Bio::EnsEMBL::ExternalData::DAS
Source
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Summary
Bio::EnsEMBL::ExternalData::DAS::Source
Package variables
No package variables defined.
Included modules
Synopsis
Description
An object representation of a DAS source.
Methods
Methods description
Arg [1] : Optional value to set (arrayref)
Description: Get/Setter for the Ensembl coordinate systems supported by the source
Returntype : arrayref of Bio::EnsEMBL::ExternalData::DAS::CoordSystem objects
Status : Stable |
Arg [1] : Optional value to set
Description: Get/Setter for the source description
Returntype : scalar
Status : Stable |
Arg [1] : Optional value to set
Description: Get/Setter for the DSN
Returntype : scalar
Exceptions : If the DSN is missing
Status : Stable |
Arg [1] : Bio::EnsEMBL::ExternalData::DAS::Source
The source to compare to for equality.
Example : if($source1->equals($source2)) { ... }
Description: Compares 2 DAS sources and returns true if they are
equivalent. The definition of equivalent is sharing the same
full URL and coordinate systems.
Returntype : 0 or 1
Exceptions : none
Caller : general
Status : Stable |
Args : none
Description: Getter for the source URL (including DSN)
Returntype : scalar
Status : Stable |
Arg [1] : Optional value to set
Description: Get/Setter for the source homepage URL
Returntype : scalar
Status : Stable |
Arg [1] : Optional value to set
Description: Get/Setter for the source label
Returntype : scalar
Status : Stable |
Arg [1] : Optional value to set
Description: Get/Setter for the logic name
Returntype : scalar
Status : Stable |
Arg [1] : Optional value to set
Description: Get/Setter for the source maintainer email address
Returntype : scalar
Status : Stable |
Arg [1] : Whole or part name string
Description: Determines whether the Source name matches a name filter. Matches
the dsn and label against a regex.
Returntype : 1 or 0
Status : Stable |
Arg [1] : Species string
Description: Determines whether the Source supports a species with at least
one of its coordinate systems.
Returntype : 1 or 0
Status : Stable |
Arg [..] : List of named arguments:
-URL - The URL (excluding source name) for the source.
-DSN - The source name.
-COORDS - (optional) The coordinate systems supported by
the source. This is an arrayref of
Bio::EnsEMBL::ExternalData::DAS::CoordSystem
objects.
-LOGIC_NAME - (optional) The logic name of the source.
-LABEL - (optional) The display name of the source.
-DESCRIPTION - (optional) The description of the source.
-HOMEPAGE - (optional) A URL link to a page with more
information about the source.
-MAINTAINER - (optional) A contact email address for the source.
Example : $src = Bio::EnsEMBL::ExternalData::DAS::Source->new(
-DSN => 'astd_exon_human_36',
-URL => 'http://www.ebi.ac.uk/das-srv/genomicdas/das',
-COORDS => [ $cs1, $cs2 ],
-LABEL => 'ASTD transcripts',
-DESCRIPTION => 'Transcripts from the ASTD database...',
-HOMEPAGE => 'http://www.ebi.ac.uk/astd',
-MAINTAINER => 'andy.jenkinson@ebi.ac.uk',
);
Description: Creates a new Source object representing a DAS source.
Returntype : Bio::EnsEMBL::ExternalData::DAS::Source
Exceptions : If the URL or DSN are missing or incorrect
Caller : general
Status : Stable |
Arg [1] : Optional value to set
Description: Get/Setter for the server URL (excluding DSN)
Returntype : scalar
Exceptions : If the URL is missing or of an incorrect format
Status : Stable |
Methods code
sub coord_systems
{ my $self = shift;
if ( @_ ) {
$self->{coords} = shift;
}
return $self->{coords} || [];} | sub description
{ my $self = shift;
if ( @_ ) {
$self->{description} = shift;
}
return $self->{description} || $self->label;} | sub dsn
{ my $self = shift;
if ( @_ ) {
my $dsn = shift || throw("No DSN specified");
$self->{dsn} = $dsn;
}
return $self->{dsn};} | sub equals
{ my ( $this, $that ) = @_;
if ($this->full_url eq $that->full_url) {
my @this_cs = sort { $a->to_string cmp $b->to_string } @{ $this->coord_systems };
my @that_cs = sort { $a->to_string cmp $b->to_string } @{ $that->coord_systems };
if ( scalar @this_cs != scalar @that_cs ) {
return 0;
}
while (my $this_cs = shift @this_cs ) {
my $that_cs = shift @that_cs;
( $this_cs && $that_cs && $this_cs->equals( $that_cs ) ) || return 0;
}
return 1;
}
return 0;
}
1;} | sub full_url
{ my $self = shift;
return $self->url . q(/). $self->dsn; } | sub homepage
{ my $self = shift;
if ( @_ ) {
$self->{homepage} = shift;
}
return $self->{homepage};} | sub label
{ my $self = shift;
if ( @_ ) {
$self->{label} = shift;
}
return $self->{label} || $self->dsn;} | sub logic_name
{ my $self = shift;
if ( @_ ) {
$self->{logic_name} = shift;
}
return $self->{logic_name} || $self->dsn;} | sub maintainer
{ my $self = shift;
if ( @_ ) {
$self->{maintainer} = shift;
}
return $self->{maintainer};} | sub matches_name
{ my ($self, $name) = @_;
return (join '', $self->dsn, $self->label) =~ m/$name/ ? 1 : 0;
} | sub matches_species
{ my ($self, $species) = @_;
if (grep { $_->matches_species( $species ) } @{ $self->coord_systems || [] }) {
return 1;
}
return 0;} | sub new
{ my $class = shift;
my $self = {};
bless $self, $class;
my ($name, $label, $url, $dsn, $coords, $desc, $homepage, $maintainer) =
rearrange(['LOGIC_NAME', 'LABEL', 'URL', 'DSN', 'COORDS', 'DESCRIPTION', 'HOMEPAGE', 'MAINTAINER'], @_);
$self->url ( $url );
$self->dsn ( $dsn );
$self->logic_name ( $name );
$self->label ( $label );
$self->description ( $desc );
$self->maintainer ( $maintainer );
$self->homepage ( $homepage );
$self->coord_systems ( $coords );
return $self;} | sub url
{ my $self = shift;
if ( @_ ) {
$_[0] || throw("No URL specified");
my ($url) = $_[0] =~ m{(.+/das)1?/*$};
$url || throw("URL is not of correct format: $_[0]");
$self->{url} = $url;
}
return $self->{url};} | General documentation