diff variant_effect_predictor/Bio/DB/RandomAccessI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/DB/RandomAccessI.pm	Thu Apr 11 02:01:53 2013 -0400
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+# POD documentation - main docs before the code
+#
+# $Id: RandomAccessI.pm,v 1.12 2002/10/22 07:38:29 lapp Exp $
+#
+
+=head1 NAME
+
+Bio::DB::RandomAccessI - Abstract interface for a sequence database
+
+=head1 SYNOPSIS
+
+  #
+  # get a database object somehow using a concrete class
+  #
+
+  $seq = $db->get_Seq_by_id('ROA1_HUMAN');
+
+  #
+  # $seq is a Bio::Seq object
+  #
+
+=head1 DESCRIPTION
+
+This is a pure interface class - in other words, all this does is define
+methods which other (concrete) classes will actually implement. 
+
+The Bio::DB::RandomAccessI class defines what methods a generic database class
+should have. At the moment it is just the ability to make Bio::Seq objects
+from a name (id) or a accession number.
+
+=head1 CONTACT
+
+Ewan Birney originally wrote this class.
+
+=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 APPENDIX
+
+The rest of the documentation details each of the object
+methods. Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+package Bio::DB::RandomAccessI;
+
+use vars qw(@ISA);
+use strict;
+
+use Bio::Root::RootI;
+use Bio::Root::Root;
+
+@ISA = qw(Bio::Root::Root);
+
+=head2 get_Seq_by_id
+
+ Title   : get_Seq_by_id
+ Usage   : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
+ Function: Gets a Bio::Seq object by its name
+ Returns : a Bio::Seq object or undef if not found
+ Args    : the id (as a string) of a sequence,
+
+=cut
+
+sub get_Seq_by_id{
+   my ($self,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 get_Seq_by_acc
+
+ Title   : get_Seq_by_acc
+ Usage   : $seq = $db->get_Seq_by_acc('X77802');
+           $seq = $db->get_Seq_by_acc(Locus => 'X77802');
+ Function: Gets a Bio::Seq object by accession number
+ Returns : A Bio::Seq object or undef if not found
+ Args    : accession number (as a string), or a two
+               element list consisting of namespace=>accession
+ Throws  : "more than one sequences correspond to this accession"
+            if the accession maps to multiple primary ids and
+            method is called in a scalar context
+
+NOTE: The two-element form allows you to choose the namespace for the
+accession number.
+
+=cut
+
+sub get_Seq_by_acc{
+   my ($self,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+
+=head2 get_Seq_by_version
+
+ Title   : get_Seq_by_version
+ Usage   : $seq = $db->get_Seq_by_version('X77802.1');
+ Function: Gets a Bio::Seq object by sequence version
+ Returns : A Bio::Seq object
+ Args    : accession.version (as a string)
+ Throws  : "acc.version does not exist" exception
+
+=cut
+
+
+sub get_Seq_by_version{
+   my ($self,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+
+
+## End of Package
+
+1;
+