All Superinterfaces:: Model, ReadOnlyInterface, WritableInterface

public interface Model
extends Model, WritableInterface

The writable model can be used to create and add additional components to a network model document. See Model for more details about the constitution of Omix network documents.
The Model provides write access to Model. Possible components of Model are Compartment and MetaboliteType. Instances of these types can be created in the Model. After creating a component it must be finally inserted into the Model by addComponent(AbstractModelComponent).

Since:: Omix 1.9.0
Author:: Dr. Peter Droste, Omix Visualization

Method Summary

Modifier and Type	Method	Description
`void`	`activatePlugin(String plugin)`	Activates the given plugin on the network model document.
`void`	`addChangeListener(ModelChangeListener listener)`	Adds a `NetworkChangeListener` which is triggered when the composition of the network changes.
`void`	`addComponent(AbstractModelComponent item)`	Created diagram items have to be inserted into the metabolic network before taking any effect. OVL definitions do not become part of a diagram component until the item is added to the diagram. After adding a `Metabolite` or `Metabolite` to the diagram, a `ModelMetaboliteType` is simultaneously added to the `Model`.
`CustomShape`	`addCustomShape(String name, List<? extends AbstractCurvePoint> points)`	Creates a new custom shape available for nodes or edge markers.
`void`	`addDiagram(Diagram diagram)`
`void`	`addMotifStamp(MotifStamp motifStamp)`
`void`	`addPublicIdentifier(PublicIdentifier publicIdentifier)`	Adds a public identifier to the model.
`List<? extends Compartment>`	`allCompartments()`	Returns an unchangeable `List` of all compartment items.
`void`	`attach(OVLEnvironment environment)`	Attaches this writable model to the OVL environment.
`UndoMacro`	`beginUndoMacro(Supplier<String> description)`
`ModelCapabilities`	`capabilities()`
`void`	`clearCapabilities(ModelCapabilities capabilities)`
`default void`	`clearCapabilities(ModelCapability... capabilities)`
`boolean`	`compartmentExists(String name)`	Determines if compartment of certain name exists.
`default Arc`	`createArc(double x, double y, double radius, double startAngle, double length)`	Create an arc with the given center, radius, start angle and length.
`Arc`	`createArc(double x, double y, double radiusX, double radiusY, double startAngle, double length)`	Create an arc with the given center, radiusX, radiusY, start angle and length.
`BezierPoint`	`createBezierPoint(double x, double y)`	Create a bezier controlpoint.
`default FluxEdge`	`createCofactorEdge(AbstractBioNode src, AbstractBioNode dst)`
`FluxEdge`	`createCofactorEdge(AbstractBioNode src, AbstractBioNode dst, double coefficient)`	Creates a new cofactor edge between a source and destination node.
`default LinkEdge`	`createCofactorEdge(AbstractBioNode src, Link dst)`
`LinkEdge`	`createCofactorEdge(AbstractBioNode src, Link dst, double coefficient)`	Creates a new link edge with flux edge appearance between a source node and destination link.
`default LinkEdge`	`createCofactorEdge(Link src, AbstractBioNode dst)`
`LinkEdge`	`createCofactorEdge(Link src, AbstractBioNode dst, double coefficient)`	Creates a new link edge with flux edge appearance between a source link and destination node.
`Compartment`	`createCompartment(String name)`	Create a new compartment item. After creating a new compartment, it must be explicitly added to the model by `addComponent(AbstractModelComponent)`.
`Compartment`	`createCompartment(String namePlainText, String nameRichText)`	Create a new compartment item. After creating a new compartment, it must be explicitly added to the model by `addComponent(AbstractModelComponent)`.
`Compartment`	`createCompartment(String namePlainText, String nameRichText, Compartment outside)`	Create a new compartment item inside another compartment. After creating a new compartment, it must be explicitly added to the model by `addComponent(AbstractModelComponent)`.
`Compartment`	`createCompartment(String name, Compartment outside)`	Create a new compartment item inside another compartment. After creating a new compartment, it must be explicitly added to the model by `addComponent(AbstractModelComponent)`.
`Diagram`	`createDiagram()`	Creates a new diagram with generic identifier.
`Diagram`	`createDiagram(String identifier)`	Creates a new diagram.
`LinkEdge`	`createEffectorEdge(Link src, Reaction dst, double effect)`	Creates a new link edge with effector edge appearance between a source link and destination node.
`LinkEdge`	`createEffectorEdge(Metabolite src, Link dst, double effect)`	Creates a new link edge with effector edge appearance between a source node and destination link.
