jp.sbi.celldesigner.plugin

Class PluginProtein

java.lang.Object

jp.sbi.celldesigner.plugin.PluginSBase

jp.sbi.celldesigner.plugin.PluginProtein

public class PluginProtein
extends PluginSBase

This class represents Protein.

Author:

The Systems Biology Institute

Field Summary

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

sbase

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	PluginProtein() Constructor
protected	PluginProtein(java.lang.String extensionId) Constructor

Method Summary

Modifier and Type	Method and Description
void	addPluginBindingRegion(PluginBindingRegion bindingRegion) Adds a PluginBindingRegion to the list.
void	addPluginModificationResidue(PluginModificationResidue residue) Adds a PluginModificationResidue to the list.
java.lang.String	getExtensionId()
PluginListOf	getListOfPluginBindingRegion()
PluginListOf	getListOfPluginResidue()
java.lang.String	getName()
int	getNumBindingRegions()
int	getNumResidues()
PluginBindingRegion	getPluginBindingRegion(int index) Gets the PluginBindingRegion with the given index.
PluginModificationResidue	getPluginModificationResidue(int index) Gets the PluginModificationResidue with the given index.
java.lang.String	getType()
void	removePluginBindingRegion(int index) Removes the PluginBindingRegion with the given index from the list.
void	removePluginBindingRegion(PluginBindingRegion bindingRegion) Removes the given PluginBindingRegion from the list.
void	removePluginModificationResidue(int index) Removes the PluginModificationResidue with the given index from the list.
void	removePluginModificationResidue(PluginModificationResidue residue) Removes the given PluginModificationResidue from the list.
void	setListOfPluginBindingRegion(PluginListOf listOfPluginBindingRegion) Sets the list of PluginBindingRegion of this PluginProtein.
void	setListOfPluginResidue(PluginListOf listOfPluginResidue) Sets the list of PluginModificationResidue of this PluginProtein.
void	setName(java.lang.String name) Sets the name of this PluginProtein.
void	setType(java.lang.String type) Sets the type of this PluginProtein.
void	update(PluginProtein rna) Update all properties of this PluginProtein to the same as the given PluginProtein

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

Constructor Detail

PluginProtein

protected PluginProtein()

Constructor

PluginProtein

protected PluginProtein(java.lang.String extensionId)

Constructor

Parameters:

extensionId - String

Method Detail

update

public void update(PluginProtein rna)

Update all properties of this PluginProtein to the same as the given PluginProtein

Parameters:

rna - PluginProtein

getExtensionId

public java.lang.String getExtensionId()

Returns:

the Id of this PluginProtein.

getName

public java.lang.String getName()

Returns:

the name of this PluginProtein.

setName

public void setName(java.lang.String name)

Sets the name of this PluginProtein.

Parameters:

name - String

getType

public java.lang.String getType()

Returns:

the type of this PluginProtein.

setType

public void setType(java.lang.String type)

Sets the type of this PluginProtein.

Parameters:

type - String

getListOfPluginResidue

public PluginListOf getListOfPluginResidue()

Returns:

the list of PluginModificationResidue of this PluginProtein.

setListOfPluginResidue

public void setListOfPluginResidue(PluginListOf listOfPluginResidue)

Sets the list of PluginModificationResidue of this PluginProtein.

Parameters:

listOfPluginResidue - PluginListOf

addPluginModificationResidue

public void addPluginModificationResidue(PluginModificationResidue residue)

Adds a PluginModificationResidue to the list.

Parameters:

residue - PluginModificationResidue

removePluginModificationResidue

public void removePluginModificationResidue(PluginModificationResidue residue)

Removes the given PluginModificationResidue from the list.

Parameters:

residue - PluginModificationResidue

removePluginModificationResidue

public void removePluginModificationResidue(int index)

Removes the PluginModificationResidue with the given index from the list.

Parameters:

index - int

getPluginModificationResidue

public PluginModificationResidue getPluginModificationResidue(int index)

Gets the PluginModificationResidue with the given index.

Parameters:

index - int

Returns:

PluginModificationResidue

getNumResidues

public int getNumResidues()

Returns:

the number of PluginModificationResidue

getListOfPluginBindingRegion

public PluginListOf getListOfPluginBindingRegion()

Returns:

the list of PluginBindingRegion of this PluginProtein.

setListOfPluginBindingRegion

public void setListOfPluginBindingRegion(PluginListOf listOfPluginBindingRegion)

Sets the list of PluginBindingRegion of this PluginProtein.

Parameters:

listOfPluginBindingRegion - PluginListOf

addPluginBindingRegion

public void addPluginBindingRegion(PluginBindingRegion bindingRegion)

Adds a PluginBindingRegion to the list.

Parameters:

bindingRegion - PluginBindingRegion

removePluginBindingRegion

public void removePluginBindingRegion(PluginBindingRegion bindingRegion)

Removes the given PluginBindingRegion from the list.

Parameters:

bindingRegion - PluginBindingRegion

removePluginBindingRegion

public void removePluginBindingRegion(int index)

Removes the PluginBindingRegion with the given index from the list.

Parameters:

index - int

getPluginBindingRegion

public PluginBindingRegion getPluginBindingRegion(int index)

Gets the PluginBindingRegion with the given index.

Parameters:

index - int

Returns:

PluginBindingRegion

getNumBindingRegions

public int getNumBindingRegions()

Returns:

num of binding regions