Bio::Polloc::RuleIO - I/O interface for the sets of rules (Bio::Polloc::RuleI)
Email lmrodriguezr at gmail dot com
Bio::Polloc::Polloc::Root
Bio::Polloc::Polloc::IO
Methods provided by the package
The basic initialization method
Arguments
The same arguments of Bio::Polloc::Polloc::IO, plus:
The format of the file
Sets/gets the prefix ID, unique for the RuleSet
Purpose
To allow the identification of children in a unique namespace
A string, supposedly unique. Any colon (:) will be changed to '_'
Returns
The prefix ID.
Appends rules to the rules set.
One or more Bio::Polloc::RuleI objects
The index of the last rule
A Bio::Polloc::Polloc::Error exception if some object is not a Bio::Polloc::RuleI
Gets the rule at the given index
The index (int)
A Bio::Polloc::RuleI object or undef
A Bio::Polloc::RuleI object
Sets/gets the group criteria objects.
A Bio::Polloc::GroupCriteria array ref (optional)
A Bio::Polloc::GroupCriteria array ref or undef
Alias of groupcriteria() (for backwards-compatibility).
Adds a grouprules object
A Bio::Polloc::GroupCriteria object
Throws
A Bio::Polloc::Polloc::Error if not a proper object
Executes the executable rules only over the whole list of genomes
Any argument supported/required by the rules, plus:
A reference to a method to be called to report the advance of the execution. The method must accept four arguments, namely:
The number of loci detected so far
The number of genomes scanned so far
The total number of genomes to scan
The ID of the running rule
A Bio::Polloc::LociGroup object.
Sets/gets a parameter of arbitrary name and value
To provide a safe interface for setting values from the parsed file
The parameter's name (case insensitive)
The value of the parameter (optional)
The value of the parameter or undef
Gets/sets some generic parameter. It is intended to provide an interface between Bio::Polloc::RuleIO's general configuration and Bio::Polloc::RuleI, regardless of the format.
The key (str) and the value (mix, optional)
The value (mix or undef)
A Bio::Polloc::Polloc::NotImplementedException if not implemented
Gets/sets the genomes to be used as analysis base.
A reference to an array of Bio::Polloc::Genome objects.
Methods intended to be used only within the scope of Bio::Polloc::*
To install Bio::Polloc::RuleI, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Polloc::RuleI
CPAN shell
perl -MCPAN -e shell install Bio::Polloc::RuleI
For more information on module installation, please visit the detailed CPAN module installation guide.