`EffectorEdge`	`createEffectorEdge(Metabolite src, Reaction dst, double effect)`	Creates a new effector edge between a source and destination node with the given effect.
`default FluxEdge`	`createFluxEdge(AbstractBioNode src, AbstractBioNode dst)`
`FluxEdge`	`createFluxEdge(AbstractBioNode src, AbstractBioNode dst, double coefficient)`	Creates a new flux edge between a source and destination node.
`default LinkEdge`	`createFluxEdge(AbstractBioNode src, Link dst)`
`LinkEdge`	`createFluxEdge(AbstractBioNode src, Link dst, double coefficient)`	Creates a new link edge with flux edge appearance between a source node and destination link.
`default LinkEdge`	`createFluxEdge(Link src, AbstractBioNode dst)`
`LinkEdge`	`createFluxEdge(Link src, AbstractBioNode dst, double coefficient)`	Creates a new link edge with flux edge appearance between a source link and destination node.
`GraphicsEdge`	`createGraphicsEdge(AbstractNode src, AbstractNode dst)`	Creates a new graphics edge between a source and destination node.
`LinkEdge`	`createGraphicsEdge(AbstractNode src, Link dst)`	Creates a new link edge between a source node and destination link.
`LinkEdge`	`createGraphicsEdge(Link src, AbstractNode dst)`	Creates a new link edge between a source link and destination node.
`GraphicsNode`	`createGraphicsNode()`	Create a new graphics node item with a generated random identifier. After creating a new node, it must be explicitly added to the model by `addComponent(AbstractModelComponent)`.
`GraphicsNode`	`createGraphicsNode(String text)`	Create a new graphics node item. After creating a new node, it must be explicitly added to the model by `addComponent(AbstractModelComponent)`.
`default Link`	`createLink(File file)`
`Link`	`createLink(File file, String description)`	Create a new link to given model file. After creating a new link, it must be explicitly added to the model by `addComponent(AbstractModelComponent)`.
`Link`	`createLink(String description)`	Create a new link. After creating a new link, it must be explicitly added to the model by `addComponent(AbstractModelComponent)`.
`default Link`	`createLink(Diagram diagram)`
`Link`	`createLink(Diagram diagram, String description)`	Create a new link to given model file. After creating a new link, it must be explicitly added to the model by `addComponent(AbstractModelComponent)`.
`Link`	`createLink(Pathway pathway)`	Create a new link to given pathway. After creating a new link, it must be explicitly added to the model by `addComponent(AbstractModelComponent)`.
`Metabolite`	`createMetabolite(String name)`	Creates a new metabolite with the given unique name and returns a visible instance of the metabolite (`Metabolite`).
`Metabolite`	`createMetabolite(String namePlainText, String nameRichText)`	Creates a new metabolite with the given unique name and returns a visible instance of the metabolite (`Metabolite`).
`Metabolite`	`createMetabolite(String namePlainText, String nameRichText, Compartment compartment)`	Creates a new metabolite with the given unique name lying in the given compartment.
`Metabolite`	`createMetabolite(String name, Compartment compartment)`	Creates a new metabolite with the given unique name lying in the given compartment.
`MetaboliteType`	`createMetaboliteType(String name)`	Creates a new metabolite type. After creating a new instance, it must be explicitly added to the model by `addComponent(AbstractModelComponent)`. When the metabolite type is added to the model, a `Metabolite` is created for each compartment in the model representing the metabolite pools.
`MetaboliteType`	`createMetaboliteType(String name, String nameFormat)`	Creates a new metabolite type. After creating a new instance, it must be explicitly added to the model by `addComponent(AbstractModelComponent)`. When the metabolite type is added to the model, a `Metabolite` is created for each compartment in the model representing the metabolite pools.
`MotifStamp`	`createMotifStamp(String name)`
`Pathway`	`createPathway(String name)`	Create a new pathway item.
`Pathway`	`createPathway(String namePlainText, String nameRichText)`	Create a new pathway item.
`Reaction`	`createReaction(String name)`	Create a new reaction item.
`Reaction`	`createReaction(String name, String nameFormat)`	Create a new reaction item.
`Reaction`	`createReaction(String namePlainText, String nameRichText, Pathway pathway)`	Create a new reaction item belonging to the given pathway. After creating a new reaction, it must be explicitly added to the model by `addComponent(AbstractModelComponent)`.
