Interface Sequence

    • Method Detail

      • getTaxon

        Taxon getTaxon()
        Returns:
        the taxon that this sequence represents (primarily used to match sequences with tree nodes)
      • getSequenceType

        SequenceType getSequenceType()
        Returns:
        the type of symbols that this sequence is made up of.
      • getString

        java.lang.String getString()
        Returns:
        a string representing the sequence of symbols.
      • getStates

        State[] getStates()
        Returns:
        an array of state objects.
      • getStateIndices

        byte[] getStateIndices()
        Returns:
        an array of state indices.
      • getState

        State getState​(int site)
        Returns:
        the state at site.
      • getLength

        int getLength()
        Get the length of the sequence
        Returns:
        the length
      • appendSequences

        static Sequence appendSequences​(Sequence sequence1,
                                        Sequence sequence2)
        Append two sequences together to create a new sequence object. New sequence has the taxon of the first sequence.
        Parameters:
        sequence1 -
        sequence2 -
        Returns:
      • getSubSequence

        static Sequence getSubSequence​(Sequence sequence,
                                       int from,
                                       int to)
        Returns a sub-sequence for states from, to (inclusive).
        Parameters:
        sequence -
        from -
        to -
        Returns:
      • stripGaps

        static Sequence stripGaps​(Sequence sequence)
        Strips a sequence of gaps
        Parameters:
        sequence - the sequence
        Returns:
        the stripped sequence
      • stripStates

        static Sequence stripStates​(Sequence sequence,
                                    java.util.List<State> stripStates)
        Strips a sequence of any states given
        Parameters:
        sequence - the sequence
        stripStates - the states to strip
        Returns:
        an array of states
      • replaceStates

        static Sequence replaceStates​(Sequence sequence,
                                      java.util.List<State> searchStates,
                                      State replaceState)
        Searchers and replaces a sequence of any states given
        Parameters:
        sequence - the sequence
        searchStates - the states to search for
        Returns:
        an array of states
      • getStateCount

        static int getStateCount​(Sequence sequence,
                                 State state)
        Counts the number of occurances of a state
        Parameters:
        sequence - the sequence string to count
        state - the state
        Returns:
        the number of occurances