diff variant_effect_predictor/Bio/Cluster/UniGeneI.pm @ 0:1f6dce3d34e0

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+++ b/variant_effect_predictor/Bio/Cluster/UniGeneI.pm	Thu Apr 11 02:01:53 2013 -0400
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+# $Id: UniGeneI.pm,v 1.9 2002/10/25 22:49:03 lapp Exp $
+#
+# BioPerl module for Bio::Cluster::UniGeneI.pm
+#
+# Cared for by Andrew Macgregor <[e-mail]>
+#
+# Copyright Andrew Macgregor, Jo-Ann Stanton, David Green
+# Molecular Embryology Group, Anatomy & Structural Biology, University of Otago
+# http://anatomy.otago.ac.nz/meg
+#
+# You may distribute this module under the same terms as perl itself
+#
+# _history
+# April 31, 2002 - Initial implementation by Andrew Macgregor
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Cluster::UniGeneI - abstract interface of UniGene object
+
+=head1 SYNOPSIS
+
+  #
+
+=head1 DESCRIPTION
+
+This is the general interface for a UniGene cluster representation in Bioperl. You cannot use this module directly, use an implementation instead.
+
+You can create UniGene cluster objects yourself by instantiating
+L<Bio::Cluster::UniGene>. If you read UniGene clusters from a
+ClusterIO parser, you will get objects implementing this interface,
+most likely instances of said UniGene class.
+
+L<Bio::Cluster::UniGeneI> inherits from L<Bio::ClusterI>, so you can
+use it wherever a cluster object is expected.
+
+=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 - Andrew Macgregor
+
+Email [e-mail]
+
+
+=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::Cluster::UniGeneI;
+use vars qw(@ISA $VERSION);
+use strict;
+
+use Bio::ClusterI;
+
+$VERSION = '1.0';
+@ISA = qw(Bio::ClusterI);
+
+
+=head2 unigene_id
+
+ Title   : unigene_id
+ Usage   : unigene_id();
+ Function: Returns the unigene_id associated with the object.
+ Example : $id = $unigene->unigene_id or $unigene->unigene_id($id)
+ Returns : A string
+ Args    : None or an id
+
+
+=cut
+
+sub unigene_id {
+	my ($self) = @_;
+	$self->throw_not_implemented;
+}
+
+
+
+=head2 title
+
+ Title   : title
+ Usage   : title();
+ Function: Returns the title associated with the object.
+ Example : $title = $unigene->title or $unigene->title($title)
+ Returns : A string
+ Args    : None or a title
+
+
+=cut
+
+sub title {
+	my ($self) = @_;
+	$self->throw_not_implemented;
+}
+
+
+=head2 gene
+
+ Title   : gene
+ Usage   : gene();
+ Function: Returns the gene associated with the object.
+ Example : $gene = $unigene->gene or $unigene->gene($gene)
+ Returns : A string
+ Args    : None or a gene
+
+
+=cut
+
+sub gene {
+	my ($self) = @_;
+	$self->throw_not_implemented;
+}
+
+
+=head2 cytoband
+
+ Title   : cytoband
+ Usage   : cytoband();
+ Function: Returns the cytoband associated with the object.
+ Example : $cytoband = $unigene->cytoband or $unigene->cytoband($cytoband)
+ Returns : A string
+ Args    : None or a cytoband
+
+
+=cut
+
+sub cytoband {
+	my ($self) = @_;
+	$self->throw_not_implemented;
+}
+
+
+=head2 mgi
+
+ Title   : mgi
+ Usage   : mgi();
+ Function: Returns the mgi associated with the object.
+ Example : $mgi = $unigene->mgi or $unigene->mgi($mgi)
+ Returns : A string
+ Args    : None or a mgi
+
+
+=cut
+
+sub mgi {
+	my ($self) = @_;
+	$self->throw_not_implemented;
+}
+
+
+=head2 locuslink
+
+ Title   : locuslink
+ Usage   : locuslink();
+ Function: Returns or stores a reference to an array containing locuslink data.
+ 		   This should really only be used by ClusterIO, not directly
+ Returns : An array reference
+ Args    : None or an array reference
+
+=cut
+
+sub locuslink {
+	my ($self) = @_;
+	$self->throw_not_implemented;
+}
+
+
+=head2 gnm_terminus
+
+ Title   : gnm_terminus
+ Usage   : gnm_terminus();
+ Function: Returns the gnm_terminus associated with the object.
