diff variant_effect_predictor/Bio/Align/StatisticsI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Align/StatisticsI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,109 @@
+# $Id: StatisticsI.pm,v 1.4 2002/10/22 07:45:10 lapp Exp $
+#
+# BioPerl module for Bio::Align::StatisticsI
+#
+# Cared for by Jason Stajich <[e-mail]>
+#
+# Copyright Jason Stajich
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Align::StatisticsI - Calculate some statistics for an alignment
+
+=head1 SYNOPSIS
+
+Give standard usage here
+
+=head1 DESCRIPTION
+
+Describe the interface here
+
+=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 - Jason Stajich
+
+Email [e-mail]
+
+Describe contact details here
+
+=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::Align::StatisticsI;
+use strict;
+use vars qw(@ISA);
+
+use Bio::Root::RootI;
+
+@ISA = qw(Bio::Root::RootI);
+
+=head2 distance
+
+ Title   : distance
+ Usage   : my $distance_mat = $stats->distance(-align  => $aln, 
+		 			       -method => $method);
+ Function: Calculates a distance matrix for all pairwise distances of
+           sequences in an alignment.
+ Returns : Array ref
+ Args    : -align  => Bio::Align::AlignI object
+           -method => String specifying specific distance method 
+                      (implementing class may assume a default)
+
+=cut
+
+sub distance{
+   my ($self,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 available_distance_methods
+
+ Title   : available_distance_methods
+ Usage   : my @methods = $stats->available_distance_methods();
+ Function: Enumerates the possible distance methods
+ Returns : Array of strings
+ Args    : none
+
+
+=cut
+
+sub available_distance_methods{
+   my ($self,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+1;