Documentation for Substitution class from SLiM
This class represents a mutation that has been fixed; Mutation objects are converted to Substitution objects upon fixation. Its properties are thus very similar to those of Mutation. Section 1.5.2 presents an overview of the conceptual role of this class. Since Substitution objects represent fixation events that occurred in the past, they are relatively immutable. However, since it may be useful to attach (possibly dynamic) state to substitutions, their tag and subpopID properties are mutable, and they also provide the same getValue() / setValue() functionality as Mutation (inherited from the Eidos class Dictionary). Values set on a Mutation object will carry over to the corresponding Substitution object automatically upon fixation. This class has the following methods (functions):
None. This class has no methods.
This class has the following properties:
A property of type integer. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The identifier for this mutation. Each mutation created during a run receives an immutable identifier that will be unique across the duration of the run, and that identifier is carried over to the Substitution object when the mutation fixes.
A property of type integer. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The tick in which this mutation fixed.
A property of type MutationType object. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The MutationType from which this mutation was drawn.
A property of type string. It is of length one (a singleton). This property is a variable, so it is modifiable. Property Description: A string representing the nucleotide associated with this mutation; this will be "A", "C", "G", or "T". If the mutation is not nucleotide-based, this property is unavailable.
A property of type integer. It is of length one (a singleton). This property is a variable, so it is modifiable. Property Description: An integer representing the nucleotide associated with this mutation; this will be 0 (A), 1 (C), 2 (G), or 3 (T). If the mutation is not nucleotide-based, this property is unavailable.
A property of type integer. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The tick in which this mutation arose.
A property of type integer. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The position in the chromosome of this mutation.
A property of type float. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The selection coefficient of the mutation, drawn from the distribution of fitness effects of its MutationType.
A property of type integer. It is of length one (a singleton). This property is a variable, so it is modifiable. Property Description: The identifier of the subpopulation in which this mutation arose. This value is carried over from the Mutation object directly; if a "tag" value was used in the Mutation object (see section 25.10.1), that value will carry over to the corresponding Substitution object. The subpopID in Substitution is a read-write property to allow it to be used as a "tag" in the same way, if the origin subpopulation identifier is not needed.
A property of type integer. It is of length one (a singleton). This property is a variable, so it is modifiable. Property Description: A user-defined integer value. The value of tag is carried over automatically from the original Mutation object. Apart from that, the value of tag is not used by SLiM; it is free for you to use.