+ Example : $gnm_terminus = $unigene->gnm_terminus or $unigene->gnm_terminus($gnm_terminus)
+ Returns : A string
+ Args    : None or a gnm_terminus
+
+=cut
+
+sub gnm_terminus {
+	my ($self) = @_;
+	$self->throw_not_implemented;
+}
+
+
+=head2 scount
+
+ Title   : scount
+ Usage   : scount();
+ Function: Returns the scount associated with the object.
+ Example : $scount = $unigene->scount or $unigene->scount($scount)
+ Returns : A string
+ Args    : None or a scount
+
+=cut
+
+sub scount {
+	my ($self) = @_;
+	$self->throw_not_implemented;
+}
+
+
+
+=head2 express
+
+ Title   : express
+ Usage   : express();
+ Function: Returns or stores a reference to an array containing tissue expression data.
+ 		   This should really only be used by ClusterIO, not directly
+ Returns : An array reference
+ Args    : None or an array reference
+
+=cut
+
+sub express {
+	my ($self) = @_;
+	$self->throw_not_implemented;
+}
+
+
+=head2 chromosome
+
+ Title   : chromosome
+ Usage   : chromosome();
+ Function: Returns or stores a reference to an array containing chromosome lines
+ 		   This should really only be used by ClusterIO, not directly
+ Returns : An array reference
+ Args    : None or an array reference
+
+=cut
+
+sub chromosome {
+	my ($self) = @_;
+	$self->throw_not_implemented;
+}
+
+
+=head2 sts
+
+ Title   : sts
+ Usage   : sts();
+ Function: Returns or stores a reference to an array containing sts lines
+ 		   This should really only be used by ClusterIO, not directly
+ Returns : An array reference
+ Args    : None or an array reference
+
+=cut
+
+sub sts {
+	my ($self) = @_;
+	$self->throw_not_implemented;
+}
+
+
+=head2 txmap
+
+ Title   : txmap
+ Usage   : txmap();
+ Function: Returns or stores a reference to an array containing txmap lines
+ Returns : An array reference
+ Args    : None or an array reference
+
+=cut
+
+sub txmap {
+	my ($self) = @_;
+	$self->throw_not_implemented;
+}
+
+
+=head2 protsim
+
+ Title   : protsim
+ Usage   : protsim();
+ Function: Returns or stores a reference to an array containing protsim lines
+ 		   This should really only be used by ClusterIO, not directly
+ Returns : An array reference
+ Args    : None or an array reference
+
+=cut
+
+sub protsim {
+	my ($self) = @_;
+	$self->throw_not_implemented;
+}
+
+
+=head2 sequence
+
+ Title   : sequence
+ Usage   : sequence();
+ Function: Returns or stores a reference to an array containing sequence data
+ 		   This should really only be used by ClusterIO, not directly
+ Returns : An array reference
+ Args    : None or an array reference
+
+=cut
+
+sub sequence {
+	my ($self) = @_;
+	$self->throw_not_implemented;
+}
+
+=head2 species
+
+ Title   : species
+ Usage   : $obj->species($newval)
+ Function: Get the species object for this Unigene cluster.
+ Example : 
+ Returns : value of species (a L<Bio::Species> object)
+ Args    : 
+
+
+=cut
+
+sub species{
+    shift->throw_not_implemented();
+}
+
+=head1 Methods inherited from L<Bio::ClusterI>
+
+=cut
+
+=head2 display_id
+
+ Title   : display_id
+ Usage   : 
+ Function: Get/set the display name or identifier for the cluster
+ Returns : a string
+ Args    : optional, on set the display ID ( a string)
+
+=cut
+
+=head2 description
+
+ Title   : description
+ Usage   : Bio::ClusterI->description("POLYUBIQUITIN")
+ Function: get/set for the consensus description of the cluster
+ Returns : the description string 
+ Args    : Optional the description string 
+
+=cut
+
+=head2 size
+
+ Title   : size
+ Usage   : Bio::ClusterI->size();
+ Function: get/set for the size of the family, 
+           calculated from the number of members
+ Returns : the size of the family 
+ Args    : 
+
+=cut
+
+=head2 cluster_score
+
+ Title   : cluster_score
+ Usage   : $cluster ->cluster_score(100);
+ Function: get/set for cluster_score which
+           represent the score in which the clustering
+           algorithm assigns to this cluster.
+ Returns : a number
+
+=cut
+
+=head2 get_members
+
+ Title   : get_members
+ Usage   : Bio::ClusterI->get_members(($seq1, $seq2));
+ Function: retrieve the members of the family by some criteria, for
+           example :
+           $cluster->get_members(-species => 'homo sapiens'); 
+
+           Will return all members if no criteria are provided.
+
+ Returns : the array of members
+ Args    : 
+
+=cut
+
+1;