Uses of Class
pal.alignment.SitePattern

Packages that use SitePattern
pal.alignment Classes dealing with sequence alignments, including methods for reading and printing in several possible formats, as well as rearranging and concatenating. 
pal.distance Classes for reading and generating distance matrices, including computation of pairwise distances for sequence data (maximum-likelihood and observed distances). 
pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters. 
 

Uses of SitePattern in pal.alignment
 

Methods in pal.alignment that return SitePattern
static SitePattern SitePattern.getSitePattern(Alignment a)
           
 

Uses of SitePattern in pal.distance
 

Methods in pal.distance with parameters of type SitePattern
 void AlignmentDistanceMatrix.recompute(SitePattern sp, AlgorithmCallback callback)
          recompute observed distances under new site pattern
 void AlignmentDistanceMatrix.recompute(SitePattern sp, SubstitutionModel model)
          recompute maximum-likelihood distances under new site pattern
 void AlignmentDistanceMatrix.recompute(SitePattern sp, SubstitutionModel model, AlgorithmCallback callback)
          recompute maximum-likelihood distances under new site pattern
 void SequencePairLikelihood.updateSitePattern(SitePattern sp)
          update site pattern
 void PairwiseDistance.updateSitePattern(SitePattern sp)
          update site pattern
 

Constructors in pal.distance with parameters of type SitePattern
AlignmentDistanceMatrix(SitePattern sp)
          compute observed distances
AlignmentDistanceMatrix(SitePattern sp, AlgorithmCallback callback)
          compute observed distances
AlignmentDistanceMatrix(SitePattern sp, SubstitutionModel m)
          compute maximum-likelihood distances
AlignmentDistanceMatrix(SitePattern sp, SubstitutionModel m, AlgorithmCallback callback)
          compute maximum-likelihood distances
JukesCantorDistanceMatrix(SitePattern sitePattern)
          compute jukes-cantor corrected distances
PairwiseDistance(SitePattern sp)
          Constructor 1 (estimate observed distances only)
PairwiseDistance(SitePattern sp, SubstitutionModel m)
          Constructor 2 (uses evolutionary model)
SequencePairLikelihood(SitePattern sp, SubstitutionModel m)
          initialisation
 

Uses of SitePattern in pal.eval
 

Methods in pal.eval that return SitePattern
 SitePattern SimpleLikelihoodCalculator.getSitePattern()
           
 SitePattern LikelihoodValue.getSitePattern()
          Returns the site pattern of this likelihood value
 

Methods in pal.eval with parameters of type SitePattern
 void LikelihoodValue.renewSitePattern(SitePattern sp)
          Set new site pattern (while keeping tree and model)
 void FastLikelihoodCalculator.updateSitePattern(SitePattern pattern)
           
 

Constructors in pal.eval with parameters of type SitePattern
DemographicLikelihoodValue(SitePattern sp)
          Parameter taking a site pattern.
FastLikelihoodCalculator(SitePattern pattern)
          Constructor taking only site pattern.
FastLikelihoodCalculator(SitePattern pattern, Tree tree, RateMatrix model)
          Constructor taking site pattern, tree and model.
LikelihoodValue(SitePattern sp)
          initialization
ModelParameters(SitePattern sp, SubstitutionModel m)
          Constructor
SimpleLikelihoodCalculator(SitePattern pattern)
          Need to use setTree(), and setModel() before using compute() if you use this constructor
SimpleLikelihoodCalculator(SitePattern pattern, Tree tree, RateMatrix model)