public static final class SimulatedAlignment.Factory
extends java.lang.Object
Constructor | Description |
---|---|
Factory(int sequenceLength,
SubstitutionModel model) |
Modifier and Type | Method | Description |
---|---|---|
SimulatedAlignment |
generateAlignment(Tree tree) |
Generate a simulated alignment based on input tree
|
SimulatedAlignment[] |
generateAlignments(Tree[] trees,
AlgorithmCallback callback) |
Generate an array of simulated alignments based on an array of input trees
|
public Factory(int sequenceLength, SubstitutionModel model)
public final SimulatedAlignment generateAlignment(Tree tree)
tree
- The tree, with branchlengths set appropriately.java.lang.IllegalArgumentException
- if trees units are not EXPECTED SUBSTITUTIONS, or UNKNOWNpublic final SimulatedAlignment[] generateAlignments(Tree[] trees, AlgorithmCallback callback)
trees
- The tree, with branchlengths set appropriately.callback
- An AlgorithmCallback for monitoring progress and premature stoppingjava.lang.IllegalArgumentException
- if trees units are not EXPECTED SUBSTITUTIONS, or UNKNOWN