Bio::SeqEvolution::FacUser(Contributed Perl DocumBio::SeqEvolution::Factory(3)NAMEBio::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 : -
perl v5.14.1 2011-07-22 Bio::SeqEvolution::Factory(3)
