Uses of Interface omix.plugin.model.Metabolite (Omix API)

Packages that use Metabolite
Package	Description
omix.plugin.diagram
omix.plugin.diagram.writable
omix.plugin.identity
omix.plugin.model
omix.plugin.model.writable
omix.util	This package contains utilities for OVL and Omix plugin development.

Uses of Metabolite in omix.plugin.diagram

Methods in omix.plugin.diagram that return Metabolite

Modifier and Type Method Description

Metabolite MetaboliteItem.modelComponent()

Uses of Metabolite in omix.plugin.diagram.writable

Methods in omix.plugin.diagram.writable with parameters of type Metabolite
Modifier and Type	Method	Description
`MetaboliteItem`	Diagram.`createMetaboliteItem(Metabolite metabolite)`	Creates another visible instance of the metabolite in the diagram (a duplicate node).
`MetaboliteItem`	Diagram.`createMetaboliteItem(Metabolite metabolite, CompartmentItem compartment)`

Uses of Metabolite in omix.plugin.identity

Methods in omix.plugin.identity with parameters of type Metabolite
Modifier and Type	Method	Description
`default Set<PublicIdentifier>`	PublicIdentifierProviderInterface.`providePublicIdentifiers(Metabolite item, PublicIdentifierManager registry)`

Uses of Metabolite in omix.plugin.model

Methods in omix.plugin.model that return Metabolite
Modifier and Type	Method	Description
`Metabolite`	Compartment.`getMetabolite(String name)`	Returns the metabolite node of the given name if available in the compartment, otherwise null.
`Metabolite`	MetaboliteType.`getMetabolite(Compartment compartment)`	Returns the metabolite pool inside the given compartment.
`Metabolite`	Model.`getMetabolite(String name)`	Returns the (compartment free) metabolite node of the given name if available, otherwise null.
`default Metabolite`	MetaboliteType.`getNonCompartmentalizedMetabolite()`

Methods in omix.plugin.model that return types with arguments of type Metabolite
Modifier and Type	Method	Description
`Collection<? extends Metabolite>`	Reaction.`getEductMetabolites()`	Returns a list of all metabolite instances being connected by incoming flux edges.
`Collection<? extends Metabolite>`	Reaction.`getEffectorMetabolites()`	Returns a list of all metabolite instances being connected by effector edges.
`List<? extends Metabolite>`	MetaboliteType.`getExistingMetabolites()`
`List<? extends Metabolite>`	MetaboliteType.`getExistingMetabolites(Diagram diagram)`
`Collection<? extends Metabolite>`	Reaction.`getProductMetabolites()`	Returns a list of all metabolite instances being connected by outgoing flux edges.
`List<? extends Metabolite>`	Compartment.`metabolites()`	Returns an unchangeable `List` of all metabolites that occur in this compartment.
`List<? extends Metabolite>`	MetaboliteType.`metabolites()`	Returns all metabolite pools of different compartments.
`List<? extends Metabolite>`	Model.`metabolites()`	Returns an unchangeable `List` of all metabolite nodes.

Uses of Metabolite in omix.plugin.model.writable

Subinterfaces of Metabolite in omix.plugin.model.writable

Modifier and Type Interface Description

interface Metabolite

Methods in omix.plugin.model.writable that return Metabolite

Modifier and Type Method Description

Metabolite Metabolite.toReadOnly()

Methods in omix.plugin.model.writable with parameters of type Metabolite

Modifier and Type Method Description

Metabolite Model.toWritable(Metabolite metabolite)
Uses of Metabolite in omix.util

Methods in omix.util with parameters of type Metabolite

Modifier and Type Method Description

static String NameUtilities.getMetaboliteName(Metabolite metabolite)