`Reaction`	`createReaction(String name, Pathway pathway)`	Create a new reaction item belonging to the given pathway. After creating a new reaction, it must be explicitly added to the model by `addComponent(AbstractModelComponent)`.
`Separator`	`createSeparator()`
`default SplinePoint`	`createSplinePoint(double x, double y)`	Create a spline point.
`SplinePoint`	`createSplinePoint(double x, double y, Smoothness smoothness)`	Create a spline point with the given smoothness.
`void`	`deactivatePlugin(String string)`
`void`	`detach(OVLEnvironment environment)`	Detaches this writable model from the OVL environment.
`List<? extends Diagram>`	`diagrams()`
`List<? extends EffectorEdge>`	`effectorEdges()`	Returns an unchangeable `List` of all effector edges.
`List<? extends FluxEdge>`	`fluxEdges()`	Returns an unchangeable `List` of all flux edges.
`List<? extends Accessory>`	`getAccessories()`	Returns all accessories of the submitted network object defined in the document embedded OVL script.
`List<? extends Accessory>`	`getAccessories(String namespace)`	Returns all accessories of the submitted network object defined in the namespace.
`Accessory`	`getAccessory(String accessoryName)`	Returns the accessory of the submitted network object defined in the document embedded OVL script.
`default <T extends Accessory> T`	`getAccessory(String accessoryName, Class<T> accessoryItemClass)`
`Accessory`	`getAccessory(String namespace, String accessoryName)`	Returns the accessory of the submitted network object defined in the namespace.
`default <T extends Accessory> T`	`getAccessory(String namespace, String accessoryName, Class<T> accessoryItemClass)`
`List<String>`	`getActivePlugins()`	Returns a list of all acive plugins.
`List<? extends Accessory>`	`getAllAccessories()`	Returns all accessories of the submitted network object defined in the document embedded OVL script and all namespaces.
`Diagram`	`getCurrentDiagram()`
`DataSourceManager`	`getDataSourceManager()`	Returns the DataSourceManager of the model.
`Diagram`	`getDiagram(String identifier)`
`String`	`getDocumentSetting(String key)`	Get a setting by key. A plugin program can read and write settings in order to realize an own document based settings management.
`String`	`getDocumentSetting(String key, String defaultValue)`	Get a setting by key. A plugin program can read and write settings in order to realize an own document based settings management.
`Set<Map.Entry<String,String>>`	`getDocumentSettings()`	Returns a set of all available settings of the document. A plugin program can read and write settings in order to realize an own document based settings management.
`Field`	`getField(String fieldName)`	Returns the field of the submitted network object defined in the document embedded OVL script.
`Field`	`getField(String namespace, String fieldName)`	Returns the field of the submitted network object defined in the give namespace.
`GraphicsBox`	`getGraphicsBox(String identifier)`	Returns the graphics item with the given identifier if available, otherwise null.
`GraphicsNode`	`getGraphicsNode(String identifier)`	Returns the graphics node by identifier if available, otherwise null.
`String`	`getIdentifier()`	Returns the name of the model
`Link`	`getLink(String identifier)`	Returns the link by identifier if available, otherwise null.
`Metabolite`	`getMetabolite(String name)`	Returns the (compartment free) metabolite node of the given name if available, otherwise null.
`MetaboliteType`	`getMetaboliteType(String name)`	Get a metabolite type by name.
`Method`	`getMethod(String methodName, Class<?>... params)`	Returns the method of the submitted network object defined in the document embedded OVL script.
`Method`	`getMethod(String namespace, String methodName, Class<?>... params)`	Returns the method of the submitted network object defined in the given namespace. Example code: OVL: `extend Model{ void myMethod(String strg, int i){...} }` can be called by: `getMethod("myMethod", String.class, int.class)` or `getMethod("myMethod(java.lang.String,int)")`
`default Method`	`getMethod(OVLMethodDefinition methodDefinition)`	Returns the method of the submitted network object defined in the document embedded OVL script.
`MotifStamp`	`getMotifStamp(String name)`
`List<String>`	`getNamespaces()`	Returns a list of all available namespaces.
`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.
`boolean`	`graphicsBoxExists(String identifier)`	Determines if graphics box of certain name exists.
`List<? extends GraphicsEdge>`	`graphicsEdges()`	Returns an unchangeable `List` of all graphics edges (connection edges).
`boolean`	`graphicsNodeExists(String identifier)`	Determines if graphics node item of certain name exists.
