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java.lang.Objectjava.util.AbstractCollection<E>
java.util.AbstractList<Symbol>
jbil.sequence.Alphabet
jbil.sequence.DNAAlphabet
public class DNAAlphabet
Class representing the basic DNA nucleotide alphabet {a,g,c,t}.
| Field Summary | |
|---|---|
static AtomicCharSymbol |
a
The atomic 'a' symbol |
static AtomicCharSymbol |
c
The atomic 'c' symbol |
static java.lang.String |
DNA_ALPHABET
The alphabet name constant |
static AtomicCharSymbol |
g
The atomic 'g' symbol |
static AtomicCharSymbol |
t
The atomic 't' symbol |
| Constructor Summary | |
|---|---|
DNAAlphabet()
Creates a DNA {a,g,c,t} alphabet. |
|
| Method Summary | |
|---|---|
AtomicCharSymbol |
a()
|
AtomicCharSymbol |
c()
|
AtomicCharSymbol |
g()
|
Symbol |
get(char ch)
Gets a symbol from its character representation. |
AtomicCharSymbol |
t()
|
| Methods inherited from class jbil.sequence.Alphabet |
|---|
add, contains, get, indexOf, intersection, isLocked, lock, remove, set, size |
| Methods inherited from class java.util.AbstractList |
|---|
add, addAll, clear, equals, hashCode, iterator, lastIndexOf, listIterator, listIterator, subList |
| Methods inherited from class java.util.AbstractCollection |
|---|
addAll, containsAll, isEmpty, remove, removeAll, retainAll, toArray, toArray, toString |
| Methods inherited from class java.lang.Object |
|---|
getClass, notify, notifyAll, wait, wait, wait |
| Methods inherited from interface java.util.List |
|---|
addAll, containsAll, isEmpty, remove, removeAll, retainAll, toArray, toArray |
| Field Detail |
|---|
public static final java.lang.String DNA_ALPHABET
public static final AtomicCharSymbol a
public static final AtomicCharSymbol g
public static final AtomicCharSymbol c
public static final AtomicCharSymbol t
| Constructor Detail |
|---|
public DNAAlphabet()
| Method Detail |
|---|
public AtomicCharSymbol a()
public AtomicCharSymbol c()
public AtomicCharSymbol g()
public AtomicCharSymbol t()
public Symbol get(char ch)
ch - The character representation of the symbol.
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