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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Cluster/FamilyI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,183 @@
+#
+# BioPerl module for Bio::Cluster::FamilyI
+#
+# 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::Cluster::FamilyI - Family 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 if for a Family object representing a family of 
+biological objects. A generic implementation for this may be
+found a Bio::Cluster::Family.
+
+
+=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
+
+
+package Bio::Cluster::FamilyI;
+use vars qw(@ISA);
+use strict;
+
+use Bio::ClusterI;
+
+@ISA = qw(Bio::ClusterI);
+
+=head2 new
+
+  We dont mandate but encourage implementors to support at least the
+  following named parameters upon object initialization.
+
+ Arguments          Description
+ ---------          -----------
+ -family_id         the name of the family
+ -description       the consensus description of the family
+ -annotation_score  the confidence by which the consensus description is 
+                    representative of the family
+ -members           the members belonging to the family
+ -alignment         the multiple alignment of the members
+
+=cut
+
+
+=head2 family_id
+
+ Title   : family_id
+ Usage   : Bio::Cluster::FamilyI->family_id("znfp");
+ Function: get/set for the family id 
+ Returns : the family id 
+ Args    : the family id
+
+=cut
+
+sub family_id{
+    shift->throw_not_implemented();
+}
+
+=head2 family_score
+
+ Title   : family_score
+ Usage   : Bio::Cluster::FamilyI->family_score(95);
+ Function: get/set for the score of algorithm used to generate
+           the family if present
+ Returns : the score
+ Args    : the score
+
+=cut
+
+sub family_score {
+    shift->throw_not_implemented();
+}
+
+
+=head1 Methods inherited from L<Bio::ClusterI>
+
+=cut
+
+=head2 display_id
+
+ Title   : display_id
+ Usage   : 
+ Function: Get the display name or identifier for the cluster
+ Returns : a string
+ Args    : 
+
+=cut
+
+=head2 get_members
+
+ Title   : get_members
+ Usage   : Bio::Cluster::FamilyI->get_members();
+ Function: get the members of the family
+ Returns : the array of members
+ Args    : the array of members
+
+=cut
+
+=head2 description
+
+ Title   : description
+ Usage   : Bio::Cluster::FamilyI->description("Zinc Finger Protein");
+ Function: get/set for the description of the family
+ Returns : the description 
+ Args    : the description
+
+=cut
+
+
+=head2 size
+
+ Title   : size
+ Usage   : Bio::Cluster::FamilyI->size();
+ Function: get/set for the description of the family
+ Returns : size 
+ 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
+
+1;