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,
                         PatternInfo centerPattern,
                         ConditionalProbabilityStore leftConditionalProbabilities,
                         ConditionalProbabilityStore rightConditionalProbabilities,
                         ConditionalProbabilityStore resultStore)

  Parameters:

  distance - the evolutionary distance

  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,
                                     int numberOfPatterns,
                                     ConditionalProbabilityStore conditionalProbabilities)

  Extend the conditionals back in time by some distance

  Parameters:

  distance - The evolutionary distance to extend by

  numberOfPatterns - the number of patterns

  conditionalProbabilities - The probabilities to extend

• calculateSingleExtendedIndirect

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

  Extend the conditionals back in time by some distance

  Parameters:

  distance - The evolutionary distance to extend by

  numberOfPatterns - the number of patterns

  baseConditionalProbabilities - The probabilities to extend

  resultConditionalProbabilities - The probabilities to extend

• calculateLogLikelihood

  double calculateLogLikelihood(double distance,
                                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 - The evolutionary distance

  centerPattern - the pattern information

  leftFlatConditionalProbabilities - The left conditional probabilities (unextended)

  rightFlatConditionalProbabilities - The right conditional probabilities (unextended)

  tempStore - may be used internally to calculate likelihood

  Returns:

  the log likelihood

• calculateLogLikelihood

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

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

  Parameters:

  centerPattern - the pattern information

  leftConditionalProbabilities - The left conditional probabilities

  rightConditionalProbabilities - The right conditional probabilities

  Returns:

  the Log likelihood

• calculateLogLikelihoodSingle

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

  Calculate the likelihood given the conditional probabilites at the root

  Parameters:

  patternWeights - the weights of each pattern

  numberOfPatterns - the number of patterns

  Returns:

  the Log likelihood

• calculateSiteDetailsRooted

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

  Calculate the conditional probabilities of each pattern for each category

  Parameters:

  centerPattern - the pattern information

  leftConditionalProbabilitiesStore - The left conditional probabilities

  rightConditionalProbabilitiesStore - The right conditional probabilities

• calculateSiteDetailsUnrooted

  SiteDetails calculateSiteDetailsUnrooted(double distance,
                                           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

  centerPattern - the pattern information

  leftConditionalProbabilitiesStore - The left conditional probabilities

  rightConditionalProbabilitiesStore - The right conditional probabilities

  tempStore - 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