Package pal.tree
Class SimulatedAlignment.Factory
- java.lang.Object
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- pal.tree.SimulatedAlignment.Factory
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- Enclosing class:
- SimulatedAlignment
public static final class SimulatedAlignment.Factory extends java.lang.Object
A utility class that can be used to generate Simulated alignments based on a tree with predefined sequence length and substitution model
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Constructor Summary
Constructors Constructor Description Factory(int sequenceLength, SubstitutionModel model)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description SimulatedAlignment
generateAlignment(Tree tree)
Generate a simulated alignment based on input treeSimulatedAlignment[]
generateAlignments(Tree[] trees, AlgorithmCallback callback)
Generate an array of simulated alignments based on an array of input trees
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Constructor Detail
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Factory
public Factory(int sequenceLength, SubstitutionModel model)
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Method Detail
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generateAlignment
public final SimulatedAlignment generateAlignment(Tree tree)
Generate a simulated alignment based on input tree- Parameters:
tree
- The tree, with branchlengths set appropriately.- Throws:
java.lang.IllegalArgumentException
- if trees units are not EXPECTED SUBSTITUTIONS, or UNKNOWN
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generateAlignments
public final SimulatedAlignment[] generateAlignments(Tree[] trees, AlgorithmCallback callback)
Generate an array of simulated alignments based on an array of input trees- Parameters:
trees
- The tree, with branchlengths set appropriately.callback
- An AlgorithmCallback for monitoring progress and premature stopping- Throws:
java.lang.IllegalArgumentException
- if trees units are not EXPECTED SUBSTITUTIONS, or UNKNOWN
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