lib/Bio/Align/StatisticsI.pm

   1 #
   2 # BioPerl module for Bio::Align::StatisticsI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Jason Stajich <jason@bioperl.org>
   7 #
   8 # Copyright Jason Stajich
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::Align::StatisticsI - Calculate some statistics for an alignment
  17
  18 =head1 SYNOPSIS
  19
  20 Give standard usage here
  21
  22 =head1 DESCRIPTION
  23
  24 Describe the interface here
  25
  26 =head1 FEEDBACK
  27
  28 =head2 Mailing Lists
  29
  30 User feedback is an integral part of the evolution of this and other
  31 Bioperl modules. Send your comments and suggestions preferably to
  32 the Bioperl mailing list.  Your participation is much appreciated.
  33
  34   bioperl-l@bioperl.org                  - General discussion
  35   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  36
  37 =head2 Support
  38
  39 Please direct usage questions or support issues to the mailing list:
  40
  41 I<bioperl-l@bioperl.org>
  42
  43 rather than to the module maintainer directly. Many experienced and
  44 reponsive experts will be able look at the problem and quickly
  45 address it. Please include a thorough description of the problem
  46 with code and data examples if at all possible.
  47
  48 =head2 Reporting Bugs
  49
  50 Report bugs to the Bioperl bug tracking system to help us keep track
  51 of the bugs and their resolution. Bug reports can be submitted via the
  52 web:
  53
  54   https://github.com/bioperl/bioperl-live/issues
  55
  56 =head1 AUTHOR - Jason Stajich
  57
  58 Email jason@bioperl.org
  59
  60 =head1 APPENDIX
  61
  62 The rest of the documentation details each of the object methods.
  63 Internal methods are usually preceded with a _
  64
  65 =cut
  66
  67
  68 # Let the code begin...
  69
  70
  71 package Bio::Align::StatisticsI;
  72
  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;