Package org.helm.notation2

Class Nucleotide

java.lang.Object

org.helm.notation2.Nucleotide

All Implemented Interfaces:

Serializable

public class Nucleotide
extends Object
implements Serializable

This is a data model class for nucleotide

Author:

ZHANGTIANHONG

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static int	ENDING_POSITION_TYPE
static int	MIDDLE_POSITION_TYPE
static int	STARTING_POSITION_TYPE

Constructor Summary

Constructors

Constructor	Description
Nucleotide()
Nucleotide(String notation, int postionType)
Nucleotide(String symbol, String notation)
Nucleotide(String symbol, String notation, int postionType)

Method Summary

Modifier and Type	Method	Description
static Nucleotide	fromJSON(String json)
Monomer	getBaseMonomer()	get the base monomer, the return value could be null if this nucleotide does not have a base
Monomer	getBaseMonomer(MonomerStore monomerStore)	get the base monomer, the return value could be null if this nucleotide does not have a base
String	getLinkerNotation()	This method returns the HELM notation for nucleotide linker
String	getNaturalAnalog()	return the natural analog of this nucleotide
String	getNaturalAnalog(MonomerStore monomerStore)	return the natural analog of this nucleotide
String	getNotation()
String	getNucleosideNotation()	This method returns the HELM notation for nucleoside
Monomer	getPhosphateMonomer()	return the phosphate monomer of this nucleotide
Monomer	getPhosphateMonomer(MonomerStore monomerStore)	return the phosphate monomer of this nucleotide
int	getPositionType()
Monomer	getSugarMonomer()	get the sugar monomer, the return value could be null if the "nucleotide" does not has a sugar
Monomer	getSugarMonomer(MonomerStore monomerStore)	get the sugar monomer, the return value could be null if the "nucleotide" does not has a sugar
String	getSymbol()
boolean	isModified()
void	setModified(boolean modified)	Deprecated.
void	setNaturalAnalog(String naturalAnalog)	Deprecated.
void	setNotation(String notation)
void	setPositionType(int positionType)
void	setSymbol(String symbol)
String	toJSON()
boolean	unmodifiedWithoutPhosphate()	Returns true if the nucleotide is unmodified except for a missing phosphate group.

Methods inherited from class java.lang.Object

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

Field Details

STARTING_POSITION_TYPE

public static final int STARTING_POSITION_TYPE

See Also:

Constant Field Values

MIDDLE_POSITION_TYPE

public static final int MIDDLE_POSITION_TYPE

See Also:

Constant Field Values

ENDING_POSITION_TYPE

public static final int ENDING_POSITION_TYPE

See Also:

Constant Field Values

Constructor Details

Nucleotide

public Nucleotide()

Nucleotide

public Nucleotide(String symbol, String notation)

Nucleotide

public Nucleotide(String notation, int postionType)

Nucleotide

public Nucleotide(String symbol, String notation, int postionType)

Method Details

getPositionType

public int getPositionType()

setPositionType

public void setPositionType(int positionType)

getSymbol

public String getSymbol()

setSymbol

public void setSymbol(String symbol)

isModified

public boolean isModified()

unmodifiedWithoutPhosphate

public boolean unmodifiedWithoutPhosphate()

Returns true if the nucleotide is unmodified except for a missing phosphate group. If the nucleotide notation is empty, it returns true.

Returns:

true or false

setModified

@Deprecated public void setModified(boolean modified)

Deprecated.

getNotation

public String getNotation()

setNotation

public void setNotation(String notation)

getNaturalAnalog

public String getNaturalAnalog()

return the natural analog of this nucleotide

Returns:

natural Analog or X if natural analog is not available

getNaturalAnalog

public String getNaturalAnalog(MonomerStore monomerStore)

return the natural analog of this nucleotide

Parameters:

monomerStore - - store in which base monomer is located

Returns:

natural Analog or X if natural analog is not available

setNaturalAnalog

@Deprecated public void setNaturalAnalog(String naturalAnalog)

Deprecated.

getPhosphateMonomer

public Monomer getPhosphateMonomer()

return the phosphate monomer of this nucleotide

Returns:

phosphate monomer

getPhosphateMonomer

public Monomer getPhosphateMonomer(MonomerStore monomerStore)

return the phosphate monomer of this nucleotide

Parameters:

monomerStore - - store in which phosphate monomer is located

Returns:

phosphate monomer

getBaseMonomer

public Monomer getBaseMonomer()

get the base monomer, the return value could be null if this nucleotide does not have a base

Returns:

base monomer, could be null

getBaseMonomer

public Monomer getBaseMonomer(MonomerStore monomerStore)

get the base monomer, the return value could be null if this nucleotide does not have a base

Parameters:

monomerStore - - store in which base monomer is located

Returns:

base monomer, could be null

getSugarMonomer

public Monomer getSugarMonomer()

get the sugar monomer, the return value could be null if the "nucleotide" does not has a sugar

Returns:

sugar monomer

getSugarMonomer

public Monomer getSugarMonomer(MonomerStore monomerStore)

get the sugar monomer, the return value could be null if the "nucleotide" does not has a sugar

Parameters:

monomerStore - - store in which sugar monomer is located

Returns:

sugar monomer

getLinkerNotation

public String getLinkerNotation()

This method returns the HELM notation for nucleotide linker

Returns:

linker notation

getNucleosideNotation

public String getNucleosideNotation()

This method returns the HELM notation for nucleoside

Returns:

nucleodie notation

fromJSON

public static Nucleotide fromJSON(String json)

toJSON

public String toJSON()