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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
interface for sequence data types
Field Summary | |
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 java.lang.String |
GENERALIZED_CODONS_DESCRIPTION
generalized codon name (for XML and human readability) |
static int |
GENERALIZEDCODONS
|
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 java.lang.String |
TWO_STATE_DESCRIPTION
two state name (for XML and human readability) |
static int |
TWOSTATES
|
static char |
UNKNOWN_CHARACTER
|
Method Summary | |
char |
getChar(int state)
get character corresponding to a given state |
java.lang.String |
getDescription()
description of data type |
int |
getNumSimpleStates()
get number of unique non-ambiguous states |
int |
getNumStates()
get number of unique 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)
|
Field Detail |
public static final char UNKNOWN_CHARACTER
public static final int NUCLEOTIDES
public static final int AMINOACIDS
public static final int TWOSTATES
public static final int IUPACNUCLEOTIDES
public static final int CODONS
public static final int GENERALIZEDCODONS
public static final java.lang.String NUCLEOTIDE_DESCRIPTION
public static final java.lang.String AMINO_ACID_DESCRIPTION
public static final java.lang.String TWO_STATE_DESCRIPTION
public static final java.lang.String IUPAC_NUCELOTIDES_DESCRIPTION
public static final java.lang.String CODON_DESCRIPTION
public static final java.lang.String GENERALIZED_CODONS_DESCRIPTION
Method Detail |
public int getNumStates()
public int getNumSimpleStates()
public int getState(char c)
c
- characterpublic char getChar(int state)
state
- state
return corresponding characterpublic boolean isAmbiguousState(int state)
public int[] getSimpleStates(int state)
public java.lang.String getDescription()
public int getTypeID()
public boolean isUnknownState(int state)
public boolean isUnknownChar(char c)
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