Module omix.api

Package omix.plugin.model.writable

Interface Reaction

All Superinterfaces:

AbstractBioNode, AbstractBioNode, AbstractModelComponent, AbstractModelComponent, AbstractNode, AbstractNode, AbstractVisibleComponent, AbstractVisibleComponent, Reaction, ReadOnlyInterface, WritableInterface

public interface Reaction
extends Reaction, AbstractBioNode

Method Summary

Modifier and Type	Method	Description
void	addPublicIdentifier(PublicIdentifier publicIdentifier)	Adds a public identifier to the item.
default void	addSynonym(String synonym)	Adds a synonym to the item.
void	addSynonym(String synonym, String htmlSynonym)	Adds a synonym to the item.
void	exchangeSynonyms(int index1, int index2)	Exchanges the position of two synonyms.
List<? extends ReactionItem>	getDiagramItems()
List<? extends ReactionItem>	getDiagramItems(Diagram diagram)
Collection<? extends Metabolite>	getEductMetabolites()	Returns a list of all metabolite instances being connected by incoming flux edges.
Collection<? extends Metabolite>	getEffectorMetabolites()	Returns a list of all metabolite instances being connected by effector edges.
Collection<? extends Metabolite>	getProductMetabolites()	Returns a list of all metabolite instances being connected by outgoing flux edges.
void	invert()	Inverts all flux edges of the reaction.
Pathway	pathway()	Returns the pathway the reaction belongs to.
void	removePublicIdentifier(PublicIdentifier publicIdentifier)	Removes the public identifier from the item.
void	removeSynonym(int synonymIndex)	Removes the synonym from the item.
void	removeSynonym(String synonym)	Removes the synonym from the item.
void	setFormattedLabel(String html)	Set items visible label in html.
void	setIdentifier(String identifier)	Changes identifier of the item.
void	setInverted(boolean inverted)	Changes the inverted state of the reaction.
void	setLocalPathwayStrength(double localPathwayStrength)	Changes the local pathway strength of the reaction.
void	setPublicIdentifiers(Collection<? extends PublicIdentifier> publicIdentifiers)	Set the public identifiers of the item.
void	setReversible(boolean reversibility)	Changes the reversibility of the reaction.
default void	setSynonym(int index, String synonymPlain)	Sets the synonym at the given position.
void	setSynonym(int index, String synonymPlain, String synonymRichText)	Sets the synonym at the given position.
Reaction	toReadOnly()

Methods inherited from interface omix.plugin.model.AbstractBioNode

getPublicIdentifiers, name, synonyms

Methods inherited from interface omix.plugin.model.writable.AbstractBioNode

effectorEdges, fluxEdges, inEdges, outEdges, setBlurDefault, setCollapsedDefault, setFillLevelDefault, setFillLevelIndicationDefault, setFontDefault, setPaintDefault, setScaleDefault, setShadowDefault, setShapeDefault, setStrokeColorDefault, setStrokeStyleDefault, setStrokeWidthDefault, setTextBrushDefault, setTextStrokeColorDefault, setTextStrokeWidthDefault, setTransparencyDefault

Methods inherited from interface omix.plugin.model.AbstractModelComponent

addChangeListener, addPropertyChangeListener, fieldExists, removeChangeListener, removePropertyChangeListener

Methods inherited from interface omix.plugin.model.writable.AbstractModelComponent

getField, getField, isChangeable, model

Methods inherited from interface omix.plugin.model.AbstractNode

blur, collapsed, fillLevel, fillLevelIndication, font, getCustomProperty, getIdentifier, hidden, paint, scale, setCustomProperty, setTmpCustomProperty, shadow, shape, strokeColor, strokeStyle, strokeWidth, textBrush, textStrokeColor, textStrokeWidth, transparency

Methods inherited from interface omix.plugin.model.writable.AbstractNode

edges, graphicsEdges, linkEdges, setBlur, setCollapsed, setFillLevel, setFillLevelIndication, setFont, setHidden, setPaint, setScale, setShadow, setShape, setStrokeColor, setStrokeStyle, setStrokeWidth, setTextBrush, setTextStrokeColor, setTextStrokeWidth, setTransparency

Methods inherited from interface omix.plugin.model.AbstractVisibleComponent

accessoryExists, getAccessory, getAccessory, hasDiagramItems, hasDiagramItems

Methods inherited from interface omix.plugin.model.writable.AbstractVisibleComponent

getAccessories, getAccessories, getAccessory, getAccessory, getAllAccessories, getCustomProperty, getMethod, getMethod, getMethod, setCustomProperty, setTmpCustomProperty

Methods inherited from interface omix.plugin.model.Reaction

inverted, localPathwayStrength, reversible

Method Details

pathway

Pathway pathway()

Returns the pathway the reaction belongs to.

Specified by:

pathway in interface Reaction

Returns:

a reference to the pathway if available

setReversible

void setReversible(boolean reversibility) throws IllegalChangeException

Changes the reversibility of the reaction.

Parameters:

reversibility -

Throws:

IllegalChangeException

See Also:

Reaction.reversible()

setInverted

void setInverted(boolean inverted) throws IllegalChangeException

Changes the inverted state of the reaction.

