsEMBL::Compara
DnaFragRegion
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Summary
Bio::EnsEMBL::Compara::DnaFragRegion - dnafrag region on one species
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
my $slice = $dnafrag_region->slice;
my $dnafrag = $dnafrag_region->dnafrag;
my $genome_db = $dnafrag_region->genome_db;
my $dnafrag_start = $dnafrag_region->dnafrag_start;
my $dnafrag_end = $dnafrag_region->dnafrag_end;
my $dnafrag_strand = $dnafrag_region->dnafrag_strand;
my $length = $dnafrag_region->length;
Description
DnaFragRegion are the objects underlying the SyntenyRegion objects. Each synteny is
represented as a Bio::EnsEMBL::Compara::SyntenyRegion object. Each of these objects
contain one Bio::EnsEMBL::Compara::DnaFragRegion object per region which defines the
synteny. For instance, for a syntenic region between human and mouse, there will be
one DnaFragRegion object for the human region and another one for the mouse one.
Methods
Methods description
Arg 1 : (optional) Bio::EnsEMBL::Compara::DBSQL::DnaFragRegioAdaptor $adaptor
Example : my $adaptor = $dnafrag->adaptor;
Description : Getter/setter for the corresponding
Bio::EnsEMBL::Compara::DBSQL::DnaFragRegioAdaptor object
Returntype : Bio::EnsEMBL::Compara::DBSQL::DnaFragRegioAdaptor object
Exceptions : none
Caller : general |
Arg 1 : (optional) Bio::EnsEMBL::Compara::DnaFrag object
Example : $dnafrag = $dnafragregion->dnafrag;
Description : Getter/setter for the Bio::EnsEMBL::Compara::DnaFrag object corresponding to this
Bio::EnsEMBL::Compara::DnaFragRegion object.
Returntype : Bio::EnsEMBL::Compara::Dnafrag object
Exceptions : warns when the corresponding Bio::EnsEMBL::Compara::GenomeDB,
coord_system_name, name or Bio::EnsEMBL::DBSQL::DBAdaptor
cannot be retrieved and returns undef.
Caller : $object->methodname |
Arg 1 : (optional) integer $dnafrag_end
Example : my $dnafrag_end = $dnafrag->dnafrag_end;
Description : Getter/setter for the dnafrag_end attribute
Returntype : integer
Exceptions : none
Caller : general |
Arg 1 : (optional) integer $dnafrag_id
Example : my $dnafrag_id = $dnafrag->dnafrag_id;
Description : Getter/setter for the dnafrag_id attribute
Returntype : integer
Exceptions : none
Caller : general |
Arg 1 : (optional) integer $dnafrag_start
Example : my $dnafrag_start = $dnafrag->dnafrag_start;
Description : Getter/setter for the dnafrag_start attribute
Returntype : integer
Exceptions : none
Caller : general |
Arg 1 : (optional) integer $dnafrag_strand
Example : my $dnafrag_strand = $dnafrag->dnafrag_strand;
Description : Getter/setter for the dnafrag_strand attribute
Returntype : integer (1 or -1)
Exceptions : none
Caller : general |
Arg 1 : -none-
Example : $genome_db = $dnafragregion->genome_db;
Description : Returns the Bio::EnsEMBL::Compara::GenomeDB object corresponding to this
Bio::EnsEMBL::Compara::DnaFragRegion object. This method is a shortcut
for $dnafragregion->dnafrag->genome_db
Returntype : Bio::EnsEMBL::Compara::GenomeDB object
Exceptions : return undef if no dnafrag can be found for this DnaFragRegion object.
See dnafrag method elsewhere in this document.
Caller : $object->methodname |
Arg 1 : -none-
Example : $length = $dnafragregion->length;
Description : Returns the lenght of this DnaFragRegion
Returntype : integer
Exceptions :
Caller : $object->methodname |
Arg 1 : hash reference $hashref
Example : none
Description : This is an ultra fast constructor which requires knowledge of
the objects internals to be used.
Returntype : Bio::EnsEMBL::Compara::DnaFragRegion object
Exceptions : none
Caller : general |
Arg 1 : -none-
Example : $slice = $dnafragregion->slice;
Description : Returns the Bio::EnsEMBL::Slice object corresponding to this
Bio::EnsEMBL::Compara::DnaFrag object.
Returntype : Bio::EnsEMBL::Slice object
Exceptions : warns when the corresponding Bio::EnsEMBL::Compara::GenomeDB,
coord_system_name, name or Bio::EnsEMBL::DBSQL::DBAdaptor
cannot be retrieved and returns undef.
