jp.sbi.celldesigner.plugin

Class PluginSpeciesAlias

java.lang.Object

jp.sbi.celldesigner.plugin.PluginSBase

jp.sbi.celldesigner.plugin.PluginSpeciesAlias

public class PluginSpeciesAlias
extends PluginSBase

PluginSpeciesAlias has drawing information such as position, color, name and type.

Author:

The Systems Biology Institute

Field Summary

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

sbase

Constructor Summary

Constructors

Modifier	Constructor and Description
	PluginSpeciesAlias(PluginSpecies parent, java.lang.String type) Constructor
protected	PluginSpeciesAlias(jp.sbi.celldesigner.SpeciesAlias speciesAlias, PluginSpecies parent) Constructor

Method Summary

Modifier and Type	Method and Description
java.lang.String	getAliasID()
java.util.Vector	getAllIncludedSpeciesAliases()
PluginAntiSenseRNA	getAntiSenseRNA()
java.awt.Color	getColor()
java.lang.String	getExtensionId()
java.lang.String	getExtensionType()
double	getFrameLineWidth()
PluginGene	getGene()
double	getHeight()
int	getHomodimer()
boolean	getHypothetical()
PluginListOf	getModifications()
java.lang.String	getName()
org.sbml.libsbml.XMLNode	getNotes()
java.lang.String	getNotesString()
PluginInformationBox	getPluginInformationBox() Gets PluginInformationBox
PluginListOf	getPluginListOfStructuralStates() Gets a list of PluginStructuralStates
PluginProtein	getProtein()
PluginRNA	getRNA()
PluginSpecies	getSpecies()
java.lang.String	getType()
double	getWidth()
double	getX()
double	getY()
boolean	isActive()
static java.util.Vector	resetAllIncludedPluginSpeciesAliases(PluginModel pluginMode, PluginSpeciesAlias someone)
void	setAllIncludedSpeciesAliases(java.util.Vector includeds)
void	setAntiSenseRNA(PluginAntiSenseRNA asrna) Sets the PluginAntiSenseRNA of this PluginSpeciesAlias.
void	setColor(java.awt.Color color) Sets the color of this PluginSpeciesAlias.
void	setFrameLineWidth(double lineWidth) Sets the FrameLineWidth of this PluginSpeciesAlias.
void	setFramePosition(double x, double y) Sets the position for this PluginSpeciesAlias.
void	setFrameSize(double width, double height) Sets the FrameSize (width & height) for this PluginSpeciesAlias
void	setGene(PluginGene gene) Sets the PluginGene of this PluginSpeciesAlias.
void	setHomodimer(int homodimer) Sets the homodimer of this PluginSpeciesAlias.
void	setHypothetical(boolean hypothetical) Sets the hypothetical of this PluginSpeciesAlias.
void	setIsActive(boolean activity) Sets activity
void	setModifications(PluginListOf modifications) Sets the list of PluginModification of this PluginSpeciesAlias.
void	setName(java.lang.String name) Sets the name of this PluginSpeciesAlias
void	setPluginInformationBox(PluginInformationBox _PluginInformationBox)
void	setPluginListOfStructuralStates(PluginListOf _listOfPluginStructuralStates) Sets a list of PluginStructuralStates
void	setProtein(PluginProtein protein) Sets the PluginProtein of this PluginSpeciesAlias.
void	setRNA(PluginRNA rna) Sets the PluginRNA of this PluginSpeciesAlias.
protected void	setSpecies(PluginSpecies parentSpecies) Sets the PluginSpecies of this PluginSpeciesAlias.
void	setType(java.lang.String type) Sets the type of this PluginSpeciesAlias.
void	update(PluginSpeciesAlias target) Update all properties of this PluginSpeciesAlias to the same as the given PluginSpeciesAlias.

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

addCVTerm, ChangeCVTermToMiriamDefinition, getAnnotation, getAnnotationString, getCVTerm, 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

PluginSpeciesAlias

public PluginSpeciesAlias(PluginSpecies parent,
                          java.lang.String type)

Constructor

Parameters:

parent - PluginSpecies as the parent of this PluginSpeciesAlias

type - the type of PluginSpeciesAlias. The type is one of the fields of PluginSpeciesSymbolType.

PluginSpeciesAlias

protected PluginSpeciesAlias(jp.sbi.celldesigner.SpeciesAlias speciesAlias,
                             PluginSpecies parent)

Constructor

Parameters:

speciesAlias - SpeciesAlias

parent - PluginSpecies

Method Detail

getAllIncludedSpeciesAliases

public java.util.Vector getAllIncludedSpeciesAliases()

setAllIncludedSpeciesAliases

public void setAllIncludedSpeciesAliases(java.util.Vector includeds)

update

public void update(PluginSpeciesAlias target)

Update all properties of this PluginSpeciesAlias to the same as the given PluginSpeciesAlias.

Parameters:

target - PluginSpeciesAlias

getSpecies

public PluginSpecies getSpecies()

Returns:

the PluginSpecies of this PluginSpeciesAlias

setSpecies

protected void setSpecies(PluginSpecies parentSpecies)

Sets the PluginSpecies of this PluginSpeciesAlias.

