Package | Description |
---|---|
pal.algorithmics | |
pal.alignment |
Classes dealing with sequence alignments, including methods for reading
and printing in several possible formats, as well as rearranging and
concatenating.
|
pal.coalescent |
Classes to model population genetic processes using the coalescent.
|
pal.distance |
Classes for reading and generating distance matrices, including computation
of pairwise distances for sequence data (maximum-likelihood and observed
distances).
|
pal.statistics |
Classes with useful for statistics (normal distribution,
Gamma distribution, chi-square distribution, exponential distribution,
likelihood-ratio test, chi-square test, descriptive statistics, bootstrap estimators etc.)
|
pal.supgma | |
pal.tree |
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
|
pal.treesearch | |
pal.util |
Utility classes for sorting etc.
|
Modifier and Type | Method and Description |
---|---|
void |
StoppingCriteria.newIteration(double currentScore,
double bestScore,
boolean maximising,
boolean externalStablized,
AlgorithmCallback callback) |
void |
SearchEngine.run(AlgorithmCallback callback,
double initialScore,
ObjectState subject,
StoppingCriteria.Factory stoppingCriteria,
Ranker ranker) |
Modifier and Type | Method and Description |
---|---|
Alignment |
AlignmentGenerator.getNextAlignment(AlgorithmCallback callback) |
Modifier and Type | Method and Description |
---|---|
SerialCoalescentGenerator.Results |
SerialCoalescentGenerator.generateResults(AlgorithmCallback callback) |
Tree[] |
SerialCoalescentGenerator.generateTrees(AlgorithmCallback callback)
If callback request stop then returns trees creating thus far
|
Modifier and Type | Method and Description |
---|---|
DistanceMatrix |
DistanceMatrixGenerator.generateNextMatrix(AlgorithmCallback callback) |
DistanceMatrix |
DistanceMatrixAccess.obtainMatrix(AlgorithmCallback callback) |
void |
AlignmentDistanceMatrix.recompute(SitePattern sp,
AlgorithmCallback callback)
recompute observed distances under new site pattern
|
void |
AlignmentDistanceMatrix.recompute(SitePattern sp,
SubstitutionModel model,
AlgorithmCallback callback)
recompute maximum-likelihood distances under new site pattern
|
Constructor and Description |
---|
AlignmentDistanceMatrix(SitePattern sp,
AlgorithmCallback callback)
compute observed distances
|
AlignmentDistanceMatrix(SitePattern sp,
SubstitutionModel m,
AlgorithmCallback callback)
compute maximum-likelihood distances
|
Modifier and Type | Method and Description |
---|---|
LikelihoodEvaluator.MLResult |
LikelihoodEvaluator.getMLOptimised(Tree tree,
Alignment alignment,
AlgorithmCallback callback) |
double[] |
TopologyTestEngine.TopologyPool.getNewReplicateLogLikelihoods(AlgorithmCallback callback) |
double[] |
GeneralTopologyPool.getNewReplicateLogLikelihoods(AlgorithmCallback callback) |
double[] |
RELLTopologyPool.getNewReplicateLogLikelihoods(AlgorithmCallback callback) |
void |
GeneralTopologyPool.optimiseOriginalTopologies(AlgorithmCallback callback) |
TopologyTestEngine.TestResult |
TopologyTestEngine.performTest(TopologyTestEngine.TopologyPool topologyPool,
int numberOfReplicates,
AlgorithmCallback callback) |
Modifier and Type | Method and Description |
---|---|
SimulatedAlignment[] |
SimulatedAlignment.Factory.generateAlignments(Tree[] trees,
AlgorithmCallback callback)
Generate an array of simulated alignments based on an array of input trees
|
Tree |
TreeGenerator.getNextTree(AlgorithmCallback callback) |
static Tree |
TreeUtils.getReplicateCladeSupport(java.lang.String attributeName,
Tree baseTree,
TreeGenerator treeGenerator,
int numberOfReplicates,
AlgorithmCallback callback)
Generates a tree which is identical to baseTree but has attributes (defined by attributeName)
at all internal nodes excluding the root node signifying (as a value between 0 and 100) the replicate
support by clade (that is the proportion of replicates that produce the sub clade under that node)
