Bio::Polloc::RuleI - Generic rules interface
Use this interface to initialize the Bio::Polloc::Rule::* objects. Any rule inherits from this Interface. Usually, rules are initialized in sets (via the Bio::Polloc::RuleIO package).
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Methods provided by the package
Bio::Polloc::Polloc::Error if unable to initialize the proper object
Can be: pattern,
See the corresponding
Bio::Polloc::Rule::* objects for further details.
Some variations can be introduced, like case variations or short versions like patt or rep.
The type of the rule,
undef if undefined.
The value returned is undef or a string from the above list,
regardless of the input variations.
Bio::Polloc::Polloc::Error if an unsupported type is received.
The context is a reference to an array of two elements (int or str), the first being: 1 => with respect to the start of the sequence 0 => somewhere within the sequence (ignores the second) -1 => with respect to the end of the sequence
And the second being the number of residues from the reference point. The second value can be positive, negative, or zero.
Three integers, or one integer equal to zero. Please note that this function is extremely tolerant, and tries to guess the context regardless of the input.
A reference to the array described above.
This function relies on
Bio::Polloc::Polloc:Error if unsupported value is received
executableproperty. A rule can be executed even if this property is false, if the Bio::Polloc::RuleI::execute method is called directly (
$rule->execute) or by other rule. This property is provided only for Bio::Polloc::RuleIO objects.
Boolean (0 or 1; optional)
1 if expicilty executable, 0 otherwise
It is advisable to have only few (ideally one) executable rules, handling all the others with the rule type operation
Name (str), the name to set
The name (str or undef)
Provide a somewhat unique but human-readable identifier
The supposedly unique ID of the rule (str), any dot (.) will be changed to _
The ID (str or undef)
The stringified object (str, off course)
The value as string
The ruleset to set (a Bio::Polloc::RuleIO object).
A Bio::Polloc::RuleIO object or
A Bio::Seq object.
An array of Bio::Polloc::LocusI objects
A Bio::Polloc::Polloc::NotImplementedException if not implemented
To provide a safe interface for setting values from the parsed file
The value of the parameter or undef
The source (str)
The source (str or
Methods intended to be used only witin the scope of Bio::Polloc::*
The supported value keys (
Provide support for children identification
The ID (str) or
undef if the ID of the current Rule is not set.