Package pal.datatype

Class Codons

java.lang.Object
pal.datatype.SimpleDataType
pal.datatype.Codons
All Implemented Interfaces:
Serializable, DataType, MolecularDataType
public class Codons extends SimpleDataType implements MolecularDataType
implements DataType for all Codons (including terminators). Characters are defined as 'A-Z' followed by 'a-z' followed by '0-9' followed by '@' and '%' Now incorporates the ungeneral code from GeneralizedCodons (which has died due to it's limited use)
Version:
$Id: Codons.java,v 1.21 2004/03/10 04:42:54 matt Exp $
Author:
Matthew Goode, Alexei Drummond
See Also:

  • Field Details

    • DEFAULT_INSTANCE

      public static final Codons DEFAULT_INSTANCE

  • Constructor Details

    • Codons

      public Codons()

  • Method Details

    • 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

    • getCharImpl

      protected char getCharImpl(int state)
      Get character corresponding to a given state
      Specified by:
      getCharImpl in class SimpleDataType

    • getDescription

      public String getDescription()
      Description copied from interface: DataType
      description of data type
      Specified by:
      getDescription in interface DataType
      Returns:
      string describing the data type

    • 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

    • 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:
      residue - states an array of states corresponding to states of this datatype
      Returns:
      the corresponding IUPAC states

    • getMolecularStatesFromIUPACNucleotides

      public final int[] getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates, int startingIndex)
      Specified by:
      getMolecularStatesFromIUPACNucleotides in interface MolecularDataType

    • getMolecularStatesFromSimpleNucleotides

      public final int[] getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates, int startingIndex)
      Specified by:
      getMolecularStatesFromSimpleNucleotides in interface MolecularDataType
      Returns:

    • isCreatesIUPACNuecleotides

      public boolean isCreatesIUPACNuecleotides()
      Specified by:
      isCreatesIUPACNuecleotides in interface MolecularDataType
      Returns:
      false

    • getNucleotideLength

      public final int getNucleotideLength()
      Specified by:
      getNucleotideLength in interface MolecularDataType
      Returns:
      3

    • getTLA

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

    • getCodonIndexFromNucleotides

      public static final int getCodonIndexFromNucleotides(char[] codon)
      The codon index is a number between 0 and 64 assigned to each different codon type
      Parameters:
      codon - a 3 element array of characters which contain Nucleotide characters
      Returns:
      -1 if the codon has unknowns, or gaps in it, or is length is less than 3

    • getCodonIndexFromNucleotideStates

      public static final int getCodonIndexFromNucleotideStates(int[] codon)
      The codon index is a number between 0 and 64 assigned to each different codon type
      Parameters:
      codon - a 3 element array of characters which contain Nucleotide states
      Returns:
      -1 if the codon has unknowns, or gaps in it, or is length is less than 3

    • getCodonIndexFromNucleotideStates

      public static final int getCodonIndexFromNucleotideStates(int[] codon, int startingPosition)
      The codon index is a number between 0 and 64 assigned to each different codon type
      Parameters:
      codon - a 3 element array of characters which contain Nucleotide states
      startingPosition - an offset into the array to start examining
      Returns:
      -1 if the codon has unknowns, or gaps in it, or is length is less than 3

    • getCodonIndexFromIUPACNucleotideStates

      public static final int getCodonIndexFromIUPACNucleotideStates(int[] codon)
      The codon index is a number between 0 and 64 assigned to each different codon type
      Parameters:
      codon - a 3 element array of characters which contain Nucleotide states
      startingPosition - an offset into the array to start examining
      Returns:
      -1 if the codon has unknowns, or gaps in it, or is length is less than 3

    • getCodonIndexFromIUPACNucleotideStates

      public static final int getCodonIndexFromIUPACNucleotideStates(int[] codon, int startingPosition)
      The codon index is a number between 0 and 64 assigned to each different codon type
      Parameters:
      codon - a 3 element array of characters which contain Nucleotide states
      startingPosition - an offset into the array to start examining
      Returns:
      -1 if the codon has unknowns, or gaps in it, or is length is less than 3

    • getNucleotidesFromCodonIndex

      public static final char[] getNucleotidesFromCodonIndex(int index)
      Translates an index into a codon
      Parameters:
      index - the codon index
      Returns:
      a char array contain 3 nucleotide characters

    • getNucleotideStatesFromCodonIndex

      public static final int[] getNucleotideStatesFromCodonIndex(int codonIndex)
      Translates an index into a codon
      Parameters:
      index - the codon index
      Returns:
      an int array contain 3 nucleotide states

    • getF1X4CodonFrequencies

      public static final double[] getF1X4CodonFrequencies(double[] nucleotideFrequencies)

    • getF3X4CodonFrequencies

      public static final double[] getF3X4CodonFrequencies(double[][] nucleotideTripletFrequencies)