Package | Description |
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pal.coalescent |
Classes to model population genetic processes using the coalescent.
|
pal.tree |
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
|
Constructor | Description |
---|---|
SerialCoalescentGenerator(TimeOrderCharacterData tocd,
DemographicModel demographicModel,
int numberOfTreesToGenerate,
TreeOperation treeFinisher) |
Results will not contain alignments
|
SerialCoalescentGenerator(TimeOrderCharacterData tocd,
DemographicModel demographicModel,
int numberOfTreesToGenerate,
TreeOperation treeFinisher,
SimulatedAlignment.Factory alignmentFactory) |
|
SerialCoalescentGenerator(TimeOrderCharacterData tocd,
DemographicModel demographicModel,
TreeOperation treeFinisher,
SimulatedAlignment.Factory alignmentFactory) |
Modifier and Type | Method | Description |
---|---|---|
static TreeOperation |
TreeOperation.Utils.createPipeline(TreeOperation first,
TreeOperation second) |
Creates a tree operation that first applies one tree operation and then applies a second operation to get it's result
|
static TreeOperation |
TreeOperation.Utils.createScale(double scaleFactor,
int resultingUnits) |
Create a tree operation that scales the input tree and changes the units
|
static TreeOperation |
TreeOperation.Utils.getNoOperation() |
Modifier and Type | Method | Description |
---|---|---|
static TreeOperation |
TreeOperation.Utils.createPipeline(TreeOperation first,
TreeOperation second) |
Creates a tree operation that first applies one tree operation and then applies a second operation to get it's result
|