diff variant_effect_predictor/Bio/IdentifiableI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/IdentifiableI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,218 @@
+# $Id: IdentifiableI.pm,v 1.6 2002/10/23 18:07:49 lapp Exp $
+
+#
+# This module is licensed under the same terms as Perl itself. You use,
+# modify, and redistribute it under the terms of the Perl Artistic License.
+#
+
+=head1 NAME
+
+Bio::IdentifiableI - interface for objects with identifiers
+
+=head1 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();
+
+    # utility function
+
+    $lsid        = $obj->lsid_string();      # gives authority:namespace:object_id
+    $ns_string   = $obj->namespace_string(); # gives namespace:object_id.version
+
+
+=head1 DESCRIPTION
+
+This interface describes methods expected on identifiable objects, ie
+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
+
+examples being
+
+ swissprot:P012334.2
+
+or
+
+ GO:0007048
+
+We also work well with LSID proposals which adds in the concept of an
+authority, being the DNS name of the organisation assigning the namespace.
+Helper functions are provided to make useful strings being
+
+
+  lsid_string - string complying to the LSID standard
+  namespace_string - string complying to the usual convention of 
+     namespace:object_id.version
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+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.
+
+  [e-mail]                       - General discussion
+  http://bio.perl.org/MailList.html           - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+the bugs and their resolution.  Bug reports can be submitted via email
+or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Ewan Birney
+
+Email [e-mail]
+
+=cut
+
+package Bio::IdentifiableI;
+use vars qw(@ISA );
+use strict;
+use Bio::Root::RootI;
+
+
+@ISA = qw(Bio::Root::RootI);
+
+=head1 Implementation Specific Functions
+
+These functions are the ones that a specific implementation must
+define.
+
+=head2 object_id
+
+ Title   : object_id
+ Usage   : $string    = $obj->object_id()
+ Function: a string which represents the stable primary identifier
+           in this namespace of this object. For DNA sequences this
+           is its accession_number, similarly for protein sequences
+
+ Returns : A scalar
+ Status  : Virtual
+
+=cut
+
+sub object_id {
+   my ($self) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 version
+
+ Title   : version
+ Usage   : $version    = $obj->version()
+ Function: a number which differentiates between versions of
+           the same object. Higher numbers are considered to be
+           later and more relevant, but a single object described
+           the same identifier should represent the same concept
+
+ Returns : A number
+ Status  : Virtual
+
+=cut
+
+sub version {
+   my ($self) = @_;
+   $self->throw_not_implemented();
+}
+
+
+=head2 authority
+
+ Title   : authority
+ Usage   : $authority    = $obj->authority()
+ Function: a string which represents the organisation which
+           granted the namespace, written as the DNS name for  
+           organisation (eg, wormbase.org)
+
+ Returns : A scalar
+ Status  : Virtual
+
+=cut
+
+sub authority {
+   my ($self) = @_;
+   $self->throw_not_implemented();
+}
+
+
+=head2 namespace
+
+ Title   : namespace
+ Usage   : $string    = $obj->namespace()
+ Function: A string representing the name space this identifier
+           is valid in, often the database name or the name
+           describing the collection 
+
+ Returns : A scalar
+ Status  : Virtual
+
+=cut
+
+sub namespace {
+   my ($self) = @_;
+   $self->throw_not_implemented();
+}
+
+
+
+=head1 Implementation optional functions
+
+These functions are helper functions that are provided by
+the interface but can be overridden if so wished
+
+=head2 lsid_string
+
+ Title   : lsid_string
+ Usage   : $string   = $obj->lsid_string()
+ Function: a string which gives the LSID standard
+           notation for the identifier of interest
+
+
+ Returns : A scalar
+
+=cut
+
+sub lsid_string {
+  my ($self) = @_;
+
+  return $self->authority.":".$self->namespace.":".$self->object_id;
+}
+
+
+
+=head2 namespace_string
+
+ Title   : namespace_string
+ Usage   : $string   = $obj->namespace_string()
+ Function: a string which gives the common notation of
+           namespace:object_id.version
+
+ Returns : A scalar
+
+=cut
+
+sub namespace_string {
+  my ($self) = @_;
+
+  return $self->namespace.":".$self->object_id .
+      (defined($self->version()) ? ".".$self->version : '');
+}
+
+1;