Field Detail

• UNIVERSAL

  static final int UNIVERSAL

  TypeID for Universal

  See Also:

  Constant Field Values

• VERTEBRATE_MITOCHONDRIAL

  static final int VERTEBRATE_MITOCHONDRIAL

  TypeID for Vertebrate Mitochondrial

  See Also:

  Constant Field Values

• YEAST

  static final int YEAST

  TypeID for Yeast

  See Also:

  Constant Field Values

• MOLD_PROTOZOAN_MITOCHONDRIAL

  static final int MOLD_PROTOZOAN_MITOCHONDRIAL

  TypeID for Mold Protozoan Mitochondrial

  See Also:

  Constant Field Values

• MYCOPLASMA

  static final int MYCOPLASMA

  TypeID for Mycoplasma

  See Also:

  Constant Field Values

• INVERTEBRATE_MITOCHONDRIAL

  static final int INVERTEBRATE_MITOCHONDRIAL

  TypeID for Invertebrate Mitochondrial

  See Also:

  Constant Field Values

• CILATE

  static final int CILATE

  TypeID for Cilate

  See Also:

  Constant Field Values

• ECHINODERM_MITOCHONDRIAL

  static final int ECHINODERM_MITOCHONDRIAL

  TypeID for Echinoderm Mitochondrial

  See Also:

  Constant Field Values

• EUPLOTID_NUCLEAR

  static final int EUPLOTID_NUCLEAR

  TypeID for Euplotid Nuclear

  See Also:

  Constant Field Values

• ASCIDIAN_MITOCHONDRIAL

  static final int ASCIDIAN_MITOCHONDRIAL

  TypeID for Ascidian Mitochondrial

  See Also:

  Constant Field Values

• FLATWORM_MITOCHONDRIAL

  static final int FLATWORM_MITOCHONDRIAL

  TypeID for Flatworm Mitochondrial

  See Also:

  Constant Field Values

• BLEPHARISMA_NUCLEAR

  static final int BLEPHARISMA_NUCLEAR

  TypeID for Blepharisma Nuclear

  See Also:

  Constant Field Values

• BACTERIAL

  static final int BACTERIAL

  TypeID for Bacterial

  See Also:

  Constant Field Values

• ALTERNATIVE_YEAST

  static final int ALTERNATIVE_YEAST

  TypeID for Alternative Yeast

  See Also:

  Constant Field Values

• ORGANISM_TYPE_NAMES

  static final java.lang.String[] ORGANISM_TYPE_NAMES

  A textual version of an organism type - type is index into array

Method Detail

• getAminoAcidChar

  char getAminoAcidChar​(char[] codon)

  Returns the char associated with AminoAcid represented by 'codon'

  Returns:

  state for '?' if codon unknown or wrong length

  See Also:

  AminoAcids

• getAminoAcidState

  int getAminoAcidState​(char[] codon)

  Returns the state associated with AminoAcid represented by 'codon'

  Returns:

  '?' if codon unknown or wrong length

  See Also:

  AminoAcids

• getCodonsFromAminoAcidState

  char[][] getCodonsFromAminoAcidState​(int aminoAcidState)

  Returns:

  all the possible codons for a given amino acid

• getCodonsFromAminoAcidChar

  char[][] getCodonsFromAminoAcidChar​(char aminoAcidChar)

• getAminoAcidCharFromCodonIndex

  char getAminoAcidCharFromCodonIndex​(int codonIndex)

  Returns the amino acid char at the corresponding codonIndex

• getAminoAcidStateFromCodonIndex

  int getAminoAcidStateFromCodonIndex​(int codonIndex)

  Returns the amino acid state at the corresponding codonIndex

• getIUPACStatesFromAminoAcidState

  int[] getIUPACStatesFromAminoAcidState​(int aminoAcid)

• getStatesFromAminoAcidState

  int[] getStatesFromAminoAcidState​(int aminoAcid)

• getAminoAcidStateFromStates

  int getAminoAcidStateFromStates​(int[] states)

  Returns:

  The AminoAcid states given the nucleotides states (array should be of size 3)

• getTerminatorIndexes

  int[] getTerminatorIndexes()

  Returns:

  the codon states of terminator amino acids.

• getNumberOfTerminatorIndexes

  int getNumberOfTerminatorIndexes()

  Returns the number of terminator amino acids.

• getOrganismTypeID

  int getOrganismTypeID()

  Returns:

  the type of this organism (see defined type constants)

• isSynonymous

  boolean isSynonymous​(int codonIndexOne,
                       int codonIndexTwo)

  Returns:

  true if the amino acids that map to two codons are the same (synonymous). False otherwise