public interface DataType
extends java.io.Serializable
Modifier and Type | Interface and Description |
---|---|
static class |
DataType.Utils
Some useful methods for implmenting classes and for DataType users
|
Modifier and Type | Field and Description |
---|---|
static java.lang.String |
AMINO_ACID_DESCRIPTION
amino acid name (for XML and human readability)
|
static int |
AMINOACIDS |
static java.lang.String |
CODON_DESCRIPTION
codon name (for XML and human readability)
|
static int |
CODONS |
static int |
GAP_BALANCED |
static java.lang.String |
GAP_BALANCED_DESCRIPTION
generalized codon name (for XML and human readability)
|
static java.lang.String |
IUPAC_NUCELOTIDES_DESCRIPTION
iupac nucleotide name (for XML and human readability)
|
static int |
IUPACNUCLEOTIDES |
static java.lang.String |
NUCLEOTIDE_DESCRIPTION
Name of nucleotide data type.
|
static int |
NUCLEOTIDES |
static int |
NUMERIC |
static char |
PRIMARY_SUGGESTED_GAP_CHARACTER
A suggested Gap character
|
static char[] |
SUGGESTED_GAP_CHARACTERS |
static int |
SUGGESTED_GAP_STATE
The gap state that should generally be used (-2),
though the DataType specification makes no requirement that this be the gap state
|
static int |
SUGGESTED_UNKNOWN_STATE
The gap state that should generally be used (-1).
|
static java.lang.String |
TWO_STATE_DESCRIPTION
two state name (for XML and human readability)
|
static int |
TWOSTATES |
static int |
UNKNOWN |
static char |
UNKNOWN_CHARACTER |
static java.lang.String |
UNKNOWN_TLA |
Modifier and Type | Method and Description |
---|---|
AmbiguousDataType |
getAmbiguousVersion() |
char |
getChar(int state)
get character corresponding to a given state
|
java.lang.String |
getDescription()
description of data type
|
int |
getNumStates()
get number of unique states
|
char |
getPreferredChar(char c)
get the preferred version of a particular character (eg a -> A)
Should not always assume that a DataType only uses Upper case characters!
|
int |
getRecommendedGapState() |
int |
getRecommendedUnknownState() |
int |
getState(char c)
get state corresponding to a character
|
int |
getTypeID()
get numerical code describing the data type
|
boolean |
hasGap() |
boolean |
isAmbiguous() |
boolean |
isGapChar(char c) |
boolean |
isGapState(int state) |
boolean |
isUnknownChar(char c) |
boolean |
isUnknownState(int state) |
static final char UNKNOWN_CHARACTER
static final java.lang.String UNKNOWN_TLA
static final char PRIMARY_SUGGESTED_GAP_CHARACTER
static final char[] SUGGESTED_GAP_CHARACTERS
static final int SUGGESTED_GAP_STATE
static final int SUGGESTED_UNKNOWN_STATE
static final int NUCLEOTIDES
static final int AMINOACIDS
static final int TWOSTATES
static final int IUPACNUCLEOTIDES
static final int CODONS
static final int GAP_BALANCED
static final int NUMERIC
static final int UNKNOWN
static final java.lang.String NUCLEOTIDE_DESCRIPTION
static final java.lang.String AMINO_ACID_DESCRIPTION
static final java.lang.String TWO_STATE_DESCRIPTION
static final java.lang.String IUPAC_NUCELOTIDES_DESCRIPTION
static final java.lang.String CODON_DESCRIPTION
static final java.lang.String GAP_BALANCED_DESCRIPTION
int getNumStates()
int getState(char c)
c
- characterchar getChar(int state)
state
- state
return corresponding characterchar getPreferredChar(char c)
java.lang.String getDescription()
int getTypeID()
boolean isUnknownState(int state)
boolean isUnknownChar(char c)
int getRecommendedUnknownState()
boolean hasGap()
boolean isGapChar(char c)
boolean isGapState(int state)
int getRecommendedGapState()
boolean isAmbiguous()
AmbiguousDataType getAmbiguousVersion()