Uses of Class
Simulations.Simulate.SimulationException

Packages that use Simulate.SimulationException
Simulations Provides a class to create simulate data. 
 

Uses of Simulate.SimulationException in Simulations
 

Methods in Simulations that throw Simulate.SimulationException
 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