`List<? extends GraphicsNode>`	`graphicsNodes()`	Returns an unchangeable `List` of all graphics nodes.
`boolean`	`graphicsPathExists(String identifier)`	Determines if graphics path (free-form curve) of certain name exists.
`List<? extends GraphicsPath>`	`graphicsPaths()`	Returns an unchangeable `List` of all graphical paths.
`boolean`	`isChangeable()`	Checks if the given element can be changed.
`boolean`	`isPluginActive(String id)`	Asks if a plugin is active on the network model.
`boolean`	`isPluginAvailable(String plugin)`	Determines if plugin is available in the current Omix session.
`List<? extends LinkEdge>`	`linkEdges()`	Returns an unchangeable `List` of all link edges.
`List<? extends Link>`	`links()`	Returns an unchangeable `List` of all links.
`List<? extends Metabolite>`	`metabolites()`	Returns an unchangeable `List` of all metabolite nodes.
`boolean`	`metaboliteTypeExists(String name)`	Determines if metabolite type of certain name exists.
`List<? extends MetaboliteType>`	`metaboliteTypes()`	All metabolite types being part of the model.
`List<? extends MotifStamp>`	`motifStamps()`
`boolean`	`pathwayExists(String name)`	Determines if pathway of certain name exists.
`List<? extends Pathway>`	`pathways()`	Returns an unchangeable `List` of all pathway items.
`void`	`performAction(UndoableAction change)`
`boolean`	`reactionExists(String name)`	Determines if reaction of certain name exists.
`List<? extends Reaction>`	`reactions()`	Returns an unchangeable `List` of all reaction nodes.
`void`	`removeChangeListener(ModelChangeListener listener)`	Removes the listener which is therefore no longer triggered.
`void`	`removeComponent(AbstractModelComponent item)`
`void`	`removeDiagram(Diagram diagram)`
`void`	`removeMotifStamp(MotifStamp motifStamp)`
`void`	`removePublicIdentifier(PublicIdentifier publicIdentifier)`	Removes the public identifier from the model.
`void`	`setCapabilities(ModelCapabilities capabilities)`
`default void`	`setCapabilities(ModelCapability... capabilities)`
`void`	`setCurrentDiagram(Diagram diagram)`
`void`	`setDocumentSetting(String key, String value)`	Set a setting of the model document. For instance: last used levels of detail, last used editing tool etc.
`void`	`setName(String name)`	Changes name of the model.
`void`	`setPublicIdentifiers(Collection<? extends PublicIdentifier> publicIdentifiers)`	Set the public identifiers of the model.
`StyleSheet`	`styleSheet()`
`Model`	`toReadOnly()`	Returns the read-only interface of this model.
`Diagram`	`toWritable(Diagram type)`
`default AbstractBioNode`	`toWritable(AbstractBioNode type)`
`default AbstractEdge`	`toWritable(AbstractEdge type)`
`default AbstractModelComponent`	`toWritable(AbstractModelComponent type)`
`default AbstractNode`	`toWritable(AbstractNode type)`
`default AbstractVisibleComponent`	`toWritable(AbstractVisibleComponent type)`
`default Accessory`	`toWritable(Accessory type)`
`default AbstractSideBox`	`toWritable(AbstractSideBox type)`
`AnnotationArray<?>`	`toWritable(AnnotationArray<?> type)`
`ChartSideBox`	`toWritable(ChartSideBox type)`
`default DataAnnotation`	`toWritable(DataAnnotation type)`
`DoubleField`	`toWritable(DoubleField type)`
`ImageField`	`toWritable(ImageField type)`
`IntegerField`	`toWritable(IntegerField type)`
`ItemGroup`	`toWritable(ItemGroup type)`
`SideBox`	`toWritable(SideBox type)`
`default SimpleValueField`	`toWritable(SimpleValueField type)`
`TextField`	`toWritable(TextField type)`
`default Array<?>`	`toWritable(Array<?> type)`
`CheckButton`	`toWritable(CheckButton type)`
`DoublePlayer`	`toWritable(DoublePlayer type)`
`DoubleSlider`	`toWritable(DoubleSlider type)`
`DoubleSpinBox`	`toWritable(DoubleSpinBox type)`
`default DoubleTrigger`	`toWritable(DoubleTrigger type)`
`default IntegerTrigger`	`toWritable(IntegerTrigger type)`
`Player`	`toWritable(Player type)`
`PushButton`	`toWritable(PushButton type)`
`Slider`	`toWritable(Slider type)`
`SpinBox`	`toWritable(SpinBox type)`
`default Trigger`	`toWritable(Trigger type)`
`TriggerArray<?>`	`toWritable(TriggerArray<?> type)`
`Compartment`	`toWritable(Compartment compartment)`
`EffectorEdge`	`toWritable(EffectorEdge edge)`
`FluxEdge`	`toWritable(FluxEdge edge)`
`GraphicsBox`	`toWritable(GraphicsBox item)`
`GraphicsEdge`	`toWritable(GraphicsEdge edge)`
`GraphicsNode`	`toWritable(GraphicsNode node)`
`Link`	`toWritable(Link node)`
`LinkEdge`	`toWritable(LinkEdge edge)`
`Metabolite`	`toWritable(Metabolite metabolite)`
`MetaboliteType`	`toWritable(MetaboliteType type)`
`default Model`	`toWritable(Model model)`
`OVLObject`	`toWritable(OVLObject ovlObject)`
`Pathway`	`toWritable(Pathway pathway)`
`Reaction`	`toWritable(Reaction reaction)`
`default WritableInterface`	`toWritable(ReadOnlyInterface type)`

