Package | Description |
---|---|
pal.eval |
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
|
pal.mep |
Classes for the analysis of "measurably evolving populations" (mep).
|
pal.misc |
Classes that don't fit elsewhere ;^)
|
pal.substmodel |
Classes describing substitution models, i.e.
|
Modifier and Type | Class | Description |
---|---|---|
class |
FastLikelihoodCalculator |
Title: Fast Likelihood Calculator
Description: A fast likelihood calculator Original code by Matthew Goode. |
class |
GeneralLikelihoodCalculator |
Title: General Likelihood Calculator
Description: A General likelihood calculator This calculates the likelihood of an topologically invariant tree (on an unchanging alignment) quickly by remembering partial likelihoods of invariant subtrees, and by essentially generating site patterns for each sub tree. |
Modifier and Type | Method | Description |
---|---|---|
void |
DeltaModel.Instance.addPalObjectListener(PalObjectListener pol) |
|
void |
DeltaModel.Instance.removePalObjectListener(PalObjectListener pol) |
Modifier and Type | Method | Description |
---|---|---|
static PalObjectListener |
PalEventMulticaster.add(PalObjectListener old,
PalObjectListener toAdd) |
For managing PalObjectListeners
Usage: PalObjectListener current = null;
...
|
static PalObjectListener |
PalEventMulticaster.remove(PalObjectListener old,
PalObjectListener toRemove) |
For managing PalObjectListeners
Usage: PalObjectListener current = null;
...
|
Modifier and Type | Method | Description |
---|---|---|
static PalObjectListener |
PalEventMulticaster.add(PalObjectListener old,
PalObjectListener toAdd) |
For managing PalObjectListeners
Usage: PalObjectListener current = null;
...
|
void |
PalObjectListener.EventGenerator.addPalObjectListener(PalObjectListener pol) |
|
static PalObjectListener |
PalEventMulticaster.remove(PalObjectListener old,
PalObjectListener toRemove) |
For managing PalObjectListeners
Usage: PalObjectListener current = null;
...
|
void |
PalObjectListener.EventGenerator.removePalObjectListener(PalObjectListener pol) |
Modifier and Type | Class | Description |
---|---|---|
class |
CachedRateMatrix |
a cached rate matrix.
|
Modifier and Type | Method | Description |
---|---|---|
void |
AbstractRateMatrix.addPalObjectListener(PalObjectListener pol) |
|
void |
CachedRateMatrix.addPalObjectListener(PalObjectListener pol) |
|
void |
GeneralRateDistributionSubstitutionModel.addPalObjectListener(PalObjectListener l) |
|
void |
RateMatrix.addPalObjectListener(PalObjectListener pol) |
Add a PalObjectListener to be notified of changes to the model.
|
void |
SingleClassSubstitutionModel.addPalObjectListener(PalObjectListener l) |
|
void |
SubstitutionModel.addPalObjectListener(PalObjectListener l) |
|
void |
AbstractRateMatrix.removePalObjectListener(PalObjectListener pol) |
|
void |
CachedRateMatrix.removePalObjectListener(PalObjectListener pol) |
|
void |
GeneralRateDistributionSubstitutionModel.removePalObjectListener(PalObjectListener l) |
|
void |
RateMatrix.removePalObjectListener(PalObjectListener pol) |
|
void |
SingleClassSubstitutionModel.removePalObjectListener(PalObjectListener l) |
|
void |
SubstitutionModel.removePalObjectListener(PalObjectListener l) |