Uses of Class
Trees.TreeException

Packages that use TreeException
Ancestors Provides classed to calculate ancestral reconstruction. 
Constraints Provides classes to constrain the state of internal nodes. 
Likelihood Provides classes for calculating the likelihood of a tree given a model and an alignment. 
Optimizers Provides classes for optimising a likelihood. 
Simulations Provides a class to create simulate data. 
Trees Provides classes to define a tree and any constraints on that tree. 
 

Uses of TreeException in Ancestors
 

Methods in Ancestors that throw TreeException
abstract  Alignment AncestralJoint.calculate(Parameters params)
          Calculates the reconstruction
 Alignment AncestralJointBB.calculate(Parameters p)
           
 Alignment AncestralJointDP.calculate(Parameters params)
           
 AncestralMarginal.Result AncestralMarginal.calculate(Parameters params)
          Calculates the reconstruction
 

Uses of TreeException in Constraints
 

Methods in Constraints that throw TreeException
 SiteConstraints Constrainer.getConstraints(Tree t, Site s)
          Gets the consraints on an the external nodes of a site given the tree and the state of the leafs.
 

Uses of TreeException in Likelihood
 

Methods in Likelihood that throw TreeException
 Likelihood Calculator.calculate(Parameters p)
          Calculates the likelihood for a given set of parameters
 Range ConfidenceInterval.getCI(Parameter param, double conf)
          Calculates the confidence interval for a single parameter
 

Constructors in Likelihood that throw TreeException
Calculator(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t)
          Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
Calculator(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t, Alignment unobserved)
          Creates a class to calculate the likelihood for a given set of models, an alignment, a tree, and unobserved data.
Calculator(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t, Alignment unobserved, java.util.Map<java.lang.String,Constrainer> con)
          Creates a class to calculate the likelihood for a given set of models, an alignment, a tree, unobserved data and a set of constraints.
Calculator(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t, java.util.Map<java.lang.String,Constrainer> con)
          Creates a class to calculate the likelihood for a given set of models, an alignment, a tree and a set of constraints.
Calculator(Model m, Alignment a, Tree t)
          Creates an object to calculate the likelihood for a given model, alignment, tree.
Calculator(Model m, Alignment a, Tree t, Alignment unobserved)
          Creates a class to calculate the likelihood for a given model, alignment, tree, missing data and constraints
Calculator(Model m, Alignment a, Tree t, Alignment unobserved, Constrainer con)
          Creates a class to calculate the likelihood for a given model, alignment, tree, unobserved data and constraints
Calculator(Model m, Alignment a, Tree t, Constrainer con)
          Creates a class to calculate the likelihood for a given model, alignment, tree and constraints
Probabilities(Model m, Tree t, Parameters p)
          Constructor
 

Uses of TreeException in Optimizers
 

Methods in Optimizers that throw TreeException
 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.
 

Uses of TreeException in Simulations
 

Methods in Simulations that throw TreeException
 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
 

Constructors in Simulations that throw TreeException
Simulate(java.util.Map<java.lang.String,Model> m, Tree t, Parameters p)
          Creates an object to simulate data for a given set of models, a tree and parameters.
Simulate(java.util.Map<java.lang.String,Model> m, Tree t, Parameters p, Alignment unobserved)
          Creates an object to simulate data for a given set of models, a tree, parameters and unobserved sattes.
Simulate(java.util.Map<java.lang.String,Model> m, Tree t, Parameters p, Alignment unobserved, java.util.Map<java.lang.String,Constrainer> con)
          Creates an object to simulate data for a given set of models, a tree, parameters, unobserved states and constrainers.
Simulate(Model m, Tree t, Parameters p)
          Creates an object to simulate data for a given model, tree and parameters.
Simulate(Model m, Tree t, Parameters p, Alignment unobserved)
          Creates an object to simulate data for a given model, tree, parameters and unobserved states.
Simulate(Model m, Tree t, Parameters p, Alignment unobserved, Constrainer con)
          Creates an object to simulate data for a given model, tree, parameters, unobserved states and constraints.
 

Uses of TreeException in Trees
 

Methods in Trees that throw TreeException
static Tree Tree.fromNewickString(java.lang.String newick)
          Creates a tree from a newick string
 Branch Tree.getBranchByChild(java.lang.String child)
          Gets the branch which has the given node as the child node
 java.util.Set<Branch> Tree.getBranchesByParent(java.lang.String parent)
          Gets the set of branches which have the passed node as a parent
 double Branch.getLength()
          Get the length of the branch
 double Tree.getLength()
          Gets the length of the tree
 Parameters Tree.getParameters()
          Returns a Parameters object containing a parameter for each branch length.
 java.lang.String Tree.getParent(java.lang.String child)
          Gets the parent node of the given node
 Tree Tree.midPointRoot(java.lang.String newRootName)
          Mid point roots the tree and returns a new tree
 java.lang.String Tree.MRCA(java.util.List<java.lang.String> leaves)
          Returns the most recent common ancestor of a set of leaves
 void TreeFigure.printSVG(java.io.File f, boolean showLengths)
          Prints the tree to the given file
 Tree Tree.scaledTo(double length)
          Returns a new tree where the lengths are scales so the total length is different
 

Constructors in Trees that throw TreeException
Tree(java.util.List<Branch> branches)
          Creates a tree from a list of branches
TreeFigure(Tree t)
          Constructor