Methods inherited from interface omix.plugin.model.Model

accessoryExists, addChangeListener, addContextMenuEntryProvider, addPropertyChangeListener, createOVLObject, customPropertyNames, customShapes, diagramExists, diagramIdentifiers, fieldExists, getCustomProperty, getCustomShape, getGraphicsPath, getOVLProgram, getOVLProgram, isNamespaceAvailable, linkExists, motifStampExists, removeChangeListener, removeContextMenuEntryProvider, removePropertyChangeListener, setCustomProperty, setTmpCustomProperty

Method Details
- createMetaboliteType
  
  MetaboliteType createMetaboliteType(String name)
  
  Creates a new metabolite type.
  After creating a new instance, it must be explicitly added to the model by addComponent(AbstractModelComponent).
  When the metabolite type is added to the model, a Metabolite is created for each compartment in the model representing the metabolite pools. Additionally, one omix.plugin.network.Metabolite is created as compartmentless metabolite pool. The Metabolite pools can be requested by ModelMetaboliteType#getMetabolite(omix.plugin.network.Compartment).
  
  Parameters:
  
  name - a unique name (identifier) of the metabolite type in the model
  
  Returns:
  
  the new metabolite
- createMetaboliteType
  
  MetaboliteType createMetaboliteType(String name, String nameFormat)
  
  Creates a new metabolite type.
  After creating a new instance, it must be explicitly added to the model by addComponent(AbstractModelComponent).
  When the metabolite type is added to the model, a Metabolite is created for each compartment in the model representing the metabolite pools. Additionally, one omix.plugin.network.Metabolite is created as compartmentless metabolite pool. The Metabolite pools can be requested by ModelMetaboliteType#getMetabolite(omix.plugin.network.Compartment).
  
  Parameters:
  
  name - a unique name (identifier) of the metabolite type in the model
  
  nameFormat - html coded format for the graphical representation of the metabolite's name.
  
  Returns:
  
  the new metabolite
  
  Since:
  
  Omix 1.8.1
- createMotifStamp
  
  MotifStamp createMotifStamp(String name)
- addCustomShape
  
  CustomShape addCustomShape(String name, List<? extends AbstractCurvePoint> points) throws ComponentExistsException, IllegalComponentException, IllegalChangeException
  
  Creates a new custom shape available for nodes or edge markers.
  
  Parameters:
  
  name - a recognizable name of the shape
  
  points - the curve points of the shape
  
  Returns:
  
  CustomShape
  
  Throws:
  
  IllegalComponentException - if points is empty or one of the point has not been created with CurveFactory.
  
  IllegalChangeException
  
  ComponentExistsException
- isPluginAvailable
  
  boolean isPluginAvailable(String plugin)
  
  Determines if plugin is available in the current Omix session.
  
  Parameters:
  
  plugin -
  
  Returns:
  
  available
- activatePlugin
  
  void activatePlugin(String plugin) throws IllegalArgumentException, IllegalAccessException
  
  Activates the given plugin on the network model document. When the plugin contains OVL definitions, these accordingly become active on the model, its components and all later inserted components.
  
  Parameters:
  
  plugin - the identifier of the plugin.
  
  Throws:
  
  IllegalArgumentException
  
  IllegalAccessException
- deactivatePlugin
  
  void deactivatePlugin(String string) throws IllegalArgumentException, IllegalAccessException
  
  Throws:
  
  IllegalArgumentException
  
  IllegalAccessException
- setDocumentSetting
  
  void setDocumentSetting(String key, String value)
  
  Set a setting of the model document.
  For instance: last used levels of detail, last used editing tool etc. A plugin program can read and write settings in order to realize an own document based settings management.
  
  Parameters:
  
  key - of the setting
  
  value - new value
- toReadOnly
  
  Model toReadOnly()
  
  Returns the read-only interface of this model. If you want to use the model outside of the writing process you need to call this method because the Model instance is invalidated thereafter.
  
  Specified by:
  
  toReadOnly in interface WritableInterface
  
  Returns:
  
  read-only model
- getDataSourceManager
  
  DataSourceManager getDataSourceManager()
  
  Returns the DataSourceManager of the model.
  
  Specified by:
  
  getDataSourceManager in interface Model
  
  Returns:
  
  DataSourceManager
- createReaction
  
  Reaction createReaction(String name)
  
  Create a new reaction item.
  
  Parameters:
  
  name - unique name (identifier) for the reaction in the diagram.
  
  Returns:
  
  reaction
- createReaction
  
  Reaction createReaction(String name, Pathway pathway) throws IllegalComponentException
  
  Create a new reaction item belonging to the given pathway.
  After creating a new reaction, it must be explicitly added to the model by addComponent(AbstractModelComponent).
  
  Parameters:
  
  name - unique name (identifier) for the reaction in the diagram.
  
  pathway - (may be null)
  
  Returns:
  
  reaction
  
  Throws:
  
  IllegalComponentException - is thrown when the submitted 'pathway' object has not been created by using the Model but, for instance, is a plugin internal implementation of Pathway.
- createReaction
  
  Reaction createReaction(String name, String nameFormat)
  
  Create a new reaction item.
  
  Parameters:
  
  name - unique name (identifier) for the reaction in the diagram.
  
  nameFormat - html coded format for the graphical representation of the reaction's name.
  
  Returns:
  
  reaction
  
  Since:
  
  Omix 1.8.1
- createReaction
  
  Reaction createReaction(String namePlainText, String nameRichText, Pathway pathway) throws IllegalComponentException
  
  Create a new reaction item belonging to the given pathway.
  After creating a new reaction, it must be explicitly added to the model by addComponent(AbstractModelComponent).
  
  Parameters:
  
  namePlainText - unique name (identifier) for the reaction in the diagram.
  
  nameRichText - html coded format for the graphical representation of the reaction's name.
  
  pathway - (may be null)
  
  Returns:
  
  reaction
  
  Throws:
  
  IllegalComponentException - is thrown when the submitted 'pathway' object has not been created by using the Model but, for instance, is a plugin internal implementation of Pathway.
  
