Method Detail

• calculateFlat

  void calculateFlat(PatternInfo centerPattern,
                     ConditionalProbabilityStore leftConditionalProbabilities,
                     ConditionalProbabilityStore rightConditionalProbabilities,
                     ConditionalProbabilityStore resultStore)

  Parameters:

  centerPattern - the pattern information

  leftConditionalProbabilities - Implementations must not overwrite or change

  rightConditionalProbabilities - Implementations must not overwrite or change

  resultStore - Where to stick the created categoryPatternState information

• calculateExtended

  void calculateExtended(double distance,
                         SubstitutionModel model,
                         PatternInfo centerPattern,
                         ConditionalProbabilityStore leftConditionalProbabilities,
                         ConditionalProbabilityStore rightConditionalProbabilities,
                         ConditionalProbabilityStore resultStore)

  Parameters:

  distance -

  model -

  centerPattern - the pattern information

  leftConditionalProbabilities - Implementations must not overwrite or change

  rightConditionalProbabilities - Implementations must not overwrite or change

  resultStore - Where to stick the created categoryPatternState information

• calculateSingleExtendedDirect

  void calculateSingleExtendedDirect(double distance,
                                     SubstitutionModel model,
                                     int numberOfPatterns,
                                     ConditionalProbabilityStore conditionalProbabilities)

  Extend the conditionals back in time by some distance, with some model

  Parameters:

  distance - The distance to extend by

  model - The model to use

  conditionalProbabilities - The probabilities to extend

• calculateSingleExtendedIndirect

  void calculateSingleExtendedIndirect(double distance,
                                       SubstitutionModel model,
                                       int numberOfPatterns,
                                       ConditionalProbabilityStore baseConditionalProbabilities,
                                       ConditionalProbabilityStore resultConditionalProbabilities)

  Extend the conditionals back in time by some distance, with some model

  Parameters:

  distance - The distance to extend by

  model - The model to use

  baseConditionalProbabilities - The probabilities to extend

  resultConditionalProbabilities - The probabilities to extend

• calculateLogLikelihood

  double calculateLogLikelihood(double distance,
                                SubstitutionModel model,
                                PatternInfo centerPattern,
                                ConditionalProbabilityStore leftFlatConditionalProbabilities,
                                ConditionalProbabilityStore rightFlatConditionalProbabilities,
                                ConditionalProbabilityStore tempStore)

  Calculate the likelihood given two sub trees (left, right) and their flat (unextend) likeihood probabilities

  Parameters:

  distance -

  model -

  centerPattern - the pattern information

  leftFlatConditionalProbabilities -

  rightFlatConditionalProbabilities -

  tempStore - may be used internally to calculate likelihood

  Returns:

  the log likelihood

• calculateLogLikelihood

  double calculateLogLikelihood(SubstitutionModel model,
                                PatternInfo centerPattern,
                                ConditionalProbabilityStore leftConditionalProbabilities,
                                ConditionalProbabilityStore rightConditionalProbabilities)

  Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilities

  Parameters:

  model -

  centerPattern - the pattern information

  leftConditionalProbabilities -

  rightConditionalProbabilities -

  Returns:

  the Log likelihood

• calculateLogLikelihoodSingle

  double calculateLogLikelihoodSingle(SubstitutionModel model,
                                      int[] patternWeights,
                                      int numberOfPatterns,
                                      ConditionalProbabilityStore conditionalProbabilityStore)

  Calculate the likelihood given the conditional probabilites at the root

  Parameters:

  model - The substitution model used

  patternWeights - the weights of each pattern

  numberOfPatterns - the number of patterns

  conditionalProbabilities - The conditionals

  Returns:

  the Log likelihood

• calculateSiteDetailsRooted

  SiteDetails calculateSiteDetailsRooted(SubstitutionModel model,
                                         PatternInfo centerPattern,
                                         ConditionalProbabilityStore leftConditionalProbabilitiesStore,
                                         ConditionalProbabilityStore rightConditionalProbabilitiesStore)

  Calculate the conditional probabilities of each pattern for each category

  Parameters:

  model -

  centerPattern - the pattern information

  leftConditionalProbabilities -

  rightConditionalProbabilities -

  categoryPatternLogLikelihoodStore - after call will hold a matrix of values in the form [cat][pattern], where [cat][pattern] represents the site probability under a particular category/class, *not* multiplied by the category probability or pattern weights

• calculateSiteDetailsUnrooted

  SiteDetails calculateSiteDetailsUnrooted(double distance,
                                           SubstitutionModel model,
                                           PatternInfo centerPattern,
                                           ConditionalProbabilityStore leftConditionalProbabilitiesStore,
                                           ConditionalProbabilityStore rightConditionalProbabilitiesStore,
                                           ConditionalProbabilityStore tempStore)

  Calculate the conditional probabilities of each pattern for each category

  Parameters:

  distance - The distance between the two nodes

  model -

  centerPattern - the pattern information

  leftConditionalProbabilities -

  rightConditionalProbabilities -

  categoryPatternLogLikelihoodStore - after call will hold a matrix of values in the form [cat][pattern], where [cat][pattern] represents the site probability under a particular category/class, *not* multiplied by the category probability or pattern weights