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java.lang.Objectpal.tree.SimulatedAlignment.Factory
public static final class SimulatedAlignment.Factory
A utility class that can be used to generate Simulated alignments based on a tree with predefined sequence length and substitution model
Constructor Summary | |
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SimulatedAlignment.Factory(int sequenceLength,
SubstitutionModel model)
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Method Summary | |
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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 |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public SimulatedAlignment.Factory(int sequenceLength, SubstitutionModel model)
Method Detail |
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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 stopping
java.lang.IllegalArgumentException
- if trees units are not EXPECTED SUBSTITUTIONS, or UNKNOWN
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