  Since:
  
  Omix 1.8.1
- createPathway
  
  Pathway createPathway(String name)
  
  Create a new pathway item.
  After creating a new pathway, it must be explicitly added to the model by addComponent(AbstractModelComponent).
  
  Parameters:
  
  name - unique name (identifier) for the pathway in the diagram.
  
  Returns:
  
  pathway
- createPathway
  
  Pathway createPathway(String namePlainText, String nameRichText)
  
  Create a new pathway item.
  After creating a new pathway, it must be explicitly added to the model by addComponent(AbstractModelComponent).
  
  Parameters:
  
  namePlainText - unique name (identifier) for the pathway in the diagram.
  
  nameRichText - html coded format for the graphical representation of the pathway's name.
  
  Returns:
  
  pathway
  
  Since:
  
  Omix 1.8.1
- createMetabolite
  
  Metabolite createMetabolite(String name)
  
  Creates a new metabolite with the given unique name and returns a visible instance of the metabolite (Metabolite). Internally, a new Metabolite object is the visible item of a Metabolite object.
  After creating a new metabolite instance, it must be explicitly added to the model by addComponent(AbstractModelComponent).
  
  Parameters:
  
  name - unique name of the new metabolite
  
  Returns:
  
  the visible instance of the new metabolite
  
  See Also:
  
  createMetabolite(String, Compartment)
- createMetabolite
  
  Metabolite createMetabolite(String namePlainText, String nameRichText)
  
  Creates a new metabolite with the given unique name and returns a visible instance of the metabolite (Metabolite). Internally, a new Metabolite object is the visible item of a Metabolite object.
  After creating a new metabolite instance, it must be explicitly added to the model by addComponent(AbstractModelComponent).
  
  Parameters:
  
  namePlainText - unique name of the new metabolite
  
  nameRichText - html coded format for the graphical representation of the metabolite's name.
  
  Returns:
  
  the visible instance of the new metabolite
  
  Since:
  
  Omix 1.8.1
  
  See Also:
  
  createMetabolite(String, Compartment)
- createMetabolite
  
  Metabolite createMetabolite(String name, Compartment compartment) throws IllegalComponentException
  
  Creates a new metabolite with the given unique name lying in the given compartment. The method returns a visible instance of the metabolite (Metabolite).
  After creating a new metabolite instance, it must be explicitly added to the model by addComponent(AbstractModelComponent).
  The Metabolite is the metabolite pool in the metabolic network diagram which is abstracted on the model layer by the Metabolite object. The Metabolite represents the metabolite pool in a certain compartment (or in uncompartmented space). Several Metabolite can be of the same ModelMetaboliteType. When the returned Metabolite is added to the diagram, the according ModelMetaboliteType is consequently added to the Model.
  
  Parameters:
  
  name - unique name of the new metabolite
  
  compartment - the compartment, the metabolite lyies in (may be null).
  
  Returns:
  
  the visible instance of the new metabolite
  
  Throws:
  
  IllegalComponentException - when the submitted 'compartment' object has not been created by using the Model but, for instance, is a plugin internal implementation of Compartment.
- createMetabolite
  
  Metabolite createMetabolite(String namePlainText, String nameRichText, Compartment compartment) throws IllegalComponentException
  
  Creates a new metabolite with the given unique name lying in the given compartment. The method returns a visible instance of the metabolite (Metabolite).
  After creating a new metabolite instance, it must be explicitly added to the model by addComponent(AbstractModelComponent).
  The Metabolite is the metabolite pool in the metabolic network diagram which is abstracted on the model layer by the Metabolite object. The Metabolite represents the metabolite pool in a certain compartment (or in uncompartmented space). Several Metabolite can be of the same ModelMetaboliteType. When the returned Metabolite is added to the diagram, the according ModelMetaboliteType is consequently added to the Model.
  
  Parameters:
  
  namePlainText - unique name of the new metabolite
  
  nameRichText - html coded format for the graphical representation of the metabolite's name.
  
  compartment - the compartment, the metabolite lyies in (may be null).
  
  Returns:
  
  the visible instance of the new metabolite
  
  Throws:
  
  IllegalComponentException - when the submitted 'compartment' object has not been created by using the Model but, for instance, is a plugin internal implementation of Compartment.
  
  Since:
  
  Omix 1.8.1
- createCompartment
  
  Compartment createCompartment(String name)
  
  Create a new compartment item.
  After creating a new compartment, it must be explicitly added to the model by addComponent(AbstractModelComponent).
  
  Parameters:
  
  name - unique name (identifier) for the compartment in the diagram.
  
  Returns:
  
  compartment
  
  See Also:
  
  createCompartment(String), createCompartment(String, Compartment)
- createCompartment
  
  Compartment createCompartment(String namePlainText, String nameRichText)
  
  Create a new compartment item.
  After creating a new compartment, it must be explicitly added to the model by addComponent(AbstractModelComponent).
  
  Parameters:
  
  namePlainText - unique name (identifier) for the compartment in the diagram.
  
  nameRichText - html coded format for the graphical representation of the compartment's name.
  
