Uses of Interface
pal.misc.Parameterized

Packages that use Parameterized
pal.coalescent Classes to model population genetic processes using the coalescent. 
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. 
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 Parameterized in pal.coalescent
 

Classes in pal.coalescent that implement Parameterized
 class ConstantPopulation
          This class models coalescent intervals for a constant population (parameter: N0=present-day population size).
 class ConstExpConst
          This class models a population that grows exponentially from an initial population size alpha N0 at time y to a size N0 at time x until the present-day.
 class ConstExpGrowth
          This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.
 class DemographicClockTree
          Provides parameter interface to a clock-like genealogy which is assumed to have some demographic pattern of theta (diversity) as well as branch parameters (the minimal node height differences at each internal node).
 class DemographicModel
          This abstract class contains methods that are of general use for modelling coalescent intervals given a demographic model.
 class ExpandingPopulation
          This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.
 class ExponentialGrowth
          This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).
 

Uses of Parameterized in pal.eval
 

Methods in pal.eval with parameters of type Parameterized
 double LikelihoodOptimiser.optimiseLogLikelihood(Parameterized parameters, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits)
           
 double LikelihoodOptimiser.optimiseLogLikelihood(Parameterized parameters, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)
           
 

Uses of Parameterized in pal.mep
 

Subinterfaces of Parameterized in pal.mep
static interface DeltaModel.Instance
           
 

Classes in pal.mep that implement Parameterized
 class ConstantMutationRate
          This class models a constant mutation rate (parameter: mu = mutation rate).
 class MutationRateModel
          This abstract class contains methods that are of general use for modelling mutation rate changes over time.
 class SteppedMutationRate
          This class models a step-wise mutation rate.
 class WindowedMutationRate
          This class models a windowed mutation rate (parameter: mu = mutation rate).
 

Uses of Parameterized in pal.misc
 

Subinterfaces of Parameterized in pal.misc
 interface NamedParameterized
          interface for class with (optimizable) named parameters
 

Classes in pal.misc that implement Parameterized
 class MultiParameterized
          Title: MultiParameterized
static class Parameterized.Null
          NullParameterized Object Can be used by subclasses to implement parameterized without actually having paramters
 

Methods in pal.misc that return Parameterized
static Parameterized Parameterized.Utils.combine(Parameterized[] bases)
          Combine multiple parameterized objects into one
static Parameterized Parameterized.Utils.combine(Parameterized baseOne, Parameterized baseTwo)
          Combine multiple parameterized objects into one
static Parameterized Parameterized.Utils.createParametizedWrapper(double[] parameters, double[] lowerLimits, double[] upperLimits, double[] defaultValues)
          Create a wrapper around a set of double arrays to create a parameterized object (changes to parameterized object change given arrays)
static Parameterized Parameterized.Utils.createParametizedWrapper(double[] parameters, double[] lowerLimits, double[] upperLimits, double[] defaultValues, double[] parametersSE)
          Create a wrapper around a set of double arrays to create a parameterized object (changes to parameterized object change given arrays)
 

Methods in pal.misc with parameters of type Parameterized
static Parameterized Parameterized.Utils.combine(Parameterized[] bases)
          Combine multiple parameterized objects into one
static Parameterized Parameterized.Utils.combine(Parameterized baseOne, Parameterized baseTwo)
          Combine multiple parameterized objects into one
static MultivariateFunction Utils.combineMultivariateFunction(MultivariateFunction base, Parameterized[] additionalParameters)
          Creates an interface between a parameterised object to allow it to act as a multivariate minimum.
protected static int MultiParameterized.countParameters(Parameterized[] ps)
           
static IndividualParameterHandler[] IndividualParameterHandler.Utils.createSimple(Parameterized[] bases)
           
static IndividualParameterHandler IndividualParameterHandler.Utils.createSimple(Parameterized base, int parameterIndex)
           
static IndividualParameterHandler IndividualParameterHandler.Utils.createSimple(Parameterized base, int parameterIndex, IndividualParameterHandler.Listener listener)
           
 double[] MultiParameterized.getBaseParameters(Parameterized base)
           
protected  int MultiParameterized.getIndex(Parameterized base)
          Get the index of a base parameterized object
static double[] Parameterized.Utils.getParameters(Parameterized source)
           
static int Parameterized.Utils.getTotalNumberOfParameters(Parameterized[] bases)
           
 void IndividualParameterHandler.Listener.parameterChanged(Parameterized base, int parameterIndex, double value)
           
 void MultiParameterized.ParameterAccessWatcher.parameterSet(Parameterized baseParameterized, double param, int localParameter)
           
protected  void Parameterized.ParameterizedUser.setParameterizedBase(Parameterized base)
          Set's the base parameterized object...
protected static void MultiParameterized.setup(Parameterized[] ps, int[] baseLookup, int[] baseParameter)
           
static void Parameterized.Utils.setupLookups(Parameterized[] bases, int[] baseLookup, int[] parameterIndexLookup, int totalNumberOfParameters)
           
