pal.tree
public static final class SimulatedAlignment.Factory extends java.lang.Object
Constructor and Description |
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SimulatedAlignment.Factory(int sequenceLength,
SubstitutionModel model) |
Modifier and Type | Method and Description |
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SimulatedAlignment |
generateAlignment(Tree tree)
Generate a simulated alignment based on input tree
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SimulatedAlignment[] |
generateAlignments(Tree[] trees,
AlgorithmCallback callback)
Generate an array of simulated alignments based on an array of input trees
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public SimulatedAlignment.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