Parameters:

parentSpecies - PluginSpecies

getType

public java.lang.String getType()

Returns:

the type of PluginSpeciesAlias. The type is one of fields of PluginSpeciesSymbolType

getExtensionType

public java.lang.String getExtensionType()

Returns:

the ExtensionType of this PluginSpeciesAlias

setType

public void setType(java.lang.String type)

Sets the type of this PluginSpeciesAlias.

Parameters:

type - String

setName

public void setName(java.lang.String name)

Sets the name of this PluginSpeciesAlias

Parameters:

name - String

getName

public java.lang.String getName()

Returns:

the name of this PluginSpeciesAlias.

getAliasID

public java.lang.String getAliasID()

Returns:

AliasID of this PluginSpeciesAlias

getX

public double getX()

Returns:

x position of this PluginSpeciesAlias.

getY

public double getY()

Returns:

y position of this PluginSpeciesAlias.

getWidth

public double getWidth()

Returns:

the width of this PluginSpeciesAlias

getHeight

public double getHeight()

Returns:

the height of this PluginSpeciesAlias

setFrameSize

public void setFrameSize(double width,
                         double height)

Sets the FrameSize (width & height) for this PluginSpeciesAlias

Parameters:

width - double

height - double

setFramePosition

public void setFramePosition(double x,
                             double y)

Sets the position for this PluginSpeciesAlias.

Parameters:

x - double

y - double

getHomodimer

public int getHomodimer()

Returns:

the homodimer of this PluginSpeciesAlias

setHomodimer

public void setHomodimer(int homodimer)

Sets the homodimer of this PluginSpeciesAlias.

Parameters:

homodimer - the number of the field "homomultimer" of Species

getHypothetical

public boolean getHypothetical()

Returns:

true if this PluginSpeciesAlias is hypothetical, false otherwise

setHypothetical

public void setHypothetical(boolean hypothetical)

Sets the hypothetical of this PluginSpeciesAlias.

Parameters:

hypothetical - true if this PluginSpeciesAlias is hypothetical, false otherwise

setColor

public void setColor(java.awt.Color color)

Sets the color of this PluginSpeciesAlias.

Parameters:

color - Color

getColor

public java.awt.Color getColor()

Returns:

color the color of this PluginSpeciesAlias

getFrameLineWidth

public double getFrameLineWidth()

Returns:

the FramelineWidth of thisPluginSpeciesAlias

setFrameLineWidth

public void setFrameLineWidth(double lineWidth)

Sets the FrameLineWidth of this PluginSpeciesAlias.

Parameters:

lineWidth - double

getExtensionId

public java.lang.String getExtensionId()

Returns:

the extensionId of this PluginSpeciesAlias

getAntiSenseRNA

public PluginAntiSenseRNA getAntiSenseRNA()

Returns:

the PluginAntiSenseRNA of this PluginSpeciesAlias

setAntiSenseRNA

public void setAntiSenseRNA(PluginAntiSenseRNA asrna)

Sets the PluginAntiSenseRNA of this PluginSpeciesAlias.

Parameters:

asrna - PluginAntiSenseRNA

getGene

public PluginGene getGene()

Returns:

the PluginGene of this PluginSpeciesAlias

setGene

public void setGene(PluginGene gene)

Sets the PluginGene of this PluginSpeciesAlias.

Parameters:

gene - PluginGene

getProtein

public PluginProtein getProtein()

Returns:

the PluginProtein of this PluginSpeciesAlias.

setProtein

public void setProtein(PluginProtein protein)

Sets the PluginProtein of this PluginSpeciesAlias.

Parameters:

protein - PluginProtein

getRNA

public PluginRNA getRNA()

Returns:

the PluginRNA of this PluginSpeciesAlias

setRNA

public void setRNA(PluginRNA rna)

Sets the PluginRNA of this PluginSpeciesAlias.

Parameters:

rna - PluginRNA

getNotesString

public java.lang.String getNotesString()

Overrides:

getNotesString in class PluginSBase

Returns:

the notes of this PluginSBase.

getNotes

public org.sbml.libsbml.XMLNode getNotes()

Overrides:

getNotes in class PluginSBase

Returns:

Notes as XMLNode

getModifications

public PluginListOf getModifications()

Returns:

the list of PluginModification

setModifications

public void setModifications(PluginListOf modifications)

Sets the list of PluginModification of this PluginSpeciesAlias.

Parameters:

modifications - PluginListOf

setIsActive

public void setIsActive(boolean activity)

Sets activity

Parameters:

activity - boolean

isActive

public boolean isActive()

Returns:

isActive

getPluginListOfStructuralStates

public PluginListOf getPluginListOfStructuralStates()

Gets a list of PluginStructuralStates

Returns:

listOfPluginStructuralStates

setPluginListOfStructuralStates

public void setPluginListOfStructuralStates(PluginListOf _listOfPluginStructuralStates)

Sets a list of PluginStructuralStates

Parameters:

_listOfPluginStructuralStates - PluginListOf

getPluginInformationBox

public PluginInformationBox getPluginInformationBox()

Gets PluginInformationBox

Returns:

PluginInformationBox

setPluginInformationBox

public void setPluginInformationBox(PluginInformationBox _PluginInformationBox)

Parameters:

_PluginInformationBox - PluginInformationBox

resetAllIncludedPluginSpeciesAliases

public static final java.util.Vector resetAllIncludedPluginSpeciesAliases(PluginModel pluginMode,
                                                                          PluginSpeciesAlias someone)