public final class IUPACDNAAlphabet extends ComplementableDiscreteAlphabet implements Singleton
Modifier and Type | Class and Description |
---|---|
static class |
IUPACDNAAlphabet.IUPACDNAAlphabetParameterSet
The parameter set for a
IUPACDNAAlphabet . |
DiscreteAlphabet.DiscreteAlphabetParameterSet
Alphabet.AlphabetParameterSet<T extends Alphabet>
Singleton.SingletonHandler
Modifier and Type | Field and Description |
---|---|
static IUPACDNAAlphabet |
SINGLETON
The only instance of this class.
|
alphabet, caseInsensitive, parameters
Modifier and Type | Method and Description |
---|---|
int |
getComplementaryCode(int code)
This method returns the code of the symbol that is the complement of the
symbol encoded by
code . |
boolean |
isPart(int query,
int code)
Indicates if
query is contained in code
according to the IUPAC DNA alphabet. |
boolean |
isPart(String query,
String code)
Indicates if
query is contained in code
according to the IUPAC DNA alphabet. |
compareTo, getCode, getCurrentParameterSet, getMaximalSymbolLength, getMin, getSymbolAt, ignoresCase, isEncodedSymbol, isSymbol, length, toString, toXML
checkConsistency
public static final IUPACDNAAlphabet SINGLETON
Singleton
public int getComplementaryCode(int code)
ComplementableDiscreteAlphabet
code
.getComplementaryCode
in class ComplementableDiscreteAlphabet
code
- the encoded symbolpublic boolean isPart(String query, String code) throws WrongAlphabetException
query
is contained in code
according to the IUPAC DNA alphabet.query
- the query symbolcode
- the reference symbolquery
is contained in code
WrongAlphabetException
- if either of the arguments is not defined in the IUPAC alphabetpublic boolean isPart(int query, int code)
query
is contained in code
according to the IUPAC DNA alphabet.query
- the code of the query symbolcode
- the code of the reference symbolquery
is contained in code