Field Detail

• NAME

  public static final java.lang.String NAME

  See Also:

  Constant Field Values

• CANONICAL_STATE_COUNT

  public static final int CANONICAL_STATE_COUNT

  See Also:

  Constant Field Values

• STATE_COUNT

  public static final int STATE_COUNT

  See Also:

  Constant Field Values

• CANONICAL_STATES

  public static final CodonState[] CANONICAL_STATES

• STATES

  public static final CodonState[] STATES

• UNKNOWN_STATE

  public static final CodonState UNKNOWN_STATE

• GAP_STATE

  public static final CodonState GAP_STATE

Constructor Detail

• Codons

  public Codons()

Method Detail

• getStateCount

  public static int getStateCount()

• getStates

  public static java.util.List<State> getStates()

• getCanonicalStateCount

  public static int getCanonicalStateCount()

• getCanonicalStates

  public static java.util.List<State> getCanonicalStates()

• getState

  public static CodonState getState​(NucleotideState nucleotide1,
                                    NucleotideState nucleotide2,
                                    NucleotideState nucleotide3)

• getState

  public static CodonState getState​(java.lang.String code)

  Gets the state object for the given code. Returns null if the code is illegal or contains ambiguous nucleotides.

  Parameters:

  code - a three-character string of non-ambiguous nucleotides in uppercase

  Returns:

  the state

• getState

  public static CodonState getState​(int index)

• getUnknownState

  public static CodonState getUnknownState()

• getGapState

  public static CodonState getGapState()

• isUnknown

  public static boolean isUnknown​(CodonState state)

• isGap

  public static boolean isGap​(CodonState state)

• toNucleotides

  public static NucleotideState[] toNucleotides​(State[] states)

• toNucleotides

  public static NucleotideState[] toNucleotides​(CodonState state)

• toStateArray

  public static CodonState[] toStateArray​(java.lang.String sequenceString)

• toStateArray

  public static CodonState[] toStateArray​(byte[] indexArray)