diff variant_effect_predictor/Bio/Seq/RichSeqI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Seq/RichSeqI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,219 @@
+# $Id: RichSeqI.pm,v 1.8 2002/10/22 07:38:40 lapp Exp $
+#
+# BioPerl module for Bio::Seq::RichSeqI
+#
+# Cared for by Ewan Birney <[e-mail]>
+#
+# Copyright Ewan Birney
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Seq::RichSeqI - RichSeq interface, mainly for database orientated sequences
+
+=head1 SYNOPSIS
+
+    @secondary   = $richseq->get_secondary_accessions;
+    $division    = $richseq->division;
+    $mol         = $richseq->molecule;
+    @dates       = $richseq->get_dates; 
+    $seq_version = $richseq->seq_version;  
+    $pid         = $richseq->pid;
+    $keywords    = $richseq->keywords;
+
+=head1 DESCRIPTION
+
+This interface extends the Bio::SeqI interface to give additional functionality
+to sequences with richer data sources, in particular from database sequences 
+(EMBL, GenBank and Swissprot).
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this
+and other Bioperl modules. Send your comments and suggestions preferably
+ to one of the Bioperl mailing lists.
+Your participation is much appreciated.
+
+  [e-mail]                 - General discussion
+  http://bio.perl.org/MailList.html             - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+ the bugs and their resolution.
+ Bug reports can be submitted via email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Ewan Birney
+
+Email [e-mail]
+
+Describe contact details here
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::Seq::RichSeqI;
+use vars qw(@ISA);
+use strict;
+use Bio::SeqI;
+
+@ISA = ('Bio::SeqI');
+
+
+=head2 get_secondary_accessions
+
+ Title   : get_secondary_accessions
+ Usage   : 
+ Function: Get the secondary accessions for a sequence.
+ Example :
+ Returns : an array of strings
+ Args    : none
+
+
+=cut
+
+sub get_secondary_accessions{
+   my ($self,@args) = @_;
+
+   $self->throw("hit get_secondary_accessions in interface definition - error");
+
+}
+
+
+=head2 division
+
+ Title   : division
+ Usage   :
+ Function: Get (and set, depending on the implementation) the divison for
+           a sequence.
+
+           Examples from GenBank are PLN (plants), PRI (primates), etc.
+ Example :
+ Returns : a string
+ Args    :
+
+
+=cut
+
+sub division{
+   my ($self,@args) = @_;
+
+   $self->throw("hit division in interface definition - error");
+
+}
+
+
+=head2 molecule
+
+ Title   : molecule
+ Usage   :
+ Function: Get (and set, depending on the implementation) the molecule
+           type for the sequence.
+
+           This is not necessarily the same as Bio::PrimarySeqI::alphabet(),
+           because it is databank-specific.
+ Example :
+ Returns : a string
+ Args    :
+
+
+=cut
+
+sub molecule{
+   my ($self,@args) = @_;
+
+   $self->throw("hit molecule in interface definition - error");
+}
+
+=head2 pid
+
+ Title   : pid
+ Usage   :
+ Function: Get (and set, depending on the implementation) the PID property
+           for the sequence.
+ Example :
+ Returns : a string
+ Args    :
+
+
+=cut
+
+sub pid {
+   my ($self,@args) = @_;
+
+   $self->throw("hit pid in interface definition - error");
+}
+
+=head2 get_dates
+
+ Title   : get_dates
+ Usage   :
+ Function: Get (and set, depending on the implementation) the dates the
+           databank entry specified for the sequence
+ Example :
+ Returns : an array of strings
+ Args    :
+
+
+=cut
+
+sub get_dates{
+   my ($self,@args) = @_;
+
+   $self->throw("hit get_dates in interface definition - error");
+
+}
+
+
+=head2 seq_version
+
+ Title   : seq_version
+ Usage   :
+ Function: Get (and set, depending on the implementation) the version string
+           of the sequence.
+ Example :
+ Returns : a string
+ Args    :
+
+
+=cut
+
+sub seq_version{
+   my ($self,@args) = @_;
+
+   $self->throw("hit seq_version in interface definition - error");
+
+}
+
+=head2 keywords
+
+ Title   : keywords
+ Usage   : $obj->keywords($newval)
+ Function: 
+ Returns : value of keywords (a string)
+ Args    : newvalue (optional) (a string)
+
+
+=cut
+
+sub keywords {
+   my ($self) = @_;
+   $self->throw("hit keywords in interface definition - error");
+}
+
+1;