Class Nucleotides

java.lang.Object
jebl.evolution.sequences.Nucleotides

public final class Nucleotides extends Object
Uninstantiable utility class with only static methods.
Version:
$Id: Nucleotides.java 986 2009-03-10 01:00:03Z matt_kearse $
Author:
Andrew Rambaut, Alexei Drummond
  • Field Details

  • 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:
    • 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:
    • 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