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>
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 : -