Package pal.datatype

Class AminoAcids

  • All Implemented Interfaces:
    java.io.Serializable, DataType
    Direct Known Subclasses:
    SpecificAminoAcids

    public class AminoAcids
    extends SimpleDataType
    implements DataType for amino acids
    Version:
    $Id: AminoAcids.java,v 1.19 2003/03/23 00:04:23 matt Exp $
    Author:
    Korbinian Strimmer, Alexei Drummond, Matthew Goode
    See Also:
    Serialized Form
    • Constructor Detail

      • AminoAcids

        public AminoAcids()
    • Method Detail

      • getNumStates

        public int getNumStates()
        Description copied from interface: DataType
        get number of unique states
        Returns:
        number of unique states
      • getStateImpl

        protected int getStateImpl​(char c)
        Description copied from class: SimpleDataType
        For sub classes to implement main functionality of getState. Gaps do not need to be considered
        Specified by:
        getStateImpl in class SimpleDataType
      • isUnknownStateImpl

        protected boolean isUnknownStateImpl​(int state)
        Description copied from class: SimpleDataType
        For subclasses to handle, without regard for gaps
        Specified by:
        isUnknownStateImpl in class SimpleDataType
      • getDescription

        public java.lang.String getDescription()
        Description copied from interface: DataType
        description of data type
        Returns:
        string describing the data type
      • getTypeID

        public int getTypeID()
        Description copied from interface: DataType
        get numerical code describing the data type
        Returns:
        numerical code
      • getTLA

        public static final java.lang.String getTLA​(int state)
        Returns:
        a three letter acronym for an AminoAcid, according to state