  Returns:
  
  compartment
  
  Since:
  
  Omix 1.8.1
  
  See Also:
  
  createCompartment(String), createCompartment(String, Compartment)
- createCompartment
  
  Compartment createCompartment(String name, Compartment outside) throws IllegalComponentException
  
  Create a new compartment item inside another compartment.
  After creating a new compartment, it must be explicitly added to the model by addComponent(AbstractModelComponent).
  
  Parameters:
  
  name - unique name (identifier) for the compartment in the diagram.
  
  outside -
  
  Returns:
  
  compartment
  
  Throws:
  
  IllegalComponentException - when the submitted 'compartment' object has not been created by using the Model but, for instance, is a plugin internal implementation of Compartment.
  
  See Also:
  
  createCompartment(String), createCompartment(String, Compartment)
- createCompartment
  
  Compartment createCompartment(String namePlainText, String nameRichText, Compartment outside) throws IllegalComponentException
  
  Create a new compartment item inside another compartment.
  After creating a new compartment, it must be explicitly added to the model by addComponent(AbstractModelComponent).
  
  Parameters:
  
  namePlainText - unique name (identifier) for the compartment in the diagram.
  
  nameRichText - html coded format for the graphical representation of the compartment's name.
  
  outside -
  
  Returns:
  
  compartment
  
  Throws:
  
  IllegalComponentException - when the submitted 'compartment' object has not been created by using the Model but, for instance, is a plugin internal implementation of Compartment.
  
  Since:
  
  Omix 1.8.1
  
  See Also:
  
  createCompartment(String), createCompartment(String, Compartment)
- createFluxEdge
  
  FluxEdge createFluxEdge(AbstractBioNode src, AbstractBioNode dst, double coefficient) throws IllegalComponentException
  
  Creates a new flux edge between a source and destination node.
  
  Parameters:
  
  src - source node
  
  dst - destination node
  
  coefficient - stoichiometric coefficient
  
  Returns:
  
  a flux edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using the Diagram but, for instance, is a plugin internal implementation.
- createFluxEdge
  
  default FluxEdge createFluxEdge(AbstractBioNode src, AbstractBioNode dst) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createCofactorEdge
  
  FluxEdge createCofactorEdge(AbstractBioNode src, AbstractBioNode dst, double coefficient) throws IllegalComponentException
  
  Creates a new cofactor edge between a source and destination node.
  
  Parameters:
  
  src - source node
  
  dst - destination node
  
  coefficient - stoichiometric coefficient
  
  Returns:
  
  a flux edge with isCofactor = true
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using the Diagram but, for instance, is a plugin internal implementation.
- createCofactorEdge
  
  default FluxEdge createCofactorEdge(AbstractBioNode src, AbstractBioNode dst) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createEffectorEdge
  
  EffectorEdge createEffectorEdge(Metabolite src, Reaction dst, double effect) throws IllegalComponentException
  
  Creates a new effector edge between a source and destination node with the given effect.
  
  Parameters:
  
  src - source node
  
  dst - destination node
  
  effect - -1.0 = inhibition, 1.0 = activation, 0.0 = unknown effect
  
  Returns:
  
  effector edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using the Model but, for instance, is a plugin internal implementation.
- createGraphicsNode
  
  GraphicsNode createGraphicsNode(String text)
  
  Create a new graphics node item.
  After creating a new node, it must be explicitly added to the model by addComponent(AbstractModelComponent).
  
  Parameters:
  
  text - displayed text. the text is used as unique identifier for the graphics node in the diagram if possible.
  
  Returns:
  
  graphics node
  
  Since:
  
  Omix 2.0
- createGraphicsNode
  
  GraphicsNode createGraphicsNode()
  
  Create a new graphics node item with a generated random identifier.
  After creating a new node, it must be explicitly added to the model by addComponent(AbstractModelComponent).
  
  Returns:
  
  graphics node
  
  Since:
  
  Omix 2.0
- createLink
  
  Link createLink(String description)
  
  Create a new link.
  After creating a new link, it must be explicitly added to the model by addComponent(AbstractModelComponent).
  
  Parameters:
  
  text - displayed text. the text is used as unique identifier for the link in the diagram if possible.
  
  Returns:
  
  link
  
  Since:
  
  Omix 2.0
- createLink
  
  Link createLink(Pathway pathway) throws IllegalComponentException
  
  Create a new link to given pathway.
  After creating a new link, it must be explicitly added to the model by addComponent(AbstractModelComponent).
  
  Returns:
  
  link
  
  Throws:
  
  IllegalComponentException
  
  Since:
  
  Omix 2.0
- createLink
  
  Link createLink(File file, String description)
  
  Create a new link to given model file.
  After creating a new link, it must be explicitly added to the model by addComponent(AbstractModelComponent).
  
