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Packages that use AlignmentException | |
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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 AlignmentException in Alignments |
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Constructors in Alignments that throw AlignmentException | |
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Alignment(java.util.List<Site> data)
Creates an alignment |
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DuplicationAlignment(java.io.File f)
Creates a duplication alignment from a file. |
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DuplicationAlignment(java.io.File f,
Ambiguous ambig)
Creates a duplication alignment which contains ambiguous data. |
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FastaAlignment(java.io.File f)
Creates a sequence alignment from a file. |
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FastaAlignment(java.io.File f,
Ambiguous ambig)
Creates a sequence alignment from a file with ambiguouis data. |
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PhylipAlignment(java.io.File f)
Creates a sequence alignment from a file. |
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PhylipAlignment(java.io.File f,
Ambiguous ambig)
Creates a sequence alignment from a file with ambiguouis data. |
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SequenceAlignment(java.io.File f)
Deprecated. Creates a sequence alignment from a file. |
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SequenceAlignment(java.io.File f,
Ambiguous ambig)
Deprecated. Creates a sequence alignment from a file with ambiguouis data. |
Uses of AlignmentException in Ancestors |
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Methods in Ancestors that throw AlignmentException | |
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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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AncestralMarginal.Result |
AncestralMarginal.calculate(Parameters params)
Calculates the reconstruction |
static AncestralJoint |
AncestralJoint.newInstance(java.util.Map<java.lang.String,Model> m,
Alignment a,
Tree t)
Returns an object of this class that can be used for joint reconstruction. |
Constructors in Ancestors that throw AlignmentException | |
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AncestralMarginal(java.util.Map<java.lang.String,Model> m,
Alignment a,
Tree t)
Creates an object to calculate an ancestral reconstruction for a given set of models, an alignment and a tree. |
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AncestralMarginal(java.util.Map<java.lang.String,Model> m,
Alignment a,
Tree t,
java.util.Map<java.lang.String,Constrainer> con)
Creates an object to calculate an ancestral reconstruction for a given set of models, an alignment, a tree and s et of constrainers. |
Uses of AlignmentException in Likelihood |
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Constructors in Likelihood that throw AlignmentException | |
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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. |
Uses of AlignmentException in Simulations |
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Methods in Simulations that throw AlignmentException | |
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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. |
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 |
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