Bio IdentifiableI
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Summary
Bio::IdentifiableI - interface for objects with identifiers
Package variables
No package variables defined.
Inherit
Bio::Root::RootI
Synopsis
    # to test this is an identifiable object
$obj->isa("Bio::IdentifiableI") || $obj->throw("$obj does not implement the Bio::IdentifiableI interface"); # Accessors $object_id = $obj->object_id(); $namespace = $obj->namespace(); $authority = $obj->authority(); $version = $obj->version(); # Gets authority:namespace:object_id $lsid = $obj->lsid_string(); # Gets namespace:object_id.version $ns_string = $obj->namespace_string();
Description
This interface describes methods expected on identifiable objects, i.e.
ones which have identifiers expected to make sense across a number of
instances and/or domains. This interface is modeled after pretty much
ubiquitous ideas for names in bioinformatics being
 databasename:object_id.version
Example:
 swissprot:P012334.2
or:
 GO:0007048
The object will also work with LSID proposals which adds the concept of an
authority, being the DNS name of the organisation assigning the namespace.
See http://lsid.sourceforge.net/.
Helper functions are provided to make useful strings:
  lsid_string - string complying to the LSID standard
namespace_string - string complying to the usual convention of namespace:object_id.version
Methods
object_idDescriptionCode
versionDescriptionCode
authorityDescriptionCode
namespaceDescriptionCode
lsid_stringDescriptionCode
namespace_stringDescriptionCode
Methods description
object_idcode    nextTop
 Title   : object_id
Usage : $string = $obj->object_id()
Function: a string which represents the stable primary identifier
in this namespace of this object. For DNA sequences this
is its accession_number, similarly for protein sequences
Returns : A scalar
Status : Virtual
versioncodeprevnextTop
 Title   : version
Usage : $version = $obj->version()
Function: a number which differentiates between versions of
the same object. Higher numbers are considered to be
later and more relevant, but a single object described
the same identifier should represent the same concept
Returns : A number
Status : Virtual
authoritycodeprevnextTop
 Title   : authority
Usage : $authority = $obj->authority()
Function: a string which represents the organisation which
granted the namespace, written as the DNS name for
organisation (eg, wormbase.org)
Returns : A scalar
Status : Virtual
namespacecodeprevnextTop
 Title   : namespace
Usage : $string = $obj->namespace()
Function: A string representing the name space this identifier
is valid in, often the database name or the name
describing the collection
Returns : A scalar
Status : Virtual
lsid_stringcodeprevnextTop
 Title   : lsid_string
Usage : $string = $obj->lsid_string()
Function: a string which gives the LSID standard
notation for the identifier of interest
Returns : A scalar
namespace_stringcodeprevnextTop
 Title   : namespace_string
Usage : $string = $obj->namespace_string()
Function: a string which gives the common notation of
namespace:object_id.version
Returns : A scalar
Methods code
object_iddescriptionprevnextTop
sub object_id {
   my ($self) = @_;
   $self->throw_not_implemented();
}
versiondescriptionprevnextTop
sub version {
   my ($self) = @_;
   $self->throw_not_implemented();
}
authoritydescriptionprevnextTop
sub authority {
   my ($self) = @_;
   $self->throw_not_implemented();
}
namespacedescriptionprevnextTop
sub namespace {
   my ($self) = @_;
   $self->throw_not_implemented();
}
lsid_stringdescriptionprevnextTop
sub lsid_string {
  my ($self) = @_;

  return $self->authority.":".$self->namespace.":".$self->object_id;
}
namespace_stringdescriptionprevnextTop
sub namespace_string {
  my ($self) = @_;

  return $self->namespace.":".$self->object_id .
      (defined($self->version()) ? ".".$self->version : '');
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Ewan BirneyTop
Email birney@ebi.ac.uk
Implementation Specific FunctionsTop
These functions are the ones that a specific implementation must
define.
Implementation optional functionsTop
These functions are helper functions that are provided by
the interface but can be overridden if so wished