Uses of Class
Likelihood.Calculator

Packages that use Calculator
Likelihood Provides classes for calculating the likelihood of a tree given a model and an alignment. 
Optimizers Provides classes for optimising a likelihood. 
 

Uses of Calculator in Likelihood
 

Constructors in Likelihood with parameters of type Calculator
ConfidenceInterval(Calculator l, Parameters p)
          Default constructor
 

Uses of Calculator in Optimizers
 

Methods in Optimizers with parameters of type Calculator
 Likelihood GoldenSection.maximise(Calculator l, Parameters params)
           
 Likelihood NelderMead.maximise(Calculator l, Parameters params)
           
 Likelihood Optimizer.maximise(Calculator l, Parameters p)
          Maximises the likelihood, logging to screen.
 Likelihood GoldenSection.maximise(Calculator l, Parameters params, java.io.File log)
           
 Likelihood NelderMead.maximise(Calculator l, Parameters params, java.io.File log)
           
 Likelihood Optimizer.maximise(Calculator l, Parameters params, java.io.File log)
          Maximises the likelihood, logging to a file.
 Likelihood GoldenSection.restart(Calculator l, java.io.File checkPoint)
           
 Likelihood NelderMead.restart(Calculator l, java.io.File checkPoint)
           
 Likelihood Optimizer.restart(Calculator l, java.io.File checkPoint)
          Maximises the likelihood starting from a checkpoint file (see Optimizer.setCheckPointFile(java.io.File), logging to the screen.
 Likelihood GoldenSection.restart(Calculator l, java.io.File checkPoint, java.io.File log)
           
 Likelihood NelderMead.restart(Calculator l, java.io.File checkPoint, java.io.File log)
           
 Likelihood Optimizer.restart(Calculator l, java.io.File checkPoint, java.io.File log)
          Maximises the likelihood starting from a checkpoint file (see Optimizer.setCheckPointFile(java.io.File), logging to a file.