Bio/SeqEvolution/EvolutionI.pm

   1 #
   2 # BioPerl module for Bio::SeqEvolution::EvolutionI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Heikki Lehvaslaiho <heikki at bioperl dot org>
   7 #
   8 # Copyright Heikki Lehvaslaiho
   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::SeqEvolution::EvolutionI - the interface for evolving sequences
  17
  18 =head1 SYNOPSIS
  19
  20     # not an instantiable class
  21
  22 =head1 DESCRIPTION
  23
  24 This is the interface that all classes that mutate sequence objects in
  25 constant fashion must implement. A good example is
  26 Bio::SeqEvolution::DNAPoint.
  27
  28 =head1 FEEDBACK
  29
  30 =head2 Mailing Lists
  31
  32 User feedback is an integral part of the evolution of this and other
  33 Bioperl modules. Send your comments and suggestions preferably to
  34 the Bioperl mailing list.  Your participation is much appreciated.
  35
  36   bioperl-l@bioperl.org                  - General discussion
  37   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  38
  39 =head2 Support
  40
  41 Please direct usage questions or support issues to the mailing list:
  42
  43 I<bioperl-l@bioperl.org>
  44
  45 rather than to the module maintainer directly. Many experienced and
  46 reponsive experts will be able look at the problem and quickly
  47 address it. Please include a thorough description of the problem
  48 with code and data examples if at all possible.
  49
  50 =head2 Reporting Bugs
  51
  52 Report bugs to the Bioperl bug tracking system to help us keep track
  53 of the bugs and their resolution. Bug reports can be submitted via the
  54 web:
  55
  56   https://github.com/bioperl/bioperl-live/issues
  57
  58 =head1 AUTHOR
  59
  60   Heikki Lehvaslaiho E<lt>heikki at bioperl dot orgE<gt>
  61
  62 =head1 CONTRIBUTORS
  63
  64 Additional contributor's names and emails here
  65
  66 =head1 APPENDIX
  67
  68 The rest of the documentation details each of the object methods.
  69 Internal methods are usually preceded with a _
  70
  71 =cut
  72
  73
  74 # Let the code begin...
  75
  76
  77 package Bio::SeqEvolution::EvolutionI;
  78 use strict;
  79
  80 use base qw(Bio::Root::RootI);
  81
  82 =head2 annotation
  83
  84  Title   : annotation
  85  Usage   : $obj->annotation($newval)
  86  Function: Get the annotation collection for this annotatable object.
  87  Example :
  88  Returns : a Bio::AnnotationCollectionI implementing object, or undef
  89  Args    : on set, new value (a Bio::AnnotationCollectionI
  90            implementing object, optional) (an implementation may not
  91            support changing the annotation collection)
  92
  93 See L<Bio::AnnotationCollectionI>
  94
  95 =cut
  96
  97
  98 =head2 seq
  99
 100  Title   : seq
 101  Usage   : $obj->seq($newval)
 102  Function: Set the sequence object for the original sequence
 103  Returns : The sequence object
 104  Args    : newvalue (optional)
 105
 106 Setting this will reset mutation and generated mutation counters.
 107
 108 =cut
 109
 110 sub seq { shift->throw_not_implemented(); }
 111
 112 =head2 next_seq
 113
 114   Title   : next_seq
 115   Usage   : $obj->next_seq
 116   Function: Evolve the reference sequence to desired level
 117   Returns : A new sequence object mutated from the reference sequence
 118   Args    : -
 119
 120 =cut
 121
 122 sub next_seq{ shift->throw_not_implemented(); }
 123
 124
 125 =head2 mutate
 126
 127   Title   : mutate
 128   Usage   : $obj->mutate
 129   Function: mutate the sequence at the given location according to the model
 130   Returns : true
 131   Args    : integer, start location of the mutation, required argument
 132
 133 Called from next_seq().
 134
 135 =cut
 136
 137 sub mutate { shift->throw_not_implemented(); }
 138
 139
 140 1;