Uses of Interface
pal.math.OrthogonalHints

Packages that use OrthogonalHints
pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters. 
pal.math Classes for math stuff such as optimisation, numerical derivatives, matrix exponentials, random numbers, special function etc. 
pal.mep Classes for the analysis of "measurably evolving populations" (mep). 
pal.substmodel Classes describing substitution models, i.e. 
pal.tree Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint). 
 

Uses of OrthogonalHints in pal.eval
 

Methods in pal.eval that return OrthogonalHints
 OrthogonalHints ChiSquareValue.getOrthogonalHints()
           
 OrthogonalHints ModelParameters.getOrthogonalHints()
           
 OrthogonalHints DemographicValue.getOrthogonalHints()
           
 

Uses of OrthogonalHints in pal.math
 

Methods in pal.math that return OrthogonalHints
static OrthogonalHints OrthogonalHints.Utils.getAdjusted(OrthogonalHints toAdjust, int adjustmentFactor)
           
static OrthogonalHints OrthogonalHints.Utils.getCombined(OrthogonalHints first, int numberOfFirstParameters, OrthogonalHints second, int numberOfSecondParameters)
           
static OrthogonalHints OrthogonalHints.Utils.getNull()
           
 OrthogonalHints BoundsCheckedFunction.getOrthogonalHints()
           
 OrthogonalHints EvaluationCounter.getOrthogonalHints()
           
 OrthogonalHints MultivariateFunction.getOrthogonalHints()
           
 

Methods in pal.math with parameters of type OrthogonalHints
static OrthogonalHints OrthogonalHints.Utils.getAdjusted(OrthogonalHints toAdjust, int adjustmentFactor)
           
static OrthogonalHints OrthogonalHints.Utils.getCombined(OrthogonalHints first, int numberOfFirstParameters, OrthogonalHints second, int numberOfSecondParameters)
           
static double[] OrthogonalHints.Utils.getInternalParameterBoundaries(OrthogonalHints base, int parameter)
           
 

Uses of OrthogonalHints in pal.mep
 

Methods in pal.mep that return OrthogonalHints
 OrthogonalHints DeltaModel.Instance.getOrthogonalHints()
           
 OrthogonalHints MutationRateModel.getOrthogonalHints()
          Overide if there is any orthogonal hint information available
 

Uses of OrthogonalHints in pal.substmodel
 

Methods in pal.substmodel that return OrthogonalHints
 OrthogonalHints CachedRateMatrix.getOrthogonalHints()
           
 OrthogonalHints SingleClassSubstitutionModel.getOrthogonalHints()
           
 OrthogonalHints SubstitutionModel.getOrthogonalHints()
          May return null
 OrthogonalHints RateMatrix.getOrthogonalHints()
           
 OrthogonalHints YangCodonModel.SimplePositiveSelection.getOrthogonalHints()
           
 OrthogonalHints YangCodonModel.SimpleNeutralSelection.getOrthogonalHints()
           
 OrthogonalHints GeneralRateDistributionSubstitutionModel.getOrthogonalHints()
           
 OrthogonalHints AbstractRateMatrix.getOrthogonalHints()
           
 

Uses of OrthogonalHints in pal.tree
 

Classes in pal.tree that implement OrthogonalHints
 class MutationRateModelTree
          Provides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node).
 

Methods in pal.tree that return OrthogonalHints
 OrthogonalHints ParameterizedTree.getOrthogonalHints()
           
 OrthogonalHints ParameterizedTree.ParameterizedTreeBase.getOrthogonalHints()
           
 OrthogonalHints MutationRateModelTree.getOrthogonalHints()