Package jebl.evolution.sequences
Class Nucleotides
java.lang.Object
jebl.evolution.sequences.Nucleotides
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
FieldsModifier and TypeFieldDescriptionstatic final NucleotideState
static final NucleotideState
static final NucleotideState
static final int
static final NucleotideState[]
Deprecated.static final NucleotideState[]
Deprecated.static final NucleotideState
static final NucleotideState
static final NucleotideState
static final NucleotideState
static final NucleotideState
static final NucleotideState
static final NucleotideState
static final String
static final NucleotideState
static final NucleotideState
static final int
static final NucleotideState[]
Deprecated.static final NucleotideState
static final NucleotideState
static final NucleotideState
static final NucleotideState
static final NucleotideState
-
Method Summary
Modifier and TypeMethodDescriptionstatic int
static List
<NucleotideState> static NucleotideState
static NucleotideState
getName()
static NucleotideState
getState
(char code) static NucleotideState
getState
(int index) static NucleotideState
static int
static NucleotideState
static boolean
static boolean
isGap
(NucleotideState state) static boolean
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
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 CodonState[]
Convert an array of nucleotide states into an array of codon statesstatic NucleotideState[]
toStateArray
(byte[] indexArray) static NucleotideState[]
toStateArray
(String sequenceString)
-
Field Details
-
NAME
- See Also:
-
CANONICAL_STATE_COUNT
public static final int CANONICAL_STATE_COUNT- See Also:
-
STATE_COUNT
public static final int STATE_COUNT- See Also:
-
A_STATE
-
C_STATE
-
G_STATE
-
T_STATE
-
R_STATE
-
Y_STATE
-
M_STATE
-
W_STATE
-
S_STATE
-
K_STATE
-
B_STATE
-
D_STATE
-
H_STATE
-
V_STATE
-
N_STATE
-
UNKNOWN_STATE
-
GAP_STATE
-
CANONICAL_STATES
Deprecated. -
STATES
Deprecated. -
COMPLEMENTARY_STATES
Deprecated.
-
-
Method Details
-
getComplementaryState
-
getStateCount
public static int getStateCount() -
getStates
- Returns:
- A list of all possible states, including the gap and ambiguity states.
-
getCanonicalStateCount
public static int getCanonicalStateCount() -
getCanonicalStates
-
getState
-
getState
-
getState
-
getUnknownState
-
getGapState
-
isUnknown
-
isGap
-
isTransition
- 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
- 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
- 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
- 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
-
isPyrimidine
-
isGCstate
-
isATstate
-
getName
-
toStateArray
-
toStateArray
-
toCodons
Convert an array of nucleotide states into an array of codon states- Parameters:
states
- the nucleotide statesreadingFrame
- the reading frame (1 to 3)- Returns:
- the codon states
-