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Packages that use TreeException | |
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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 |
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Methods in Ancestors that throw TreeException | |
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abstract Alignment |
AncestralJoint.calculate(Parameters params)
Calculates the reconstruction |
Alignment |
AncestralJointBB.calculate(Parameters p)
|
Alignment |
AncestralJointDP.calculate(Parameters params)
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AncestralMarginal.Result |
AncestralMarginal.calculate(Parameters params)
Calculates the reconstruction |
Uses of TreeException in Constraints |
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Methods in Constraints that throw TreeException | |
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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 |
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Methods in Likelihood that throw TreeException | |
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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 | |
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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. |
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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. |
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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. |
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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. |
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Calculator(Model m,
Alignment a,
Tree t)
Creates an object to calculate the likelihood for a given model, alignment, tree. |
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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 |
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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 |
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Calculator(Model m,
Alignment a,
Tree t,
Constrainer con)
Creates a class to calculate the likelihood for a given model, alignment, tree and constraints |
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Probabilities(Model m,
Tree t,
Parameters p)
Constructor |
Uses of TreeException in Optimizers |
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Methods in Optimizers that throw TreeException | |
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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 |
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Methods in Simulations that throw TreeException | |
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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 |
Constructors in Simulations that throw TreeException | |
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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. |
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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. |
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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. |
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Simulate(Model m,
Tree t,
Parameters p)
Creates an object to simulate data for a given model, tree and parameters. |
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Simulate(Model m,
Tree t,
Parameters p,
Alignment unobserved)
Creates an object to simulate data for a given model, tree, parameters and unobserved states. |
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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 |
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Methods in Trees that throw TreeException | |
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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 | |
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Tree(java.util.List<Branch> branches)
Creates a tree from a list of branches |
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TreeFigure(Tree t)
Constructor |
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