public class AminoAcids extends SimpleDataType
DataType.Utils
Modifier and Type | Field and Description |
---|---|
static AminoAcids |
DEFAULT_INSTANCE |
static char |
TERMINATE_CHARACTER |
static int |
TERMINATE_STATE |
AMINO_ACID_DESCRIPTION, AMINOACIDS, CODON_DESCRIPTION, CODONS, GAP_BALANCED, GAP_BALANCED_DESCRIPTION, IUPAC_NUCELOTIDES_DESCRIPTION, IUPACNUCLEOTIDES, NUCLEOTIDE_DESCRIPTION, NUCLEOTIDES, NUMERIC, PRIMARY_SUGGESTED_GAP_CHARACTER, SUGGESTED_GAP_CHARACTERS, SUGGESTED_GAP_STATE, SUGGESTED_UNKNOWN_STATE, TWO_STATE_DESCRIPTION, TWOSTATES, UNKNOWN, UNKNOWN_CHARACTER, UNKNOWN_TLA
Constructor and Description |
---|
AminoAcids() |
Modifier and Type | Method and Description |
---|---|
protected char |
getCharImpl(int state) |
java.lang.String |
getDescription()
description of data type
|
int |
getNumStates()
get number of unique states
|
protected int |
getStateImpl(char c)
For sub classes to implement main functionality of getState.
|
static java.lang.String |
getTLA(int state) |
int |
getTypeID()
get numerical code describing the data type
|
protected boolean |
isUnknownStateImpl(int state)
For subclasses to handle, without regard for gaps
|
getAmbiguousVersion, getChar, getPreferredChar, getPreferredCharImpl, getRecommendedGapState, getRecommendedUnknownState, getState, hasGap, isAmbiguous, isGapChar, isGapState, isUnknownChar, isUnknownState, toString
public static final AminoAcids DEFAULT_INSTANCE
public static final char TERMINATE_CHARACTER
public static final int TERMINATE_STATE
public int getNumStates()
DataType
protected int getStateImpl(char c)
SimpleDataType
getStateImpl
in class SimpleDataType
protected char getCharImpl(int state)
getCharImpl
in class SimpleDataType
protected boolean isUnknownStateImpl(int state)
SimpleDataType
isUnknownStateImpl
in class SimpleDataType
public java.lang.String getDescription()
DataType
public int getTypeID()
DataType
public static final java.lang.String getTLA(int state)