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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--pal.datatype.IUPACNucleotides
implements DataType for nucleotides with ambiguous characters
Fields inherited from interface pal.datatype.DataType |
AMINO_ACID_DESCRIPTION, AMINOACIDS, CODON_DESCRIPTION, CODONS, GENERALIZED_CODONS_DESCRIPTION, GENERALIZEDCODONS, IUPAC_NUCELOTIDES_DESCRIPTION, IUPACNUCLEOTIDES, NUCLEOTIDE_DESCRIPTION, NUCLEOTIDES, TWO_STATE_DESCRIPTION, TWOSTATES, UNKNOWN_CHARACTER |
Constructor Summary | |
IUPACNucleotides()
|
Method Summary | |
char |
getChar(int state)
get character corresponding to a given state |
java.lang.String |
getDescription()
description of data type |
int |
getNumSimpleStates()
returns the number of true non-ambiguous states. |
int |
getNumStates()
Get number of states. |
int[] |
getSimpleStates(int state)
returns an array containing the non-ambiguous states that this state represents. |
int |
getState(char c)
get state corresponding to a character |
int |
getTypeID()
get numerical code describing the data type |
boolean |
isAmbiguousState(int state)
returns true if this state is an ambiguous state. |
boolean |
isUnknownChar(char c)
|
boolean |
isUnknownState(int state)
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
public IUPACNucleotides()
Method Detail |
public int getNumStates()
getNumStates
in interface DataType
pal.datatype.DataType
public boolean isUnknownState(int state)
isUnknownState
in interface DataType
pal.datatype.DataType
public int getNumSimpleStates()
getNumSimpleStates
in interface DataType
pal.datatype.DataType
public final int getState(char c)
DataType
getState
in interface DataType
pal.datatype.DataType
c
- characterpublic char getChar(int state)
DataType
getChar
in interface DataType
pal.datatype.DataType
state
- state
return corresponding characterpublic java.lang.String getDescription()
DataType
getDescription
in interface DataType
pal.datatype.DataType
public int getTypeID()
DataType
getTypeID
in interface DataType
pal.datatype.DataType
public boolean isAmbiguousState(int state)
isAmbiguousState
in interface DataType
public int[] getSimpleStates(int state)
getSimpleStates
in interface DataType
public boolean isUnknownChar(char c)
isUnknownChar
in interface DataType
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