Module omix.api

Package omix.lang.model

Interface Model

All Superinterfaces:

Component, Item

@OVLExtensible
public interface Model
extends Component

This class represents the network model. This Java interface represents a Model in OVL. It contain all methods available in OVL.

Author:

Dr. Peter Droste, Omix Visualization

Method Summary

Modifier and Type	Method	Description
List<? extends Compartment>	allCompartments()	Returns an unchangeable List of all compartment items.
List<? extends EffectorEdge>	effectorEdges()	Returns an unchangeable List of all effector edges.
List<? extends FluxEdge>	fluxEdges()	Returns an unchangeable List of all flux edges.
default Compartment	getCompartment(String name)	Deprecated.
GraphicsBox	getGraphicsBox(String identifier)
default GraphicsItem	getGraphicsItem(String identifier)	Deprecated.
GraphicsNode	getGraphicsNode(String identifier)	Returns the graphics node item with the given identifier if available, otherwise null.
Metabolite	getMetabolite(String name)	Returns the (compartment free) metabolite node of the given name if available, otherwise null.
String	getName()	Returns the name of the model.
Pathway	getPathway(String name)	Returns the pathway of the given name if available, otherwise null.
Set<? extends PublicIdentifier>	getPublicIdentifiers()	Returns the components public identifiers
Reaction	getReaction(String name)	Returns the reaction nodes of the given name if available, otherwise null.
Compartment	getTopLevelCompartment(String name)	Returns a toplevel compartment of the given name if available, otherwise null.
List<? extends GraphicsBox>	graphicsBoxes()	Returns an unchangeable List of all graphical boxes.
List<? extends GraphicsEdge>	graphicsEdges()	Returns an unchangeable List of all graphics edges (connection edges).
default List<? extends GraphicsItem>	graphicsItems()	Deprecated.
List<? extends GraphicsNode>	graphicsNodes()	Returns an unchangeable List of all graphics node items.
List<? extends GraphicsPath>	graphicsPaths()	Returns an unchangeable List of all graphical paths.
default Model	metabolicNetwork()	Deprecated.
List<? extends Metabolite>	metabolites()	Returns an unchangeable List of all metabolite nodes.
List<? extends MetaboliteType>	metaboliteTypes()	Returns all metabolite types of the model.
List<? extends Pathway>	pathways()	Returns an unchangeable List of all pathway items.
List<? extends Reaction>	reactions()	Returns an unchangeable List of all reaction nodes.

Methods inherited from interface omix.lang.model.Component

customPropertyNames, getCustomProperty, getIdentifier, id, onload, setCustomProperty, setTmpCustomProperty

Method Details

metabolites

List<? extends Metabolite> metabolites()

Returns an unchangeable List of all metabolite nodes.

Returns:

list of metabolites

reactions

List<? extends Reaction> reactions()

Returns an unchangeable List of all reaction nodes.

Returns:

list of reactions

pathways

List<? extends Pathway> pathways()

Returns an unchangeable List of all pathway items.

Returns:

list of pathways

allCompartments

List<? extends Compartment> allCompartments()

Returns an unchangeable List of all compartment items.

Returns:

list of compartments

graphicsNodes

List<? extends GraphicsNode> graphicsNodes()

Returns an unchangeable List of all graphics node items.

Returns:

list of node items

Since:

Omix 1.8.0

graphicsEdges

List<? extends GraphicsEdge> graphicsEdges()

Returns an unchangeable List of all graphics edges (connection edges).

Returns:

list of graphics edges

Since:

Omix 1.8.0

fluxEdges

List<? extends FluxEdge> fluxEdges()

Returns an unchangeable List of all flux edges.

Returns:

list of flux edges

effectorEdges

List<? extends EffectorEdge> effectorEdges()

Returns an unchangeable List of all effector edges.

Returns:

list of effector edges

graphicsItems

@Deprecated(since="Omix 2.0") @ReplacedBy("graphicsBoxes()") default List<? extends GraphicsItem> graphicsItems()

Deprecated.

Returns an unchangeable List of all graphical items.

Returns:

list of graphical items

graphicsBoxes

List<? extends GraphicsBox> graphicsBoxes()

Returns an unchangeable List of all graphical boxes.

Returns:

list of graphical boxes

graphicsPaths

List<? extends GraphicsPath> graphicsPaths()

Returns an unchangeable List of all graphical paths.

Returns:

list of graphical paths

getMetabolite

Metabolite getMetabolite(String name)

Returns the (compartment free) metabolite node of the given name if available, otherwise null. In order to get access to metabolites contained in a compartment call Compartment.getMetabolite(String).

Parameters:

name - of metabolite

Returns:

found metabolite

getReaction

Reaction getReaction(String name)

Returns the reaction nodes of the given name if available, otherwise null.

Parameters:

name - of the reaction

Returns:

found reaction

getPathway

Pathway getPathway(String name)

Returns the pathway of the given name if available, otherwise null.

Parameters:

name - of the pathway

Returns:

found pathway

getTopLevelCompartment

Compartment getTopLevelCompartment(String name)

Returns a toplevel compartment of the given name if available, otherwise null. In order to get access to a sub compartment call Compartment.getSubCompartment(String).

Parameters:

name - of the compartment

Returns:

found compartment

getCompartment

@Deprecated default Compartment getCompartment(String name)

Deprecated.

getGraphicsNode

GraphicsNode getGraphicsNode(String identifier)

Returns the graphics node item with the given identifier if available, otherwise null.

Parameters:

identifier - of the graphics node

Returns:

found graphics node

getGraphicsItem

@Deprecated(since="Omix 2.0") default GraphicsItem getGraphicsItem(String identifier)

Deprecated.

Returns the graphics item with the given identifier if available, otherwise null.

Parameters:

identifier - of the graphics item

Returns:

found graphics item

Since:

Omix 1.8.0

getGraphicsBox

GraphicsBox getGraphicsBox(String identifier)

getName

String getName()

Returns the name of the model.

Returns:

name

metabolicNetwork

@Deprecated default Model metabolicNetwork()

Deprecated.

returns the metabolic network layer of the model.

Returns:

metabolic network

metaboliteTypes

List<? extends MetaboliteType> metaboliteTypes()

Returns all metabolite types of the model.

Returns:

list of all metabolite types

getPublicIdentifiers

Set<? extends PublicIdentifier> getPublicIdentifiers()

Returns the components public identifiers

Returns:

set of public identifiers

Since:

Omix 1.9.0