- mutation counters
- Internal methods
Bio::SeqEvolution::Factory - Factory object to instantiate sequence evolving classes
# not an instantiable class
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.
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.
email@example.com - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
Heikki Lehvaslaiho E<lt>heikki at bioperl dot orgE<gt>
Additional contributor's names and emails here
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
Title : _load_format_module Usage : *INTERNAL SeqIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args :
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.
The next three methods set a value to limit the number of mutations introduced the the input sequence.
Title : identity Usage : $obj->identity($newval) Function: Set the desired identity between original and mutated sequence Returns : value of identity Args : newvalue (optional)
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.
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)
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.
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.
Title : get_mutation_counter Usage : $obj->get_mutation_counter() Function: Get the count of sequences created Returns : value of counter Args : -
Title : reset_mutation_counter Usage : $obj->reset_mutation_counter() Function: Resert the counter of mutations Returns : value of counter Args : -
Title : get_sequence_counter Usage : $obj->get_sequence_counter() Function: Get the count of sequences created Returns : value of counter Args : -
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.
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 : -
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
Title : _increase_mutation_counter Usage : $obj->_increase_mutation_counter() Function: Internal method to increase the counter of mutations performed Returns : value of counter Args : -
Title : _increase_sequence_counter Usage : $obj->_increase_sequence_counter() Function: Internal method to increase the counter of sequences created Returns : value of counter Args : -