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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/ClusterI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,178 @@
+# $Id: ClusterI.pm,v 1.3 2002/10/25 01:29:37 lapp Exp $
+#
+# BioPerl module for Bio::ClusterI
+#
+# Cared for by Shawn Hoon <[e-mail]>
+#
+# Copyright Shawn Hoon
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::ClusterI - Cluster Interface 
+
+=head1 SYNOPSIS
+
+# see the implementations of this interface for details but
+# basically
+
+    my $cluster= $cluster->new(-description=>"POLYUBIQUITIN",
+                               -members    =>[$seq1,$seq2]);
+    my @members = $cluster->get_members();
+    my @sub_members = $cluster->get_members(-species=>"homo sapiens");
+
+
+
+=head1 DESCRIPTION
+
+This interface is the basic structure for a cluster of bioperl objects.
+In this case it is up to the implementer to check arguments
+and initialize whatever new object the implementing class is designed for.
+
+=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
+the Bioperl mailing list.  Your participation is much appreciated.
+
+  [e-mail]              - General discussion
+  http://bioperl.org/MailList.shtml  - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+of the bugs and their resolution. Bug reports can be submitted via
+email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Shawn Hoon
+
+Email [e-mail]
+
+
+=head1 CONTRIBUTORS
+
+Additional contributors names and emails 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::ClusterI;
+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 new
+
+  We dont mandate but encourage implementors to support at least the
+  following named parameters upon object initialization.
+
+  Argument        Description
+  --------        -----------
+  -display_id     the display ID or name for the cluster
+  -description    the consensus description or name of the cluster
+  -members        the array of objects belonging to the family
+
+=cut
+
+=head2 display_id
+
+ Title   : display_id
+ Usage   : 
+ Function: Get the display name or identifier for the cluster
+ Returns : a string
+ Args    : 
+
+=cut
+
+sub display_id{
+    shift->throw_not_implemented();
+}
+
+
+=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
+
+sub description{
+    shift->throw_not_implemented();
+}
+
+=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
+
+sub size {
+    shift->throw_not_implemented();
+}
+
+=head2 cluster_score
+
+ Title   : cluster_score
+ Usage   : $cluster ->cluster_score(100);
+ Function: get/set for cluster_score which
+           represent the score in which the clustering
+           algorithm assigns to this cluster.
+ Returns : a number
+
+=cut
+
+sub cluster_score{
+    shift->throw_not_implemented();
+}
+
+=head2 get_members
+
+ Title   : get_members
+ Usage   : Bio::ClusterI->get_members(($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
+
+sub get_members {
+    shift->throw_not_implemented();
+}
+
+1;