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Packages that use Site | |
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Alignments | Provides class for dealing with "alignments" and the sites in an alignment. |
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. |
Simulations | Provides a class to create simulate data. |
Uses of Site in Alignments |
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Subclasses of Site in Alignments | |
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class |
Alignment.UniqueSite
Used to represent a unique site in an alignment. |
Fields in Alignments with type parameters of type Site | |
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protected java.util.List<Site> |
Alignment.data
The list of sites in the alignment |
Methods in Alignments that return Site | |
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Site |
Alignment.getSite(int s)
Returns the site at a given position in the alignment |
Site |
Site.limitToTaxa(java.util.Collection<java.lang.String> limit)
Returns a new Site which is the same as this one except it is limited to certain taxa |
Site |
Site.recode(java.util.Map<java.lang.String,java.lang.String> recode)
Recodes the site and returns it |
Site |
Site.recode(java.util.Map<java.lang.String,java.lang.String> recode,
Ambiguous ambig)
Recodes the alignment and returns it and also allows the definition of new ambiguous states |
Methods in Alignments that return types with arguments of type Site | |
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java.util.Iterator<Site> |
Alignment.iterator()
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Methods in Alignments with parameters of type Site | |
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int |
Alignment.getCount(Site s)
Gets a count of hoften a site occurs in the alignment |
Constructors in Alignments with parameters of type Site | |
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Alignment.UniqueSite(Site s,
int c)
Default constructor |
Constructor parameters in Alignments with type arguments of type Site | |
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Alignment(java.util.List<Site> data)
Creates an alignment |
Uses of Site in Ancestors |
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Methods in Ancestors that return Site | |
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Site |
AncestralMarginal.SiteResult.getSite()
Returns the reconstructed site |
Methods in Ancestors with parameters of type Site | |
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AncestralMarginal.SiteResult |
AncestralMarginal.Result.getSiteResult(Site s)
Gets the site results for a given site |
Uses of Site in Constraints |
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Methods in Constraints with parameters of type Site | |
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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. |
SiteConstraints |
NoConstraints.getConstraints(Tree t,
Site s)
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boolean |
SiteConstraints.meetsConstrains(Site s)
Tests whether a given site (that should include data for internal nodes) meets the defined constraints |
Uses of Site in Likelihood |
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Methods in Likelihood with parameters of type Site | |
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Likelihood.SiteLikelihood |
Likelihood.getMissingLikelihood(Site s)
Gets the likelihood result for a given missing site |
Likelihood.SiteLikelihood |
Likelihood.getSiteLikelihood(Site s)
Gets the likelihood result for a given site |
Constructors in Likelihood with parameters of type Site | |
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Calculator.SiteCalculator(Site s,
Tree t,
SiteConstraints con,
Probabilities tp)
Constructor mainly for backwards compitability although also still used by some of the ancestral calculations. |
Uses of Site in Simulations |
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Methods in Simulations that return Site | |
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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 |
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