|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.ObjectSimulations.Simulate
public class Simulate
Class for constructing simulated data
Constructor Summary | |
---|---|
Simulate(Model m,
Tree t,
Parameters p)
Creates an object to simulate data for a given model, tree and parameters. |
|
Simulate(Model m,
Tree t,
Parameters p,
Alignment unobserved)
Creates an object to simulate data for a given model, tree, parameters and unobserved states. |
|
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. |
Method Summary | |
---|---|
Alignment |
getAlignment(int length)
Gets a simulated alignment, not returing the state of internal nodes |
Alignment |
getAlignment(int length,
boolean internal)
Gets a simulated alignment |
Alignment |
getAlignment(int length,
boolean internal,
java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated alignment. |
Alignment |
getAlignment(int length,
java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated alignment, not returing the state of internal nodes. |
Site |
getSite()
Gets a simulated site without returning the state of the internal nodes |
Site |
getSite(boolean internal)
Gets a simulated site |
Site |
getSite(boolean internal,
java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated site. |
Site |
getSite(java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated site without returning the state of the internal nodes. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
---|
public Simulate(Model m, Tree t, Parameters p) throws RateCategory.RateException, Model.ModelException, TreeException, Parameters.ParameterException
m
- The modelt
- The treep
- The parameters
RateCategory.RateException
- Thrown if there is an issue with
a rate category in the model (e.g. a badly formatted rate).
Model.ModelException
- Thrown if there is a problem with the
model (e.g. the rate categories differ in their states)
TreeException
- Thrown if there is a problem with the tree.
Parameters.ParameterException
- Thrown if there is a problem
with the parameters (e.g. a requied parameter is not present)public Simulate(Model m, Tree t, Parameters p, Alignment unobserved) throws RateCategory.RateException, Model.ModelException, TreeException, Parameters.ParameterException
m
- The modelt
- The treep
- The parametersunobserved
- The unobserved states
RateCategory.RateException
- Thrown if there is an issue with
a rate category in the model (e.g. a badly formatted rate).
Model.ModelException
- Thrown if there is a problem with the
model (e.g. the rate categories differ in their states)
TreeException
- Thrown if there is a problem with the tree.
Parameters.ParameterException
- Thrown if there is a problem
with the parameters (e.g. a requied parameter is not present)public Simulate(Model m, Tree t, Parameters p, Alignment unobserved, Constrainer con) throws RateCategory.RateException, Model.ModelException, TreeException, Parameters.ParameterException
m
- The modelt
- The treep
- The parametersunobserved
- The unobserved statescon
- The constraints
RateCategory.RateException
- Thrown if there is an issue with
a rate category in the model (e.g. a badly formatted rate).
Model.ModelException
- Thrown if there is a problem with the
model (e.g. the rate categories differ in their states)
TreeException
- Thrown if there is a problem with the tree.
Parameters.ParameterException
- Thrown if there is a problem
with the parameters (e.g. a requied parameter is not present)Method Detail |
---|
public Site getSite() throws TreeException
TreeException
- Thrown if the constrainer has a problem with the treepublic Site getSite(java.util.Map<java.lang.String,java.lang.String> recode) throws TreeException
recode
- Map of recodings
TreeException
- Thrown if the constrainer has a problem with the treepublic Site getSite(boolean internal) throws TreeException
internal
- Whether to return the state of the internal nodes
TreeException
- Thrown if the constrainer has a problem with the treepublic Site getSite(boolean internal, java.util.Map<java.lang.String,java.lang.String> recode) throws TreeException
recode
- Map of recodingsinternal
- Whether to return the state of the internal nodes
TreeException
- Thrown if the constrainer has a problem with the treepublic Alignment getAlignment(int length) throws AlignmentException, TreeException
length
- The length of the alignment
AlignmentException
- Thrown if there is a problem with the alignment
TreeException
- Thrown if the constrainer has a problem with the treepublic Alignment getAlignment(int length, boolean internal) throws AlignmentException, TreeException
length
- The length of the alignmentinternal
- Whether to return the state of the internal nodes
AlignmentException
- Thrown if there is a problem with the alignment
TreeException
- Thrown if the constrainer has a problem with the treepublic Alignment getAlignment(int length, java.util.Map<java.lang.String,java.lang.String> recode) throws AlignmentException, TreeException
length
- The length of the alignmentrecode
- Map of recodings
AlignmentException
- Thrown if there is a problem with the alignment
TreeException
- Thrown if the constrainer has a problem with the treepublic Alignment getAlignment(int length, boolean internal, java.util.Map<java.lang.String,java.lang.String> recode) throws AlignmentException, TreeException
length
- The length of the alignmentinternal
- Whether to return the state of the internal nodesrecode
- Map of recodings
AlignmentException
- Thrown if there is a problem with the alignment
TreeException
- Thrown if the constrainer has a problem with the tree
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |