jebl.evolution.sequences
Class Nucleotides

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

public final class Nucleotides
extends java.lang.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 Summary
static NucleotideState A_STATE
           
static NucleotideState B_STATE
           
static NucleotideState C_STATE
           
static int CANONICAL_STATE_COUNT
           
static NucleotideState[] CANONICAL_STATES
          Deprecated. 
static NucleotideState[] COMPLEMENTARY_STATES
          Deprecated. 
static NucleotideState D_STATE
           
static NucleotideState G_STATE
           
static NucleotideState GAP_STATE
           
static NucleotideState H_STATE
           
static NucleotideState K_STATE
           
static NucleotideState M_STATE
           
static NucleotideState N_STATE
           
static java.lang.String NAME
           
static NucleotideState R_STATE
           
static NucleotideState S_STATE
           
static int STATE_COUNT
           
static NucleotideState[] STATES
          Deprecated. 
static NucleotideState T_STATE
           
static NucleotideState UNKNOWN_STATE
           
static NucleotideState V_STATE
           
static NucleotideState W_STATE
           
static NucleotideState Y_STATE
           
 
Method Summary
static int getCanonicalStateCount()
           
static java.util.List<NucleotideState> getCanonicalStates()
           
static NucleotideState getComplementaryState(NucleotideState state)
           
static NucleotideState getGapState()
           
 java.lang.String getName()
           
static NucleotideState getState(char code)
           
static NucleotideState getState(int index)
           
static NucleotideState getState(java.lang.String code)
           
static int getStateCount()
           
static java.util.List<State> getStates()
           
static NucleotideState getUnknownState()
           
static boolean isATstate(State state)
           
static boolean isGap(NucleotideState state)
           
static boolean isGCstate(State state)
           
static boolean isPossibleTransition(char c1, char c2)
           
static boolean isPossibleTransition(State s1, State s2)
           
static boolean isPossibleTransversion(char c1, char c2)
           
static boolean isPossibleTransversion(State s1, State s2)
           
static boolean isPurine(State state)
           
static boolean isPyrimidine(State state)
           
static boolean isTransition(State state1, State state2)
           
static boolean isTransversion(State state1, State state2)
           
static boolean isUnknown(NucleotideState state)
           
static NucleotideState[] toStateArray(byte[] indexArray)
           
static NucleotideState[] toStateArray(java.lang.String sequenceString)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

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

A_STATE

public static final NucleotideState A_STATE

C_STATE

public static final NucleotideState C_STATE

G_STATE

public static final NucleotideState G_STATE

T_STATE

public static final NucleotideState T_STATE

R_STATE

public static final NucleotideState R_STATE

Y_STATE

public static final NucleotideState Y_STATE

M_STATE

public static final NucleotideState M_STATE

W_STATE

public static final NucleotideState W_STATE

S_STATE

public static final NucleotideState S_STATE

K_STATE

public static final NucleotideState K_STATE

B_STATE

public static final NucleotideState B_STATE

D_STATE

public static final NucleotideState D_STATE

H_STATE

public static final NucleotideState H_STATE

V_STATE

public static final NucleotideState V_STATE

N_STATE

public static final NucleotideState N_STATE

UNKNOWN_STATE

public static final NucleotideState UNKNOWN_STATE

GAP_STATE

public static final NucleotideState GAP_STATE

CANONICAL_STATES

@Deprecated
public static final NucleotideState[] CANONICAL_STATES
Deprecated. 

STATES

@Deprecated
public static final NucleotideState[] STATES
Deprecated. 

COMPLEMENTARY_STATES

@Deprecated
public static final NucleotideState[] COMPLEMENTARY_STATES
Deprecated. 
Method Detail

getComplementaryState

public static NucleotideState getComplementaryState(NucleotideState state)

getStateCount

public static int getStateCount()

getStates

public static java.util.List<State> getStates()
Returns:
A list of all possible states, including the gap and ambiguity states.

getCanonicalStateCount

public static int getCanonicalStateCount()

getCanonicalStates

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

getState

public static NucleotideState getState(char code)

getState

public static NucleotideState getState(java.lang.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 java.lang.String getName()

toStateArray

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

toStateArray

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


http://code.google.com/p/jebl2/