 

Constructors in pal.misc with parameters of type Parameterized
MultiParameterized(Parameterized[] bases)
           
MultiParameterized(Parameterized[] bases, MultiParameterized.ParameterAccessWatcher watcher)
           
MultiParameterized(Parameterized b1, Parameterized b2)
           
Parameterized.ParameterizedUser(Parameterized base)
           
ParameterizedNeoWrapper(Parameterized base)
           
 

Uses of Parameterized in pal.substmodel
 

Subinterfaces of Parameterized in pal.substmodel
 interface RateMatrix
          abstract base class for all rate matrices
 interface SubstitutionModel
          model of sequence substitution (rate matrix + rate variation).
 

Classes in pal.substmodel that implement Parameterized
 class AbstractRateMatrix
          abstract base class for all rate matrices
 class AminoAcidModel
          base class of rate matrices for amino acids
 class BLOSUM62
          BLOSUM62 model of amino acid evolution
 class CachedRateMatrix
          a cached rate matrix.
 class CodonModel
          base class for nucleotide rate matrices
 class CPREV
          CPREV model of amino acid evolution (J.Adachi et al.
 class Dayhoff
          Dayhoff model for amino acid evolution Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C.
 class F81
          Felsenstein 1981 model of nucleotide evolution
 class F84
          Felsenstein 1984 (PHYLIP) model of nucleotide evolution
 class GammaRates
          discrete Gamma distribution (Z.
 class GeneralRateDistributionSubstitutionModel
           
 class GTR
          GTR (general time reversible) model of nucleotide evolution Lanave, C., G.
 class HKY
          Hasegawa-Kishino-Yano model of nucleotide evolution Hasegawa, M., H.
 class InvariableSites
          invariable sites model (two-rate model with mean rate = 1.0)
 class JTT
          JTT model of amino acid evolution Jones, D.
 class MTREV24
          MTREV24 model of amino acid evolution
 class NucleotideModel
          base class for nucleotide rate matrices
 class RateDistribution
          abstract base class for models of rate variation over sites employing a discrete rate distribution
 class RateMatrixHandler
           
 class SingleClassSubstitutionModel
           
 class TN
          Tamura-Nei model of nucleotide evolution Tamura, K.
 class TwoStateModel
          implements the most general reversible rate matrix for two-state data
 class UniformRate
          uniform rate distribution
 class VT
          VT (variable time matrix) model of amino acid evolution Modeling Amino Acid Replacement Mueller, T.
 class WAG
          WAG model of amino acid evolution (S.
 class YangCodonModel
          Yang's model of codon evolution More advanced codon Substitution Models (of Neilson and Yang) are now included (the M1, and M2 models).
static class YangCodonModel.SimpleNeutralSelection
          A Substitution Model which can be used to implment the Neutral Model (with out continuous rate stuff) Codon model of [1] which uses the weighted sum of trwo base YangCodon models where omega=0, omega=1 repectively
[1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene.
static class YangCodonModel.SimplePositiveSelection
          A Substitution Model which can be used to implment the Postitive Selection (with out continuous rate stuff) Codon model of [1] which uses the weighted sum of a three base Codon model where omega=0, omega=1 and omega=free
[1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene.
 

Uses of Parameterized in pal.tree
 

Subinterfaces of Parameterized in pal.tree
 interface ParameterizedTree
          abstract base class for a tree with an Parameterized interface
 

Classes in pal.tree that implement Parameterized
 class ClockTree
          provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)
 class LogParameterizedTree
          This class logarithmically transforms tree parameters.
 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).
static class ParameterizedTree.ParameterizedTreeBase
          For parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...)
 class UnconstrainedTree
          provides parameter interface to an unconstrained tree (parameters are all available branch lengths)