jp.sbi.celldesigner.plugin

Class PluginModification

java.lang.Object

jp.sbi.celldesigner.plugin.PluginSBase

jp.sbi.celldesigner.plugin.PluginModification

public class PluginModification
extends PluginSBase

 
 ProteinModification
 An instance represents <modification> tag.
 

Author:

The Systems Biology Institute

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	STATE_ACETYLATED for state field
static java.lang.String	STATE_DONT_CARE for state field
static java.lang.String	STATE_EMPTY for state field
static java.lang.String	STATE_GLYCOSYLATED stateフィールド用の定数
static java.lang.String	STATE_HISTON1 for state field
static java.lang.String	STATE_HISTON2 for state field
static java.lang.String	STATE_HYDROXYLATED for state field
static java.lang.String	STATE_METHYLATED for state field
static java.lang.String	STATE_MYRISTOYLATED stateフィールド用の定数
static java.lang.String	STATE_PALMYTOYLATED stateフィールド用の定数
static java.lang.String	STATE_PHOSPHORYLATED for state field
static java.lang.String	STATE_PRENYLATED stateフィールド用の定数
static java.lang.String	STATE_PROTONATED stateフィールド用の定数
static java.lang.String	STATE_SULFATED stateフィールド用の定数
static java.lang.String	STATE_UBIQUITINATED for state field
static java.lang.String	STATE_UNKNOWN for state field

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

sbase

Constructor Summary

Constructors

Constructor and Description
PluginModification() Constructor
PluginModification(java.lang.String residue) Constructor
PluginModification(java.lang.String residue, java.lang.String state) Constructor

Method Summary

Modifier and Type	Method and Description
protected void	clone(jp.sbi.celldesigner.sbmlExtension.Modification modification) Clones this PluginModification
boolean	equals(PluginModification target) Compares the given PluginModification to this PluginModification
java.lang.String	getLabel() Gets the text of label for the state
java.lang.String	getResidue()
java.lang.String	getState()
void	setResidue(java.lang.String residue) Sets the id of residue of this PluginModification.
void	setState(java.lang.String state) Sets the state of this PluginModification to the given string.

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

STATE_PHOSPHORYLATED

public static final java.lang.String STATE_PHOSPHORYLATED

for state field

See Also:

Constant Field Values

STATE_ACETYLATED

public static final java.lang.String STATE_ACETYLATED

for state field

See Also:

Constant Field Values

STATE_UBIQUITINATED

public static final java.lang.String STATE_UBIQUITINATED

for state field

See Also:

Constant Field Values

STATE_METHYLATED

public static final java.lang.String STATE_METHYLATED

for state field

See Also:

Constant Field Values

STATE_HYDROXYLATED

public static final java.lang.String STATE_HYDROXYLATED

for state field

See Also:

Constant Field Values

STATE_EMPTY

public static final java.lang.String STATE_EMPTY

for state field

See Also:

Constant Field Values

STATE_DONT_CARE

public static final java.lang.String STATE_DONT_CARE

for state field

See Also:

Constant Field Values

STATE_UNKNOWN

public static final java.lang.String STATE_UNKNOWN

for state field

See Also:

Constant Field Values

STATE_GLYCOSYLATED

public static final java.lang.String STATE_GLYCOSYLATED

stateフィールド用の定数

See Also:

Constant Field Values

STATE_MYRISTOYLATED

public static final java.lang.String STATE_MYRISTOYLATED

stateフィールド用の定数

See Also:

Constant Field Values

STATE_PALMYTOYLATED

public static final java.lang.String STATE_PALMYTOYLATED

stateフィールド用の定数

See Also:

Constant Field Values

STATE_PRENYLATED

public static final java.lang.String STATE_PRENYLATED

stateフィールド用の定数

See Also:

Constant Field Values

STATE_PROTONATED

public static final java.lang.String STATE_PROTONATED

stateフィールド用の定数

See Also:

Constant Field Values

STATE_SULFATED

public static final java.lang.String STATE_SULFATED

stateフィールド用の定数

See Also:

Constant Field Values

STATE_HISTON1

public static final java.lang.String STATE_HISTON1

for state field

See Also:

Constant Field Values

STATE_HISTON2

public static final java.lang.String STATE_HISTON2

for state field

See Also:

Constant Field Values

Constructor Detail

PluginModification

public PluginModification()

Constructor

PluginModification

public PluginModification(java.lang.String residue)

Constructor

Parameters:

residue - the id of PluginModificationResidue

PluginModification

public PluginModification(java.lang.String residue,
                          java.lang.String state)

Constructor

Parameters:

residue - the id of PluginModificationResidue

state - the type of state. state is the one of the following fields of this PluginModification: STATE_PHOSPHORYLATED, STATE_ACETYLATED, STATE_UBIQUITINATED, STATE_METHYLATED, STATE_HYDROXYLATED, STATE_EMPTY, STATE_DONT_CARE, STATE_UNKNOWN, STATE_HISTON1 and STATE_HISTON2

Method Detail

clone

protected void clone(jp.sbi.celldesigner.sbmlExtension.Modification modification)

Clones this PluginModification

Parameters:

modification - Modification

equals

public boolean equals(PluginModification target)

Compares the given PluginModification to this PluginModification

Parameters:

target - PluginModification

Returns:

true if two PluginModification are same, false otherwise.

setResidue

public void setResidue(java.lang.String residue)

Sets the id of residue of this PluginModification.

Parameters:

residue - the id of residue

getResidue

public java.lang.String getResidue()

Returns:

the id of residue of this PluginModification.

setState

public void setState(java.lang.String state)

Sets the state of this PluginModification to the given string. The state is one of the following fields of this PluginModification: STATE_PHOSPHORYLATED, STATE_ACETYLATED, STATE_UBIQUITINATED, STATE_METHYLATED, STATE_HYDROXYLATED, STATE_EMPTY, STATE_DONT_CARE, STATE_UNKNOWN, STATE_HISTON1 and STATE_HISTON2

Parameters:

state - String

getState

public java.lang.String getState()

Returns:

state See setState.

getLabel

public java.lang.String getLabel()

Gets the text of label for the state

Returns:

the text of label.