Package pal.eval

Class SimpleLikelihoodCalculator

    • Constructor Detail

      • SimpleLikelihoodCalculator

        public SimpleLikelihoodCalculator​(SitePattern pattern)
        Need to use setTree(), and setModel() before using compute() if you use this constructor
    • Method Detail

      • calculateLogLikelihood

        public double calculateLogLikelihood()
        compute log-likelihood for current tree (fixed branch lengths and model) return log-likelihood
        Specified by:
        calculateLogLikelihood in interface LikelihoodCalculator
      • getTree

        public Tree getTree()
      • setRateMatrix

        public void setRateMatrix​(RateMatrix m)
        define model (a site pattern must have been set before calling this method)
        Parameters:
        m - model of substitution (rate matrix + rate distribution)
      • setTree

        public void setTree​(Tree t)
        define tree ,(must only be called only after a site pattern has been defined).
        Parameters:
        t - tree
      • modelUpdated

        public final void modelUpdated()
      • treeUpdated

        public final void treeUpdated()
      • getPartial

        protected double[][] getPartial​(Node branch)
        get partial likelihood of a branch
      • getNextBranch

        protected Node getNextBranch​(Node branch,
                                     Node center)
        get next branch around a center node (center may be root, but root is never returned)
      • productPartials

        protected void productPartials​(Node center)
        multiply partials into the neighbour of branch
      • partialsInternal

        protected void partialsInternal​(Node center)
        compute partials for branch around center node (it is assumed that multiplied partials are available in the neighbor branch)
      • partialsExternal

        protected void partialsExternal​(Node branch)
        compute partials for external branch