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Packages that use Alignment | |
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Alignments | Provides class for dealing with "alignments" and the sites in an alignment. |
Ancestors | Provides classed to calculate ancestral reconstruction. |
Likelihood | Provides classes for calculating the likelihood of a tree given a model and an alignment. |
Simulations | Provides a class to create simulate data. |
Uses of Alignment in Alignments |
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Subclasses of Alignment in Alignments | |
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class |
DuplicationAlignment
Represents a duplication "alignment" - a set of gene families with their associated size in each species |
class |
SequenceAlignment
Represents a sequence alignment |
Methods in Alignments that return Alignment | |
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Alignment |
Alignment.recode(java.util.Map<java.lang.String,java.lang.String> recode)
Recodes the alignment and returns it |
Methods in Alignments with parameters of type Alignment | |
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static void |
DuplicationAlignment.writeFile(Alignment a,
java.io.File f)
Writes a alignment to a file in the duplication alignment format described above. |
static void |
SequenceAlignment.writeFile(Alignment a,
java.io.File f)
Writes a alignment to a file in the format described in SequenceAlignment.SequenceAlignment(java.io.File) . |
Uses of Alignment in Ancestors |
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Methods in Ancestors that return Alignment | |
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abstract Alignment |
AncestralJoint.calculate(Parameters params)
Calculates the reconstruction |
Alignment |
AncestralJointBB.calculate(Parameters p)
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Alignment |
AncestralJointDP.calculate(Parameters params)
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Alignment |
AncestralMarginal.Result.getAlignment()
Gets the reconstructed alignment |
Methods in Ancestors with parameters of type Alignment | |
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static AncestralJoint |
AncestralJoint.newInstance(Model m,
Alignment a,
Tree t)
Returns an object of this class that can be used for joint reconstruction. |
Constructors in Ancestors with parameters of type Alignment | |
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AncestralMarginal(Model m,
Alignment a,
Tree t)
Creates an object to calculate an ancestral reconstruction for a given model, alignment and tree |
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AncestralMarginal(Model m,
Alignment a,
Tree t,
Constrainer con)
Creates an object to calculate an ancestral reconstruction for a given model, alignment, tree and constraints |
Uses of Alignment in Likelihood |
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Constructors in Likelihood with parameters of type Alignment | |
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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 |
Uses of Alignment in Simulations |
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Methods in Simulations that return Alignment | |
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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. |
Constructors in Simulations with parameters of type Alignment | |
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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. |
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