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, toStringpublic static final AminoAcids DEFAULT_INSTANCE
public static final char TERMINATE_CHARACTER
public static final int TERMINATE_STATE
public int getNumStates()
DataTypeprotected int getStateImpl(char c)
SimpleDataTypegetStateImpl in class SimpleDataTypeprotected char getCharImpl(int state)
getCharImpl in class SimpleDataTypeprotected boolean isUnknownStateImpl(int state)
SimpleDataTypeisUnknownStateImpl in class SimpleDataTypepublic java.lang.String getDescription()
DataTypepublic int getTypeID()
DataTypepublic static final java.lang.String getTLA(int state)