jebl.evolution.sequences
public final class Nucleotides extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
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 |
Modifier and Type | Method and Description |
---|---|
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) |
public static final java.lang.String NAME
public static final int CANONICAL_STATE_COUNT
public static final int STATE_COUNT
public static final NucleotideState A_STATE
public static final NucleotideState C_STATE
public static final NucleotideState G_STATE
public static final NucleotideState T_STATE
public static final NucleotideState R_STATE
public static final NucleotideState Y_STATE
public static final NucleotideState M_STATE
public static final NucleotideState W_STATE
public static final NucleotideState S_STATE
public static final NucleotideState K_STATE
public static final NucleotideState B_STATE
public static final NucleotideState D_STATE
public static final NucleotideState H_STATE
public static final NucleotideState V_STATE
public static final NucleotideState N_STATE
public static final NucleotideState UNKNOWN_STATE
public static final NucleotideState GAP_STATE
@Deprecated public static final NucleotideState[] CANONICAL_STATES
@Deprecated public static final NucleotideState[] STATES
@Deprecated public static final NucleotideState[] COMPLEMENTARY_STATES
public static NucleotideState getComplementaryState(NucleotideState state)
public static int getStateCount()
public static java.util.List<State> getStates()
public static int getCanonicalStateCount()
public static java.util.List<NucleotideState> getCanonicalStates()
public static NucleotideState getState(char code)
public static NucleotideState getState(java.lang.String code)
public static NucleotideState getState(int index)
public static NucleotideState getUnknownState()
public static NucleotideState getGapState()
public static boolean isUnknown(NucleotideState state)
public static boolean isGap(NucleotideState state)
public static boolean isTransition(State state1, State state2)
isPossibleTransition(State, State)
public static boolean isTransversion(State state1, State state2)
isPossibleTransversion(State, State)
public static boolean isPossibleTransition(char c1, char c2)
public static boolean isPossibleTransversion(char c1, char c2)
public static boolean isPossibleTransition(State s1, State s2)
public static boolean isPossibleTransversion(State s1, State s2)
public static boolean isPurine(State state)
public static boolean isPyrimidine(State state)
public static boolean isGCstate(State state)
public static boolean isATstate(State state)
public java.lang.String getName()
public static NucleotideState[] toStateArray(java.lang.String sequenceString)
public static NucleotideState[] toStateArray(byte[] indexArray)
http://code.google.com/p/jebl2/