Bio/SeqEvolution/EvolutionI.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::SeqEvolution::EvolutionI
   4 #
   5 # Cared for by Heikki Lehvaslaiho <heikki at bioperl dot org>
   6 #
   7 # Copyright Heikki Lehvaslaiho
   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::SeqEvolution::EvolutionI - the interface for evolving sequences
  16
  17 =head1 SYNOPSIS
  18
  19     # not an instantiable class
  20
  21 =head1 DESCRIPTION
  22
  23 This is the interface that all classes that mutate sequence objects in
  24 constant fashion must implement. A good example is
  25 Bio::SeqEvolution::DNAPoint.
  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/MailList.shtml  - About the mailing lists
  37
  38 =head2 Reporting Bugs
  39
  40 Report bugs to the Bioperl bug tracking system to help us keep track
  41 of the bugs and their resolution. Bug reports can be submitted via the
  42 web:
  43
  44   http://bugzilla.bioperl.org/
  45
  46 =head1 AUTHOR
  47
  48   Heikki Lehvaslaiho E<lt>heikki at bioperl dot orgE<gt>
  49
  50 =head1 CONTRIBUTORS
  51
  52 Additional contributor's names and emails here
  53
  54 =head1 APPENDIX
  55
  56 The rest of the documentation details each of the object methods.
  57 Internal methods are usually preceded with a _
  58
  59 =cut
  60
  61
  62 # Let the code begin...
  63
  64
  65 package Bio::SeqEvolution::EvolutionI;
  66 use strict;
  67
  68 use base qw(Bio::Root::RootI);
  69
  70 =head2 annotation
  71
  72  Title   : annotation
  73  Usage   : $obj->annotation($newval)
  74  Function: Get the annotation collection for this annotatable object.
  75  Example :
  76  Returns : a Bio::AnnotationCollectionI implementing object, or undef
  77  Args    : on set, new value (a Bio::AnnotationCollectionI
  78            implementing object, optional) (an implementation may not
  79            support changing the annotation collection)
  80
  81 See L<Bio::AnnotationCollectionI>
  82
  83 =cut
  84
  85
  86 =head2 seq
  87
  88  Title   : seq
  89  Usage   : $obj->seq($newval)
  90  Function: Set the sequence object for the original sequence
  91  Returns : The sequence object
  92  Args    : newvalue (optional)
  93
  94 Setting this will reset mutation and generated mutation counters.
  95
  96 =cut
  97
  98 sub seq { shift->throw_not_implemented(); }
  99
 100 =head2 next_seq
 101
 102   Title   : next_seq
 103   Usage   : $obj->next_seq
 104   Function: Evolve the reference sequence to desired level
 105   Returns : A new sequence object mutated from the reference sequence
 106   Args    : -
 107
 108 =cut
 109
 110 sub next_seq{ shift->throw_not_implemented(); }
 111
 112
 113 =head2 mutate
 114
 115   Title   : mutate
 116   Usage   : $obj->mutate
 117   Function: mutate the sequence at the given location according to the model
 118   Returns : true
 119   Args    : integer, start location of the mutation, required argument
 120
 121 Called from next_seq().
 122
 123 =cut
 124
 125 sub mutate { shift->throw_not_implemented(); }
 126
 127
 128 1;