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Packages that use Simulate.SimulationException | |
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Simulations | Provides a class to create simulate data. |
Uses of Simulate.SimulationException in Simulations |
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Methods in Simulations that throw Simulate.SimulationException | |
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Alignment |
Simulate.getAlignment(int length)
Gets a simulated alignment, not returing the state of internal nodes |
Alignment |
Simulate.getAlignment(int length,
boolean internal)
Gets a simulated alignment |
Alignment |
Simulate.getAlignment(int length,
boolean internal,
java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated alignment. |
Alignment |
Simulate.getAlignment(int length,
java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated alignment, not returing the state of internal nodes. |
Alignment |
Simulate.getAlignment(java.util.List<java.lang.String> siteClasses)
Gets a simulated alignment, not returning the state of the internal nodes. |
Alignment |
Simulate.getAlignment(java.util.List<java.lang.String> siteClasses,
boolean internal)
Gets a simulated alignment. |
Alignment |
Simulate.getAlignment(java.util.List<java.lang.String> siteClasses,
boolean internal,
java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated alignment. |
Alignment |
Simulate.getAlignment(java.util.List<java.lang.String> siteClasses,
java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated alignment, not returning the state of the internal nodes. |
Site |
Simulate.getSite()
Gets a simulated site without returning the state of the internal nodes |
Site |
Simulate.getSite(boolean internal)
Gets a simulated site |
Site |
Simulate.getSite(boolean internal,
java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated site. |
Site |
Simulate.getSite(boolean internal,
java.util.Map<java.lang.String,java.lang.String> recode,
java.lang.String siteClass)
Gets a simulated site. |
Site |
Simulate.getSite(boolean internal,
java.lang.String siteClass)
Gets a simulated site |
Site |
Simulate.getSite(java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated site without returning the state of the internal nodes. |
Site |
Simulate.getSite(java.util.Map<java.lang.String,java.lang.String> recode,
java.lang.String siteClass)
Gets a simulated site without returning the state of the internal nodes. |
Site |
Simulate.getSite(java.lang.String siteClass)
Gets a simulated site without returning the state of the internal nodes |
double |
HypothesisTest.test(Tree t,
Alignment a,
Alignment unobserved,
Parameters nullParams,
Parameters altParams)
Does a hpyothesis test on the given data and gives a p-value |
double |
HypothesisTest.test(Tree t,
Alignment a,
Alignment unobserved,
Parameters nullParams,
Parameters altParams,
java.util.Map<java.lang.String,java.lang.String> recode)
Does a hpyothesis test on the given data and gives a p-value |
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