Package pal.datatype

Class GapBalanced

  • All Implemented Interfaces:
    java.io.Serializable, DataType, MolecularDataType
    public class GapBalanced
extends SimpleDataType
implements MolecularDataType
    implements a ResidueDataType for GapBalanced notation. The terminate character IS included as a state
    Version:
    $Id: GapBalanced.java,v 1.6 2003/03/23 00:04:23 matt Exp $
    Author:
    Matthew Goode
    See Also:
    Serialized Form

    • Field Detail

      • DEFAULT_INSTANCE

        public static final GapBalanced DEFAULT_INSTANCE

    • Constructor Detail

      • GapBalanced

        public GapBalanced​(CodonTable translationTable)

    • Method Detail

      • getNumStates

        public int getNumStates()
        Description copied from interface: DataType
        get number of unique states
        Specified by:
        getNumStates in interface DataType
        Returns:
        number of unique states

      • getStateImpl

        public 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 final 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
        Specified by:
        getDescription in interface DataType
        Returns:
        string describing the data type

      • getTypeID

        public int getTypeID()
        Description copied from interface: DataType
        get numerical code describing the data type
        Specified by:
        getTypeID in interface DataType
        Returns:
        numerical code

      • getNucleotideStates

        public int[] getNucleotideStates​(int[] residueStates)
        Specified by:
        getNucleotideStates in interface MolecularDataType
        Parameters:
        residueStates - an array of states corresponding to states of this datatype
        Returns:
        the corresponding IUPAC states

      • getMolecularStatesFromIUPACNucleotides

        public final int[] getMolecularStatesFromIUPACNucleotides​(int[] nucleotideStates,
                                                          int startingIndex)
        Currently converts ambiguous states to a simple version (IE takes the first possible simple state for the ambiguous state)
        Specified by:
        getMolecularStatesFromIUPACNucleotides in interface MolecularDataType