Package pal.tree
Class SimulatedAlignment.Factory
java.lang.Object
pal.tree.SimulatedAlignment.Factory
- Enclosing class:
SimulatedAlignment
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 -
Method Summary
Modifier and TypeMethodDescriptionfinal SimulatedAlignment
generateAlignment
(Tree tree) Generate a simulated alignment based on input treefinal SimulatedAlignment[]
generateAlignments
(Tree[] trees, AlgorithmCallback callback) Generate an array of simulated alignments based on an array of input trees
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Constructor Details
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Factory
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Method Details
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generateAlignment
Generate a simulated alignment based on input tree- Parameters:
tree
- The tree, with branchlengths set appropriately.- Throws:
IllegalArgumentException
- if trees units are not EXPECTED SUBSTITUTIONS, or UNKNOWN
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generateAlignments
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:
IllegalArgumentException
- if trees units are not EXPECTED SUBSTITUTIONS, or UNKNOWN
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