Bio/Align/StatisticsI.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Align::StatisticsI
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Jason Stajich <jason@bioperl.org>
   8 #
   9 # Copyright Jason Stajich
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::Align::StatisticsI - Calculate some statistics for an alignment
  18
  19 =head1 SYNOPSIS
  20
  21 Give standard usage here
  22
  23 =head1 DESCRIPTION
  24
  25 Describe the interface here
  26
  27 =head1 FEEDBACK
  28
  29 =head2 Mailing Lists
  30
  31 User feedback is an integral part of the evolution of this and other
  32 Bioperl modules. Send your comments and suggestions preferably to
  33 the Bioperl mailing list.  Your participation is much appreciated.
  34
  35   bioperl-l@bioperl.org                  - General discussion
  36   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  37
  38 =head2 Support
  39
  40 Please direct usage questions or support issues to the mailing list:
  41
  42 I<bioperl-l@bioperl.org>
  43
  44 rather than to the module maintainer directly. Many experienced and
  45 reponsive experts will be able look at the problem and quickly
  46 address it. Please include a thorough description of the problem
  47 with code and data examples if at all possible.
  48
  49 =head2 Reporting Bugs
  50
  51 Report bugs to the Bioperl bug tracking system to help us keep track
  52 of the bugs and their resolution. Bug reports can be submitted via the
  53 web:
  54
  55   http://bugzilla.open-bio.org/
  56
  57 =head1 AUTHOR - Jason Stajich
  58
  59 Email jason@bioperl.org
  60
  61 =head1 APPENDIX
  62
  63 The rest of the documentation details each of the object methods.
  64 Internal methods are usually preceded with a _
  65
  66 =cut
  67
  68
  69 # Let the code begin...
  70
  71
  72 package Bio::Align::StatisticsI;
  73 use strict;
  74
  75
  76 use base qw(Bio::Root::RootI);
  77
  78 =head2 distance
  79
  80  Title   : distance
  81  Usage   : my $distance_mat = $stats->distance(-align  => $aln,
  82                                                -method => $method);
  83  Function: Calculates a distance matrix for all pairwise distances of
  84            sequences in an alignment.
  85  Returns : Array ref
  86  Args    : -align  => Bio::Align::AlignI object
  87            -method => String specifying specific distance method
  88                       (implementing class may assume a default)
  89
  90 =cut
  91
  92 sub distance{
  93    my ($self,@args) = @_;
  94    $self->throw_not_implemented();
  95 }
  96
  97 =head2 available_distance_methods
  98
  99  Title   : available_distance_methods
 100  Usage   : my @methods = $stats->available_distance_methods();
 101  Function: Enumerates the possible distance methods
 102  Returns : Array of strings
 103  Args    : none
 104
 105
 106 =cut
 107
 108 sub available_distance_methods{
 109    my ($self,@args) = @_;
 110    $self->throw_not_implemented();
 111 }
 112
 113 1;