jp.sbi.celldesigner.plugin

Class PluginModificationRegion

java.lang.Object

jp.sbi.celldesigner.plugin.PluginSBase

jp.sbi.celldesigner.plugin.PluginModificationRegion

public class PluginModificationRegion
extends PluginSBase

 Class for region.
 An instance corresponds a <region> tag.

Author:

The Systems Biology Institute

CellDesigner extention of SBML definition

region

id : SId name : string {use="optional"} type : string {use="optional"} size : double {use="optional"} pos : double {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 double	MINIMUM_SIZE_ANY constants for minimum size
static double	MINIMUM_SIZE_DNAMETYLATION constants for minimum size
static double	MINIMUM_SIZE_EMPTY constants for minimum size
static java.lang.String	TYPE_CODING_REGION
static java.lang.String	TYPE_MODIFICATION_SITE
static java.lang.String	TYPE_PROTEIN_BINDING_DOMAIN constants for type field
static java.lang.String	TYPE_REGULATORY_REGION
static java.lang.String	TYPE_TRANSCRIPTION_STARTING_SITE_L
static java.lang.String	TYPE_TRANSCRIPTION_STARTING_SITE_R

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

sbase

Constructor Summary

Constructors

Constructor and Description
PluginModificationRegion(PluginAntiSenseRNA rna) Constructor
PluginModificationRegion(PluginGene gene) Constructor
PluginModificationRegion(PluginRNA rna) Constructor

Method Summary

Modifier and Type	Method and Description
boolean	getActive() Gets a state for transcriptional starting site.
java.lang.String	getId()
java.lang.String	getName()
PluginSBase	getParentExtensionSBase()
java.lang.String	getParentID()
double	getPos()
double	getSize()
java.lang.String	getType()
void	setActive(boolean active) Sets a state for transcriptional starting site.
protected void	setId(java.lang.String id) Sets the id of this PluginModificationRegion.
void	setName(java.lang.String name) Sets the name of this PluginModificationRegion
void	setPos(double pos) Sets the position of this PluginModificationRegion.
void	setSize(double size) Sets the size of this PluginModificationRegion
void	setType(java.lang.String type) Sets type of this PluginModificationRegion

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

TYPE_PROTEIN_BINDING_DOMAIN

public static final java.lang.String TYPE_PROTEIN_BINDING_DOMAIN

constants for type field

See Also:

Constant Field Values

TYPE_MODIFICATION_SITE

public static final java.lang.String TYPE_MODIFICATION_SITE

See Also:

Constant Field Values

TYPE_CODING_REGION

public static final java.lang.String TYPE_CODING_REGION

See Also:

Constant Field Values

TYPE_REGULATORY_REGION

public static final java.lang.String TYPE_REGULATORY_REGION

See Also:

Constant Field Values

TYPE_TRANSCRIPTION_STARTING_SITE_L

public static final java.lang.String TYPE_TRANSCRIPTION_STARTING_SITE_L

See Also:

Constant Field Values

TYPE_TRANSCRIPTION_STARTING_SITE_R

public static final java.lang.String TYPE_TRANSCRIPTION_STARTING_SITE_R

See Also:

Constant Field Values

MINIMUM_SIZE_EMPTY

public static final double MINIMUM_SIZE_EMPTY

constants for minimum size

See Also:

Constant Field Values

MINIMUM_SIZE_ANY

public static final double MINIMUM_SIZE_ANY

constants for minimum size

See Also:

Constant Field Values

MINIMUM_SIZE_DNAMETYLATION

public static final double MINIMUM_SIZE_DNAMETYLATION

constants for minimum size

See Also:

Constant Field Values

Constructor Detail

PluginModificationRegion

public PluginModificationRegion(PluginGene gene)

Constructor

Parameters:

gene - PluginGene

PluginModificationRegion

public PluginModificationRegion(PluginRNA rna)

Constructor

Parameters:

rna - PluginRNA

PluginModificationRegion

public PluginModificationRegion(PluginAntiSenseRNA rna)

Constructor

Parameters:

rna - PluginAntiSenseRNA

Method Detail

setName

public void setName(java.lang.String name)

Sets the name of this PluginModificationRegion

Parameters:

name - String

getName

public java.lang.String getName()

Returns:

the name of this PluginModificationRegion

setType

public void setType(java.lang.String type)

Sets type of this PluginModificationRegion

Parameters:

type - the type is the following static field of this PluginModificationRegion: TYPE_EMPTY, TYPE_PROMOTOR, TYPE_CODING_REGION, TYPE_TRANSCRIPTION_STARTING_POINT_L TYPE_TRANSCRIPTION_STARTING_POINT_R, TYPE_EXON and TYPE_PROTEIN_BINDING_DOMAIN

getType

public java.lang.String getType()

Returns:

the type of this PluginModificationRegion. See setType

setSize

public void setSize(double size)

Sets the size of this PluginModificationRegion

Parameters:

size - double

getSize

public double getSize()

Returns:

the size of this PluginModificationRegion.

setPos

public void setPos(double pos)

Sets the position of this PluginModificationRegion.

Parameters:

pos - the position of this PluginModificationRegion

getPos

public double getPos()

Returns:

the positon of this PluginModificationRegion.

getId

public java.lang.String getId()

Returns:

the id of this PluginModificationRegion.

setId

protected void setId(java.lang.String id)

Sets the id of this PluginModificationRegion.

Parameters:

id - String

getParentID

public java.lang.String getParentID()

Returns:

the ParentID of this PluginModificationRegion

getParentExtensionSBase

public PluginSBase getParentExtensionSBase()

Returns:

the ParentExtensionSBase if ParentSBase is PluginGene, PluginRNA or PluginAntiSenseRNA, null otherwise

setActive

public void setActive(boolean active)

Sets a state for transcriptional starting site.

Parameters:

active - boolean

getActive

public boolean getActive()

Gets a state for transcriptional starting site.

Returns:

active