Package pal.datatype

Class AminoAcids

java.lang.Object
pal.datatype.SimpleDataType
pal.datatype.AminoAcids
All Implemented Interfaces:
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:

  • Field Details

  • Constructor Details

    • AminoAcids

      public AminoAcids()

  • Method Details

    • 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

    • getCharImpl

      protected char getCharImpl(int state)
      Specified by:
      getCharImpl 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 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 String getTLA(int state)
      Returns:
      a three letter acronym for an AminoAcid, according to state