Provided by: libbio-perl-perl_1.7.2-3_all
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.
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Heikki Lehvaslaiho E<lt>heikki at bioperl dot orgE<gt>
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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.
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
_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 : -