jp.sbi.celldesigner.plugin

Class PluginModificationResidue

java.lang.Object

jp.sbi.celldesigner.plugin.PluginSBase

jp.sbi.celldesigner.plugin.PluginModificationResidue

public class PluginModificationResidue
extends PluginSBase

 Class for modification residue.
 An instance corresponds a <modificationResidue> tag.

Author:

The Systems Biology Institute

CellDesigner extention of SBML definition

ModificationResidue

id : SId name : string {use="optional"} side : string {use="optional"}

The "id" which may a SId type string in the SBML definition, is treated as a String. When it is input or output, format check is done. If it fails, an SIdFormatException is thrown.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	SIDE_INSIDE constants for side field
static java.lang.String	SIDE_NONE constants for side field
static java.lang.String	SIDE_OUTSIDE constants for side field
static java.lang.String	TYPE_BINDINGREGION constants for type field
static java.lang.String	TYPE_RESIDUE constants for type field

Fields inherited from class jp.sbi.celldesigner.plugin.PluginSBase

sbase

Constructor Summary

Constructors

Constructor and Description
PluginModificationResidue(PluginProtein parentProtein) Constructor

Method Summary

Modifier and Type	Method and Description
double	getAngle()
java.lang.String	getId()
java.lang.String	getName()
java.lang.String	getParentID()
PluginProtein	getParentProtein()
java.lang.String	getSide()
double	getSize() gets size
java.lang.String	getType() gets type
void	setAngle(double angle) Sets the angle of this PluginModificationResidue.
protected void	setId(java.lang.String id) Sets the id of this PluginModificationResidue.
void	setName(java.lang.String name) Sets the name of this PluginModificationResidue.
void	setSide(java.lang.String side) Sets the type of side of this PluginModificationResidue
void	setSize(double size) sets size
void	setType(java.lang.String type) sets type

Methods inherited from class jp.sbi.celldesigner.plugin.PluginSBase

addCVTerm, ChangeCVTermToMiriamDefinition, getAnnotation, getAnnotationString, getCVTerm, getNotes, getNotesString, getNumCVTerms, getParentSBase, getRelationFromCVTerm, setAnnotation, setAnnotationString, setCVTerm, setNotes, setNotes, setParentSBase, toSBML

Methods inherited from class java.lang.Object

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

Field Detail

SIDE_NONE

public static final java.lang.String SIDE_NONE

constants for side field

See Also:

Constant Field Values

SIDE_INSIDE

public static final java.lang.String SIDE_INSIDE

constants for side field

See Also:

Constant Field Values

SIDE_OUTSIDE

public static final java.lang.String SIDE_OUTSIDE

constants for side field

See Also:

Constant Field Values

TYPE_RESIDUE

public static final java.lang.String TYPE_RESIDUE

constants for type field

See Also:

Constant Field Values

TYPE_BINDINGREGION

public static final java.lang.String TYPE_BINDINGREGION

constants for type field

See Also:

Constant Field Values

Constructor Detail

PluginModificationResidue

public PluginModificationResidue(PluginProtein parentProtein)

Constructor

Parameters:

parentProtein - the PluginProtein as the parent of this PluginModificationResidue

Method Detail

setName

public void setName(java.lang.String name)

Sets the name of this PluginModificationResidue.

Parameters:

name - String

getName

public java.lang.String getName()

Returns:

the name of this PluginModificationResidue

setType

public void setType(java.lang.String type)

sets type

Parameters:

type - String

getType

public java.lang.String getType()

gets type

Returns:

type

setSize

public void setSize(double size)

sets size

Parameters:

size - double

getSize

public double getSize()

gets size

Returns:

size

setSide

public void setSide(java.lang.String side)

Sets the type of side of this PluginModificationResidue

Parameters:

side - A side is the following static field for side of PluginModificationResidue: SIDE_NONE, SIDE_INSIDE and SIDE_OUTSIDE

getSide

public java.lang.String getSide()

Returns:

the side of this PluginModificationResidue

setAngle

public void setAngle(double angle)

Sets the angle of this PluginModificationResidue.

Parameters:

angle - double

getAngle

public double getAngle()

Returns:

the angle of this PluginModificationResidue.

getId

public java.lang.String getId()

Returns:

the id of this PluginModificationResidue.

setId

protected void setId(java.lang.String id)

Sets the id of this PluginModificationResidue.

Parameters:

id - String

getParentID

public java.lang.String getParentID()

Returns:

the ParentID of this PluginModificationResidue.

getParentProtein

public PluginProtein getParentProtein()

Returns:

the ParentProtein if ParentSBase is PluginProtein, null otherwise.