Constructor Detail

• SimpleLikelihoodCalculator

  public SimpleLikelihoodCalculator​(SitePattern pattern)

  Need to use setTree(), and setModel() before using compute() if you use this constructor

• SimpleLikelihoodCalculator

  public SimpleLikelihoodCalculator​(SitePattern pattern,
                                    Tree tree,
                                    RateMatrix model)

Method Detail

• release

  public void release()

  Doesn't do anything...

  Specified by:

  release in interface LikelihoodCalculator

• calculateLogLikelihood

  public double calculateLogLikelihood()

  compute log-likelihood for current tree (fixed branch lengths and model) return log-likelihood

  Specified by:

  calculateLogLikelihood in interface LikelihoodCalculator

• getSitePattern

  public SitePattern getSitePattern()

• 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