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 Detail

      • getSequenceType

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

        int getLength()
      • getTaxa

        java.util.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

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

        java.util.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