Caller : $object->methodname |
Arg 1 : (optional) integer $synteny_region_id
Example : my $synteny_region_id = $dnafrag->synteny_region_id;
Description : Getter/setter for the synteny_region_id attribute
Returntype : integer
Exceptions : none
Caller : general |
Methods code
sub adaptor
{ my $obj = shift;
if (@_) {
my $value = shift;
$obj->{'adaptor'} = $value;
}
return $obj->{'adaptor'};} | sub dnafrag
{ my ($self) = shift @_;
if (@_) {
$self->{'_dnafrag'} = shift @_;
} elsif (!defined $self->{'_dnafrag'}) {
if (!defined($self->dnafrag_id)) {
warn "Cannot get the Bio::EnsEMBL::Compara::DnaFrag object without dbID";
return undef;
}
my $dfa = $self->adaptor->db->get_DnaFragAdaptor;
if (!defined($dfa)) {
warn "Cannot get the Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor";
return undef;
}
$self->{'_dnafrag'} = $dfa->fetch_by_dbID($self->dnafrag_id);
}
return $self->{'_dnafrag'};} | sub dnafrag_end
{ my $obj = shift;
if (@_) {
my $value = shift;
$obj->{'dnafrag_end'} = $value;
}
return $obj->{'dnafrag_end'};} | sub dnafrag_id
{ my $obj = shift;
if (@_) {
my $value = shift;
$obj->{'dnafrag_id'} = $value;
}
return $obj->{'dnafrag_id'};} | sub dnafrag_start
{ my $obj = shift;
if (@_) {
my $value = shift;
$obj->{'dnafrag_start'} = $value;
}
return $obj->{'dnafrag_start'};} | sub dnafrag_strand
{ my $obj = shift;
if (@_) {
my $value = shift;
$obj->{'dnafrag_strand'} = $value;
}
return $obj->{'dnafrag_strand'};} | sub genome_db
{ my ($self) = @_;
if ($self->dnafrag) {
return $self->dnafrag->genome_db;
}
return undef;} | sub length
{ my ($self) = @_;
return $self->dnafrag_end - $self->dnafrag_start + 1;
}
1; } | sub new
{ my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
if (scalar @args) {
my ($adaptor, $synteny_region_id, $dnafrag_id, $dnafrag_start, $dnafrag_end, $dnafrag_strand) = rearrange([qw(ADAPTOR SYNTENY_REGION_ID DNAFRAG_ID DNAFRAG_START DNAFRAG_END DNAFRAG_STRAND)], @args);
$adaptor && $self->adaptor($adaptor);
$synteny_region_id && $self->synteny_region_id($synteny_region_id);
$dnafrag_id && $self->dnafrag_id($dnafrag_id);
$dnafrag_start && $self->dnafrag_start($dnafrag_start);
$dnafrag_end && $self->dnafrag_end($dnafrag_end);
$dnafrag_strand && $self->dnafrag_strand($dnafrag_strand);
}
return $self; } | sub new_fast
{ my ($class, $hashref) = @_;
return bless $hashref, $class; } | sub slice
{ my ($self) = @_;
unless (defined $self->{'_slice'}) {
if (!defined($self->dnafrag->genome_db)) {
warn "Cannot get the Bio::EnsEMBL::Compara::GenomeDB object corresponding to [".$self."]";
return undef;
}
if (!defined($self->dnafrag->coord_system_name)) {
warn "Cannot get the coord_system_name corresponding to [".$self."]";
return undef;
}
if (!defined($self->dnafrag->name)) {
warn "Cannot get the name corresponding to [".$self."]";
return undef;
}
my $dba = $self->dnafrag->genome_db->db_adaptor;
if (!defined($dba)) {
warn "Cannot get the Bio::EnsEMBL::DBSQL::DBAdaptor corresponding to [".$self->dnafrag->genome_db."]";
return undef;
}
$self->{'_slice'} = $dba->get_SliceAdaptor->fetch_by_region($self->dnafrag->coord_system_name, $self->dnafrag->name,$self->dnafrag_start, $self->dnafrag_end, $self->dnafrag_strand);
}
return $self->{'_slice'};} | sub synteny_region_id
{ my $obj = shift;
if (@_) {
my $value = shift;
$obj->{'synteny_region_id'} = $value;
}
return $obj->{'synteny_region_id'};} | General documentation
adaptor
Bio::EnsEMBL::Compara::DBSQL::DnaFragRegionAdaptor object to access DB
synteny_region_id
corresponds to dnafrag.synteny_region_id (external ref.)
dnafrag_id
corresponds to dnafrag.dnafrag_id (external ref.)
dnafrag
Bio::EnsEMBL::Compara::DnaFrag object corresponding to dnafrag_id
dnafrag_start
corresponds to dnafrag_region.dnafrag_start
dnafrag_end
corresponds to dnafrag_region.dnafrag_end
dnafrag_strand
corresponds to dnafrag_region.dnafrag_strand
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _