Bio::SeqEvolution::Factory.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::SeqEvolution::Factory - Factory object to instantiate sequence evolving classes

SYNOPSIS

     # not an instantiable class
 
 

DESCRIPTION

This is the factory class that can be used to call for a specific model to mutate a sequence.

Bio::SeqEvolution::DNAPoint is the default for nucleotide sequences and the only implementation at this point.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR

   Heikki Lehvaslaiho E<lt>heikki at bioperl dot orgE<gt>
 
 

CONTRIBUTORS

Additional contributor's names and emails here

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

   Title   : new
   Usage   : my $obj = Bio::SeqEvolution::Factory->new();
   Function: Builds a new Bio:SeqEvolution::EvolutionI object
   Returns : Bio:SeqEvolution::EvolutionI object
   Args    : -type           => class name
 
 

See <Bio:SeqEvolution::EvolutionI>

_load_format_module

  Title   : _load_format_module
  Usage   : *INTERNAL SeqIO stuff*
  Function: Loads up (like use) a module at run time on demand
  Example :
  Returns :
  Args    :
 
 

type

  Title   : type
  Usage   : $obj->type($newval)
  Function: Set used evolution model. It is set by giving a
            valid Bio::SeqEvolution::* class name 
  Returns : value of type
  Args    : newvalue (optional)
 
 

Defaults to Bio::SeqEvolution::DNAPoint.

mutation counters

The next three methods set a value to limit the number of mutations introduced the the input sequence.

identity

  Title   : identity
  Usage   : $obj->identity($newval)
  Function: Set the desired identity between original and mutated sequence
  Returns : value of identity
  Args    : newvalue (optional)
 
 

pam

  Title   : pam
  Usage   : $obj->pam($newval)
  Function: Set the wanted Percentage of Accepted Mutations, PAM
  Returns : value of PAM
  Args    : newvalue (optional)
 
 

When you are measuring sequence divergence, PAM needs to be estimated. When you are generating sequences, PAM is simply the count of mutations introduced to the reference sequence normalised to the original sequence lenght.

mutation_count

  Title   : mutation_count
  Usage   : $obj->mutation_count($newval)
  Function: Set the number of wanted mutations to the sequence 
  Returns : value of mutation_count
  Args    : newvalue (optional)
 
 

seq

  Title   : seq
  Usage   : $obj->seq($newval)
  Function: Set the sequence object for the original sequence
  Returns : The sequence object
  Args    : newvalue (optional)
 
 

Setting this will reset mutation and generated mutation counters.

seq_type

  Title   : seq_type
  Usage   : $obj->seq_type($newval)
  Function: Set the returned seq_type to one needed
  Returns : value of seq_type
  Args    : newvalue (optional)
 
 

Defaults to Bio::PrimarySeq.

get_mutation_counter

  Title   : get_mutation_counter
  Usage   : $obj->get_mutation_counter()
  Function: Get the count of sequences created
  Returns : value of counter
  Args    : -
 
 

reset_mutation_counter

  Title   : reset_mutation_counter
  Usage   : $obj->reset_mutation_counter()
  Function: Resert the counter of mutations
  Returns : value of counter
  Args    : -
 
 

get_sequence_counter

  Title   : get_sequence_counter
  Usage   : $obj->get_sequence_counter()
  Function: Get the count of sequences created
  Returns : value of counter
  Args    : -
 
 

reset_sequence_counter

  Title   : reset_sequence_counter
  Usage   : $obj->reset_sequence_counter()
  Function: Resert the counter of sequences created
  Returns : value of counter
  Args    : -
 
 

This is called when ever mutated sequences are reassigned new values using methods seq() and mutated_seq(). As a side affect, this method also recreates the intermal alignment that is used to calculate the sequence identity.

each_seq

  Title   : each_seq
  Usage   : $obj->each_seq($int)
  Function:
  Returns : an array of sequences mutated from the reference sequence
            according to evolutionary parameters given
  Args    : -
 
 

each_mutation

   Title   : each_mutation
   Usage   : $obj->each_mutation
   Function: return the mutations leading to the last generated 
             sequence in objects 
   Returns : an array of Bio::Variation::DNAMutation objects
   Args    : optional argument to return an array of  stringified names
 
 

Internal methods

_increase_mutation_counter

  Title   : _increase_mutation_counter
  Usage   : $obj->_increase_mutation_counter()
  Function: Internal method to increase the counter of mutations performed
  Returns : value of counter
  Args    : -
 
 

_increase_sequence_counter

  Title   : _increase_sequence_counter
  Usage   : $obj->_increase_sequence_counter()
  Function: Internal method to increase the counter of sequences created
  Returns : value of counter
  Args    : -