|
Modifier and Type | Method and Description |
---|---|
Tree |
TreeSearchTool.basicUnrootedTreeMLSearch(Alignment a,
SubstitutionModel sm,
boolean optimiseModel,
AlgorithmCallback callback)
Do a basic tree search using maximum likelihood on an unrooted tree space, without a given starting tree
|
Tree |
TreeSearchTool.basicUnrootedTreeMLSearch(Tree baseTree,
Alignment a,
SubstitutionModel sm,
boolean optimiseModel,
AlgorithmCallback callback)
Do a basic tree search using maximum likelihood on an unrooted tree space, with a given starting tree
|
double |
GeneralLikelihoodSearcher.optimiseAllFullHeirarchy(StoppingCriteria mainStopper,
StoppingCriteria subStopper,
MultivariateMinimum rateMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback,
SearchMonitor monitor,
MinimiserMonitor rateMonitor) |
double |
GeneralLikelihoodSearcher.optimiseAllPlusSubstitutionModel(StoppingCriteria stopper,
MultivariateMinimum rateMinimiser,
MultivariateMinimum substitutionModelMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback,
SearchMonitor monitor,
int substitutionModelOptimiseFrequency,
MinimiserMonitor substitutionModelMonitor,
MinimiserMonitor rateMonitor) |
double |
GeneralLikelihoodSearcher.optimiseAllSimple(StoppingCriteria stopper,
MultivariateMinimum rateMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback) |
double |
GeneralLikelihoodSearcher.optimiseAllSimple(StoppingCriteria stopper,
MultivariateMinimum rateMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback,
SearchMonitor monitor,
MinimiserMonitor rateMonitor) |
double |
GeneralLikelihoodSearcher.optimiseAllSimple(StoppingCriteria stopper,
MultivariateMinimum rateMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback,
SearchMonitor monitor,
MinimiserMonitor rateMonitor,
int groupOptimistionType) |
double |
GeneralLikelihoodSearcher.optimiseAllSimpleHeirarchy(StoppingCriteria stopper,
MultivariateMinimum rateMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback,
SearchMonitor monitor,
MinimiserMonitor rateMonitor) |
static Tree |
TreeSearchTool.optimiseClockConstrainedFixed(Tree tree,
Alignment alignment,
SubstitutionModel model,
boolean optimiseModel,
AlgorithmCallback callback)
Optimise the branches of a tree with regard to maximum likelihood, with the contraints of a global molecular clock - that is, all the tips terminate at the same point.
|
double |
GeneralLikelihoodSearcher.optimiseGeneral(StoppingCriteria stopper,
int fracDigits,
AlgorithmCallback callback) |
double |
GeneralLikelihoodSearcher.optimiseGeneral(StoppingCriteria stopper,
int fracDigits,
AlgorithmCallback callback,
SearchMonitor monitor) |
static Tree |
TreeSearchTool.optimiseUnrootedFixed(Tree tree,
Alignment alignment,
SubstitutionModel model,
boolean optimiseModel,
AlgorithmCallback callback)
Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).
|
double |
UnrootedMLSearcher.simpleOptimiseLikelihood(double epsilon,
AlgorithmCallback callback)
Optimise the branch lengths of the tree to obtain the maximum likelihood.
|
double |
UnrootedMLSearcher.simpleOptimiseLikelihood(StoppingCriteria stopper,
AlgorithmCallback callback)
Optimise the branch lengths of the tree to obtain the maximum likelihood.
|
Modifier and Type | Method and Description |
---|---|
static AlgorithmCallback |
AlgorithmCallback.Utils.getNullCallback() |
static AlgorithmCallback |
AlgorithmCallback.Utils.getPrintWriterCallback(java.io.PrintWriter pw)
Construct an algorithm callback that redirects status reports to a print writer
|
static AlgorithmCallback |
AlgorithmCallback.Utils.getSubCallback(AlgorithmCallback parent,
java.lang.String id,
double minProgress,
double maxProgress) |
static AlgorithmCallback |
AlgorithmCallback.Utils.getSystemOutCallback() |
Modifier and Type | Method and Description |
---|---|
static AlgorithmCallback |
AlgorithmCallback.Utils.getSubCallback(AlgorithmCallback parent,
java.lang.String id,
double minProgress,
double maxProgress) |