jebl.evolution.sequences
Class Nucleotides
java.lang.Object
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
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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.
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/