Package | Description |
---|---|
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.
|
Modifier and Type | Field and Description |
---|---|
protected java.util.List<Site> |
Alignment.data
The list of sites in the alignment
|
Modifier and Type | Method and Description |
---|---|
Site |
Alignment.getSite(int s)
Returns the site at a given position in the alignment
|
Site |
Site.recode(java.util.Map<java.lang.String,java.lang.String> recode)
Recodes the site and returns it
|
Modifier and Type | Method and Description |
---|---|
java.util.Set<Site> |
Alignment.getUniqueSites()
Returns a list of unique sites in the aligment.
|
java.util.Iterator<Site> |
Alignment.iterator() |
Modifier and Type | Method and Description |
---|---|
int |
Alignment.getCount(Site s)
Gets a count of hoften a site occurs in the alignment
|
Constructor and Description |
---|
Alignment(java.util.List<Site> data)
Creates an alignment
|
Modifier and Type | Method and Description |
---|---|
Site |
AncestralMarginal.SiteResult.getSite()
Returns the reconstructed site
|
Modifier and Type | Method and Description |
---|---|
AncestralMarginal.SiteResult |
AncestralMarginal.Result.getSiteResult(Site s)
Gets the site results for a given site
|
Modifier and Type | Method and Description |
---|---|
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) |
boolean |
SiteConstraints.meetsConstrains(Site s)
Tests whether a given site (that should include data for internal nodes)
meets the defined constraints
|
Modifier and Type | Method and Description |
---|---|
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
|
Constructor and Description |
---|
Calculator.SiteCalculator(Site s,
Tree t,
SiteConstraints con,
Probabilities tp)
Standard constructor
|
Modifier and Type | Method and Description |
---|---|
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(java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated site without returning the state of the internal nodes.
|