Interface Pattern


public interface Pattern
An interface representing a list of states for a list of taxa (e.g. an alignment column).
Version:
$Id: Pattern.java 658 2007-03-20 03:27:20Z twobeers $
Author:
Andrew Rambaut, Alexei Drummond
  • Method Details

    • getSequenceType

      SequenceType getSequenceType()
      Returns:
      the data type of the states in this pattern.
    • getLength

      int getLength()
    • getTaxa

      List<Taxon> getTaxa()
      Returns:
      the list of taxa that the state values correspond to.
    • getState

      State getState(int index)
      Get the state for the ith taxon
      Parameters:
      index -
      Returns:
      the state
    • getStates

      List<State> getStates()
      Returns:
      the list of state values of this pattern.
    • getStateSet

      Set<State> getStateSet()
      Returns:
      the set of state values of this pattern.
    • getWeight

      double getWeight()
      Get the weight of this pattern
      Returns:
      the weight
    • getMostFrequentState

      State getMostFrequentState()
      Returns the most frequent state in this pattern
      Returns:
      the most frequent state
    • getMostFrequentState

      State getMostFrequentState(boolean includeAmbiguous)
      Returns the most frequent state in this pattern, optionally including ambiguous states
      Parameters:
      includeAmbiguous - whether to include ambiguous states
      Returns:
      the most frequent state
    • getStateFrequency

      double getStateFrequency(State state)
      Returns the frequent of the given state in this pattern
      Parameters:
      state -
      Returns:
      the frequency
    • getStateCount

      int getStateCount(State state)
      Returns the count of the given state in this pattern
      Parameters:
      state -
      Returns:
      the count