ur_rna.RNAstructure

Class Nucleobase

java.lang.Object

ur_rna.RNAstructure.Nucleobase

public class Nucleobase
extends java.lang.Object

Nucleobase symbols and corresponding numeric values (as per the RNA backend)

Field Summary

Fields

Modifier and Type	Field and Description
static int	A
static char[]	allowedSymbols
static int	Break Represents and intermolecular break between separate strands ("I")
static int	C
static char[]	dnaSymbols
static char[]	dnaSymbolsLc
static int	G
static char[]	rnaSymbols
static char[]	rnaSymbolsLc
static int	T
static int	Unknown

Constructor Summary

Constructors

Constructor and Description
Nucleobase()

Method Summary

Modifier and Type	Method and Description
static java.lang.String	getSymbol(int backendValue)
static java.lang.String	getSymbol(int backendValue, boolean isRNA)
static java.lang.String	getSymbol(int backendValue, boolean isRNA, boolean upper)
static char	getVerifiedSymbol(java.lang.String symbol)
static char	getVerifiedSymbol(java.lang.String symbol, char defaultIfInvalid)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

A

public static final int A

See Also:

Constant Field Values

allowedSymbols

public static final char[] allowedSymbols

Break

public static final int Break

Represents and intermolecular break between separate strands ("I")

See Also:

Constant Field Values

C

public static final int C

See Also:

Constant Field Values

dnaSymbols

public static final char[] dnaSymbols

dnaSymbolsLc

public static final char[] dnaSymbolsLc

G

public static final int G

See Also:

Constant Field Values

rnaSymbols

public static final char[] rnaSymbols

rnaSymbolsLc

public static final char[] rnaSymbolsLc

T

public static final int T

See Also:

Constant Field Values

Unknown

public static final int Unknown

See Also:

Constant Field Values

Constructor Detail

Nucleobase

public Nucleobase()

Method Detail

getSymbol

public static final java.lang.String getSymbol(int backendValue)

getSymbol

public static final java.lang.String getSymbol(int backendValue,
                                               boolean isRNA)

getSymbol

public static final java.lang.String getSymbol(int backendValue,
                                               boolean isRNA,
                                               boolean upper)

getVerifiedSymbol

public static char getVerifiedSymbol(java.lang.String symbol)

getVerifiedSymbol

public static char getVerifiedSymbol(java.lang.String symbol,
                                     char defaultIfInvalid)