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1 # $Id: StatisticsI.pm,v 1.4 2002/10/22 07:45:10 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Align::StatisticsI
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4 #
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5 # Cared for by Jason Stajich <jason@bioperl.org>
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6 #
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7 # Copyright Jason Stajich
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::Align::StatisticsI - Calculate some statistics for an alignment
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16
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17 =head1 SYNOPSIS
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18
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19 Give standard usage here
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20
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21 =head1 DESCRIPTION
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22
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23 Describe the interface here
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24
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25 =head1 FEEDBACK
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26
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27 =head2 Mailing Lists
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28
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29 User feedback is an integral part of the evolution of this and other
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30 Bioperl modules. Send your comments and suggestions preferably to
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31 the Bioperl mailing list. Your participation is much appreciated.
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32
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33 bioperl-l@bioperl.org - General discussion
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34 http://bioperl.org/MailList.shtml - About the mailing lists
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35
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36 =head2 Reporting Bugs
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37
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38 Report bugs to the Bioperl bug tracking system to help us keep track
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39 of the bugs and their resolution. Bug reports can be submitted via
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40 email or the web:
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41
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42 bioperl-bugs@bioperl.org
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43 http://bugzilla.bioperl.org/
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44
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45 =head1 AUTHOR - Jason Stajich
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46
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47 Email jason@bioperl.org
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48
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49 Describe contact details here
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50
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51 =head1 CONTRIBUTORS
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52
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53 Additional contributors names and emails here
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54
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55 =head1 APPENDIX
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56
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57 The rest of the documentation details each of the object methods.
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58 Internal methods are usually preceded with a _
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59
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60 =cut
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61
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62
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63 # Let the code begin...
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64
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65
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66 package Bio::Align::StatisticsI;
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67 use strict;
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68 use vars qw(@ISA);
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69
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70 use Bio::Root::RootI;
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71
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72 @ISA = qw(Bio::Root::RootI);
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73
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74 =head2 distance
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75
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76 Title : distance
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77 Usage : my $distance_mat = $stats->distance(-align => $aln,
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78 -method => $method);
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79 Function: Calculates a distance matrix for all pairwise distances of
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80 sequences in an alignment.
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81 Returns : Array ref
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82 Args : -align => Bio::Align::AlignI object
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83 -method => String specifying specific distance method
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84 (implementing class may assume a default)
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85
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86 =cut
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87
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88 sub distance{
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89 my ($self,@args) = @_;
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90 $self->throw_not_implemented();
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91 }
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92
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93 =head2 available_distance_methods
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94
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95 Title : available_distance_methods
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96 Usage : my @methods = $stats->available_distance_methods();
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97 Function: Enumerates the possible distance methods
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98 Returns : Array of strings
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99 Args : none
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100
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101
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102 =cut
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103
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104 sub available_distance_methods{
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105 my ($self,@args) = @_;
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106 $self->throw_not_implemented();
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107 }
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108
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109 1;
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