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:

         https://github.com/bioperl/bioperl-live/issues

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 length.

   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    : -