Interface SequenceType


  • public interface SequenceType
    Interface for sequences data types.
    Version:
    $Id: SequenceType.java 849 2007-12-06 00:10:14Z twobeers $
    Author:
    Andrew Rambaut, Alexei Drummond
    • Method Detail

      • getStateCount

        int getStateCount()
        Get number of states including ambiguous states
        Returns:
        number of states
      • getStates

        java.util.List<? extends State> getStates()
        Get a list of states ordered by their indices.
        Returns:
        a list of states
      • getCanonicalStateCount

        int getCanonicalStateCount()
        Get number of canonical states
        Returns:
        number of states
      • getCanonicalStates

        java.util.List<? extends State> getCanonicalStates()
        Get a list of canonical states ordered by their indices.
        Returns:
        a list of states
      • getState

        State getState​(java.lang.String code)
        Get state corresponding to a string code
        Parameters:
        code - a string code
        Returns:
        the state with the given code, or null if there is no such state
      • getState

        State getState​(char code)
        Get state whose code is the one-character string consisting only of code.
        Parameters:
        code -
        Returns:
        the state with the given code, or null if there is no such state
      • getCodeLength

        int getCodeLength()
        Returns:
        the length, in characters, of a state, when encoded as a string. i.e. 1 for Nucleotides and AminoAcids and 3 for Codons.
      • getState

        State getState​(int index)
        Get state corresponding to a state index
        Parameters:
        index - a state index
        Returns:
        the state
      • getUnknownState

        State getUnknownState()
        Get state corresponding to an unknown
        Returns:
        the state
      • getGapState

        State getGapState()
        Get state corresponding to a gap
        Returns:
        state
      • isUnknown

        boolean isUnknown​(State state)
        Returns:
        true if this state is an unknown state
      • isGap

        boolean isGap​(State state)
        Returns:
        true if this state is a gap
      • getName

        java.lang.String getName()
        name of data type
        Returns:
        string describing the data type
      • getNexusDataType

        java.lang.String getNexusDataType()
        Returns:
        datatype inside a nexus characters block, if any.
      • toStateArray

        State[] toStateArray​(java.lang.String sequenceString)
        Converts a string of state codes into an array of State objects for this SequenceType
        Parameters:
        sequenceString -
        Returns:
        the State array
      • toStateArray

        State[] toStateArray​(byte[] indexArray)
        Converts an array of state indices into an array of State objects for this SequenceType
        Parameters:
        indexArray -
        Returns:
        the State array