Package | Description |
---|---|
pal.math |
Classes for math stuff such as optimisation, numerical derivatives, matrix exponentials,
random numbers, special function etc.
|
pal.tree |
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
|
Modifier and Type | Method and Description |
---|---|
OrderEnumerator |
OrderEnumerator.OEFactory.createOrderEnumerator(int size)
For generating an ordering from 0..size-1.
|
static OrderEnumerator |
OrderEnumerator.Utils.getAdjusted(OrderEnumerator toAdjust,
int adjustmentFactor) |
static OrderEnumerator |
OrderEnumerator.Utils.getAlternating(OrderEnumerator primary,
OrderEnumerator secondary) |
static OrderEnumerator |
OrderEnumerator.Utils.getBiasAlternating(OrderEnumerator primary,
OrderEnumerator secondary) |
static OrderEnumerator |
OrderEnumerator.Utils.getConstant(int index) |
static OrderEnumerator |
OrderEnumerator.Utils.getOrdered(int size) |
static OrderEnumerator |
OrderEnumerator.Utils.getRestricted(OrderEnumerator toRestrict,
int minimum,
int range) |
static OrderEnumerator |
OrderEnumerator.Utils.getShuffled(int size) |
OrderEnumerator |
OrthogonalHints.getSuggestedOrdering(OrderEnumerator defaultOrdering)
If there is a "best" ordering to use it can be specified here,
if not should return null
|
static OrderEnumerator |
OrderEnumerator.Utils.getZero() |
Modifier and Type | Method and Description |
---|---|
static OrderEnumerator |
OrderEnumerator.Utils.getAdjusted(OrderEnumerator toAdjust,
int adjustmentFactor) |
static OrderEnumerator |
OrderEnumerator.Utils.getAlternating(OrderEnumerator primary,
OrderEnumerator secondary) |
static OrderEnumerator |
OrderEnumerator.Utils.getBiasAlternating(OrderEnumerator primary,
OrderEnumerator secondary) |
static OrderEnumerator |
OrderEnumerator.Utils.getRestricted(OrderEnumerator toRestrict,
int minimum,
int range) |
OrderEnumerator |
OrthogonalHints.getSuggestedOrdering(OrderEnumerator defaultOrdering)
If there is a "best" ordering to use it can be specified here,
if not should return null
|
Modifier and Type | Method and Description |
---|---|
OrderEnumerator |
MutationRateModelTree.getSuggestedOrdering(OrderEnumerator defaultOrdering) |
Modifier and Type | Method and Description |
---|---|
OrderEnumerator |
MutationRateModelTree.getSuggestedOrdering(OrderEnumerator defaultOrdering) |