Bio/Align/StatisticsI.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Align::StatisticsI
   4 #
   5 # Cared for by Jason Stajich <jason@bioperl.org>
   6 #
   7 # Copyright Jason Stajich
   8 #
   9 # You may distribute this module under the same terms as perl itself
  10
  11 # POD documentation - main docs before the code
  12
  13 =head1 NAME
  14
  15 Bio::Align::StatisticsI - Calculate some statistics for an alignment
  16
  17 =head1 SYNOPSIS
  18
  19 Give standard usage here
  20
  21 =head1 DESCRIPTION
  22
  23 Describe the interface here
  24
  25 =head1 FEEDBACK
  26
  27 =head2 Mailing Lists
  28
  29 User feedback is an integral part of the evolution of this and other
  30 Bioperl modules. Send your comments and suggestions preferably to
  31 the Bioperl mailing list.  Your participation is much appreciated.
  32
  33   bioperl-l@bioperl.org                  - General discussion
  34   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  35
  36 =head2 Reporting Bugs
  37
  38 Report bugs to the Bioperl bug tracking system to help us keep track
  39 of the bugs and their resolution. Bug reports can be submitted via the
  40 web:
  41
  42   http://bugzilla.open-bio.org/
  43
  44 =head1 AUTHOR - Jason Stajich
  45
  46 Email jason@bioperl.org
  47
  48 =head1 APPENDIX
  49
  50 The rest of the documentation details each of the object methods.
  51 Internal methods are usually preceded with a _
  52
  53 =cut
  54
  55
  56 # Let the code begin...
  57
  58
  59 package Bio::Align::StatisticsI;
  60 use strict;
  61
  62
  63 use base qw(Bio::Root::RootI);
  64
  65 =head2 distance
  66
  67  Title   : distance
  68  Usage   : my $distance_mat = $stats->distance(-align  => $aln,
  69                                                -method => $method);
  70  Function: Calculates a distance matrix for all pairwise distances of
  71            sequences in an alignment.
  72  Returns : Array ref
  73  Args    : -align  => Bio::Align::AlignI object
  74            -method => String specifying specific distance method
  75                       (implementing class may assume a default)
  76
  77 =cut
  78
  79 sub distance{
  80    my ($self,@args) = @_;
  81    $self->throw_not_implemented();
  82 }
  83
  84 =head2 available_distance_methods
  85
  86  Title   : available_distance_methods
  87  Usage   : my @methods = $stats->available_distance_methods();
  88  Function: Enumerates the possible distance methods
  89  Returns : Array of strings
  90  Args    : none
  91
  92
  93 =cut
  94
  95 sub available_distance_methods{
  96    my ($self,@args) = @_;
  97    $self->throw_not_implemented();
  98 }
  99
 100 1;