Class Nucleotides

Method Details

• getComplementaryState

  public static NucleotideState getComplementaryState(NucleotideState state)

• getStateCount

  public static int getStateCount()

• getStates

  public static List<State> getStates()

  Returns:

  A list of all possible states, including the gap and ambiguity states.

• getCanonicalStateCount

  public static int getCanonicalStateCount()

• getCanonicalStates

  public static List<NucleotideState> getCanonicalStates()

• getState

  public static NucleotideState getState(char code)

• getState

  public static NucleotideState getState(String code)

• getState

  public static NucleotideState getState(int index)

• getUnknownState

  public static NucleotideState getUnknownState()

• getGapState

  public static NucleotideState getGapState()

• isUnknown

  public static boolean isUnknown(NucleotideState state)

• isGap

  public static boolean isGap(NucleotideState state)

• isTransition

  public static boolean isTransition(State state1, State state2)

  Returns:

  true if state1 and state2 are different non-ambigous states that are a transition. (i.e. A-G or C-T)

  See Also:

  • isPossibleTransition(State, State)

• isTransversion

  public static boolean isTransversion(State state1, State state2)

  Returns:

  true if state1 and state2 are different non-ambigous states that are a transversion. (i.e. A-C or A-T or G-C or G-T)

  See Also:

  • isPossibleTransversion(State, State)

• isPossibleTransition

  public static boolean isPossibleTransition(char c1, char c2)

  Returns:

  true if there is a possible transition betwen these states. Possible transition means there is at least 1 transition between at least one of the possible combintaitons of non-ambiguous cannonical states represented by the ambiguity symbols. If neither state is ambigous this method returns true if and only if the states are a transversion.

• isPossibleTransversion

  public static boolean isPossibleTransversion(char c1, char c2)

  Returns:

  true if there is a possible transversion betwen these states. Possible transversion means there is at least 1 transversion between at least one of the possible combintaitons of non-ambiguous cannonical states represented by the ambiguity symbols. If neither state is ambigous this method returns true if and only if the states are a transversion.

• isPossibleTransition

  public static boolean isPossibleTransition(State s1, State s2)

  Returns:

  true if there is a possible transition betwen these states. Possible transition means there is at least 1 transition between at least one of the possible combintaitons of non-ambiguous cannonical states represented by the ambiguity symbols. If neither state is ambigous this method returns true if and only if the states are a transversion.

• isPossibleTransversion

  public static boolean isPossibleTransversion(State s1, State s2)

  Returns:

  true if there is a possible transversion betwen these states. Possible transversion means there is at least 1 transversion between at least one of the possible combintaitons of non-ambiguous cannonical states represented by the ambiguity symbols. If neither state is ambigous this method returns true if and only if the states are a transversion.

• isPurine

  public static boolean isPurine(State state)

• isPyrimidine

  public static boolean isPyrimidine(State state)

• isGCstate

  public static boolean isGCstate(State state)

• isATstate

  public static boolean isATstate(State state)

• getName

  public String getName()

• toStateArray

  public static NucleotideState[] toStateArray(String sequenceString)

• toStateArray

  public static NucleotideState[] toStateArray(byte[] indexArray)

• toCodons

  public static CodonState[] toCodons(State[] states, int readingFrame)

  Convert an array of nucleotide states into an array of codon states

  Parameters:

  states - the nucleotide states

  readingFrame - the reading frame (1 to 3)

  Returns:

  the codon states