Parameters:

inverted -

Throws:

IllegalChangeException

See Also:

Reaction.inverted()

setLocalPathwayStrength

void setLocalPathwayStrength(double localPathwayStrength) throws IllegalChangeException

Changes the local pathway strength of the reaction.

Parameters:

localPathwayStrength - value range: 0.0 to 1.0

Throws:

IllegalChangeException

See Also:

Reaction.localPathwayStrength()

setIdentifier

void setIdentifier(String identifier) throws ComponentExistsException, IllegalChangeException

Changes identifier of the item.

Parameters:

identifier - the new name of the item. CAUTION, the name must be unique in the network.

Throws:

ComponentExistsException

IllegalChangeException

setFormattedLabel

void setFormattedLabel(String html) throws IllegalChangeException

Set items visible label in html.

Parameters:

html - item's label in HTML

Throws:

IllegalChangeException

addSynonym

default void addSynonym(String synonym) throws IllegalChangeException

Adds a synonym to the item.

Parameters:

synonym -

Throws:

IllegalChangeException

addSynonym

void addSynonym(String synonym, String htmlSynonym) throws IllegalChangeException

Adds a synonym to the item.

Parameters:

synonym -

html -

Throws:

IllegalChangeException

removeSynonym

void removeSynonym(String synonym) throws IllegalChangeException

Removes the synonym from the item.

Parameters:

synonym -

Throws:

IllegalChangeException

removeSynonym

void removeSynonym(int synonymIndex) throws IllegalChangeException

Removes the synonym from the item.

Parameters:

synonym - index

Throws:

IllegalChangeException

exchangeSynonyms

void exchangeSynonyms(int index1, int index2) throws IllegalChangeException

Exchanges the position of two synonyms.

Parameters:

index1 -

index2 -

Throws:

IllegalChangeException

setSynonym

default void setSynonym(int index, String synonymPlain) throws IllegalChangeException

Sets the synonym at the given position.

Parameters:

index -

synonymPlain - plain text

Throws:

IllegalChangeException

setSynonym

void setSynonym(int index, String synonymPlain, String synonymRichText) throws IllegalChangeException

Sets the synonym at the given position.

Parameters:

index -

synonymPlain - plain text

synonymRichText - rich text

Throws:

IllegalChangeException

addPublicIdentifier

void addPublicIdentifier(PublicIdentifier publicIdentifier) throws IllegalChangeException

Adds a public identifier to the item.

Parameters:

publicIdentifier -

Throws:

IllegalChangeException

setPublicIdentifiers

void setPublicIdentifiers(Collection<? extends PublicIdentifier> publicIdentifiers) throws IllegalChangeException

Set the public identifiers of the item.

Parameters:

publicIdentifiers -

Throws:

IllegalChangeException

removePublicIdentifier

void removePublicIdentifier(PublicIdentifier publicIdentifier) throws IllegalChangeException

Removes the public identifier from the item.

Parameters:

publicIdentifier -

Throws:

IllegalChangeException

invert

void invert() throws IllegalChangeException

Inverts all flux edges of the reaction.

Throws:

IllegalChangeException

getDiagramItems

List<? extends ReactionItem> getDiagramItems()

Specified by:

getDiagramItems in interface AbstractBioNode

Specified by:

getDiagramItems in interface AbstractBioNode

Specified by:

getDiagramItems in interface AbstractNode

Specified by:

getDiagramItems in interface AbstractNode

Specified by:

getDiagramItems in interface AbstractVisibleComponent

Specified by:

getDiagramItems in interface AbstractVisibleComponent

Specified by:

getDiagramItems in interface Reaction

getDiagramItems

List<? extends ReactionItem> getDiagramItems(Diagram diagram)

Specified by:

getDiagramItems in interface AbstractBioNode

Specified by:

getDiagramItems in interface AbstractBioNode

Specified by:

getDiagramItems in interface AbstractNode

Specified by:

getDiagramItems in interface AbstractNode

Specified by:

getDiagramItems in interface AbstractVisibleComponent

Specified by:

getDiagramItems in interface AbstractVisibleComponent

Specified by:

getDiagramItems in interface Reaction

toReadOnly

Reaction toReadOnly()

Specified by:

toReadOnly in interface AbstractBioNode

Specified by:

toReadOnly in interface AbstractModelComponent

Specified by:

toReadOnly in interface AbstractNode

Specified by:

toReadOnly in interface AbstractVisibleComponent

Specified by:

toReadOnly in interface WritableInterface

getProductMetabolites

Collection<? extends Metabolite> getProductMetabolites()

Returns a list of all metabolite instances being connected by outgoing flux edges.

Specified by:

getProductMetabolites in interface Reaction

Returns:

unmodifiable list of product metabolites

getEductMetabolites

Collection<? extends Metabolite> getEductMetabolites()

Returns a list of all metabolite instances being connected by incoming flux edges.

Specified by:

getEductMetabolites in interface Reaction

Returns:

unmodifiable list of educt metabolites

getEffectorMetabolites

Collection<? extends Metabolite> getEffectorMetabolites()

Returns a list of all metabolite instances being connected by effector edges.

Specified by:

getEffectorMetabolites in interface Reaction

Returns:

unmodifiable list of effector metabolites

Since:

Omix 1.9.0