Module omix.api

Package omix.plugin.model

Interface Reaction

All Superinterfaces:

AbstractBioNode, AbstractModelComponent, AbstractNode, AbstractVisibleComponent, ReadOnlyInterface

All Known Subinterfaces:

Reaction

public interface Reaction
extends AbstractBioNode

Method Summary

Modifier and Type	Method	Description
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.
boolean	inverted()	When the inverted option is set, all flux edges of the reaction display their direction in opposition to their nominal direction.
double	localPathwayStrength()	The pathway's shape can have local divergent thicknesses according the reaction's local pathway strength.
Pathway	pathway()	Returns the pathway the reaction belongs to.
boolean	reversible()	Reversibility of the enzymatic reaction.

Methods inherited from interface omix.plugin.model.AbstractBioNode

effectorEdges, fluxEdges, getPublicIdentifiers, inEdges, name, outEdges, synonyms

Methods inherited from interface omix.plugin.model.AbstractModelComponent

addChangeListener, addPropertyChangeListener, fieldExists, getField, getField, model, removeChangeListener, removePropertyChangeListener

Methods inherited from interface omix.plugin.model.AbstractNode

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

Methods inherited from interface omix.plugin.model.AbstractVisibleComponent

accessoryExists, getAccessories, getAccessories, getAccessory, getAccessory, getAccessory, getAccessory, getAllAccessories, hasDiagramItems, hasDiagramItems

Method Details

localPathwayStrength

double localPathwayStrength()

The pathway's shape can have local divergent thicknesses according the reaction's local pathway strength. value range: 0.0 to 1.0

reversible

boolean reversible()

Reversibility of the enzymatic reaction.

inverted

boolean inverted()

When the inverted option is set, all flux edges of the reaction display their direction in opposition to their nominal direction. This property can be used to invert reactions temporarily without changing the network topology.

pathway

Pathway pathway()

Returns the pathway the reaction belongs to.

Returns:

a reference to the pathway if available

getProductMetabolites

Collection<? extends Metabolite> getProductMetabolites()

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

Returns:

unmodifiable list of product metabolites

getEductMetabolites

Collection<? extends Metabolite> getEductMetabolites()

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

Returns:

unmodifiable list of educt metabolites

getEffectorMetabolites

Collection<? extends Metabolite> getEffectorMetabolites()

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

Returns:

unmodifiable list of effector metabolites

Since:

Omix 1.9.0

getDiagramItems

List<? extends ReactionItem> getDiagramItems()

Specified by:

getDiagramItems in interface AbstractBioNode

Specified by:

getDiagramItems in interface AbstractNode

Specified by:

getDiagramItems in interface AbstractVisibleComponent

getDiagramItems

List<? extends ReactionItem> getDiagramItems(Diagram diagram)

Specified by:

getDiagramItems in interface AbstractBioNode

Specified by:

getDiagramItems in interface AbstractNode

Specified by:

getDiagramItems in interface AbstractVisibleComponent