  Returns:
  
  link
  
  Since:
  
  Omix 2.0
- createLink
  
  default Link createLink(File file)
- createLink
  
  Link createLink(Diagram diagram, String description) throws IllegalComponentException
  
  Create a new link to given model file.
  After creating a new link, it must be explicitly added to the model by addComponent(AbstractModelComponent).
  
  Returns:
  
  link
  
  Throws:
  
  IllegalComponentException
  
  Since:
  
  Omix 2.0
- createLink
  
  default Link createLink(Diagram diagram) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createGraphicsEdge
  
  GraphicsEdge createGraphicsEdge(AbstractNode src, AbstractNode dst) throws IllegalComponentException
  
  Creates a new graphics edge between a source and destination node.
  
  Parameters:
  
  src - source node
  
  dst - destination node
  
  Returns:
  
  graphics edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Model.
  
  Since:
  
  Omix 2.0
- createFluxEdge
  
  LinkEdge createFluxEdge(Link src, AbstractBioNode dst, double coefficient) throws IllegalComponentException
  
  Creates a new link edge with flux edge appearance between a source link and destination node.
  
  Parameters:
  
  src - source link
  
  dst - destination node
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Model.
  
  Since:
  
  Omix 2.0
- createFluxEdge
  
  default LinkEdge createFluxEdge(Link src, AbstractBioNode dst) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createFluxEdge
  
  LinkEdge createFluxEdge(AbstractBioNode src, Link dst, double coefficient) throws IllegalComponentException
  
  Creates a new link edge with flux edge appearance between a source node and destination link.
  
  Parameters:
  
  src - source node
  
  dst - destination link
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Model.
  
  Since:
  
  Omix 2.0
- createFluxEdge
  
  default LinkEdge createFluxEdge(AbstractBioNode src, Link dst) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createCofactorEdge
  
  LinkEdge createCofactorEdge(Link src, AbstractBioNode dst, double coefficient) throws IllegalComponentException
  
  Creates a new link edge with flux edge appearance between a source link and destination node.
  
  Parameters:
  
  src - source link
  
  dst - destination node
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Model.
  
  Since:
  
  Omix 2.0
- createCofactorEdge
  
  default LinkEdge createCofactorEdge(Link src, AbstractBioNode dst) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createCofactorEdge
  
  LinkEdge createCofactorEdge(AbstractBioNode src, Link dst, double coefficient) throws IllegalComponentException
  
  Creates a new link edge with flux edge appearance between a source node and destination link.
  
  Parameters:
  
  src - source node
  
  dst - destination link
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Model.
  
  Since:
  
  Omix 2.0
- createCofactorEdge
  
  default LinkEdge createCofactorEdge(AbstractBioNode src, Link dst) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createEffectorEdge
  
  LinkEdge createEffectorEdge(Link src, Reaction dst, double effect) throws IllegalComponentException
  
  Creates a new link edge with effector edge appearance between a source link and destination node.
  
  Parameters:
  
  src - source link
  
  dst - destination node
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Model.
  
  Since:
  
  Omix 2.0
- createEffectorEdge
  
  LinkEdge createEffectorEdge(Metabolite src, Link dst, double effect) throws IllegalComponentException
  
  Creates a new link edge with effector edge appearance between a source node and destination link.
  
  Parameters:
  
  src - source node
  
  dst - destination link
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Model.
  
  Since:
  
  Omix 2.0
- createGraphicsEdge
  
  LinkEdge createGraphicsEdge(Link src, AbstractNode dst) throws IllegalComponentException
  
  Creates a new link edge between a source link and destination node.
  
  Parameters:
  
  src - source link
  
  dst - destination node
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Model.
  
  Since:
  
  Omix 2.0
- createGraphicsEdge
  
  LinkEdge createGraphicsEdge(AbstractNode src, Link dst) throws IllegalComponentException
  
  Creates a new link edge between a source node and destination link.
  
  Parameters:
  
  src - source node
  
  dst - destination link
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Model.
  
  Since:
  
  Omix 2.0
- createDiagram
  
  Diagram createDiagram(String identifier) throws ComponentExistsException
  
  Creates a new diagram.
  
  Parameters:
  
  identifier -
  
  Returns:
  
  new diagram
  
  Throws:
  
  ComponentExistsException - when identifier is already in use
  
  Since:
  
  Omix 2.0
- createDiagram
  
  Diagram createDiagram()
  
  Creates a new diagram with generic identifier.
  
  Returns:
  
  new diagram
  
  Since:
  
  Omix 2.0
- diagrams
  
  List<? extends Diagram> diagrams()
  
  Specified by:
  
  diagrams in interface Model
- getDiagram
  
  Diagram getDiagram(String identifier)
  
  Specified by:
  
  getDiagram in interface Model
- getCurrentDiagram
  
  Diagram getCurrentDiagram()
  
  Specified by:
  
  getCurrentDiagram in interface Model
- setCurrentDiagram
  
  void setCurrentDiagram(Diagram diagram) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- addComponent
  
  void addComponent(AbstractModelComponent item) throws ComponentExistsException, IllegalComponentException, IllegalStateException
  
  Created diagram items have to be inserted into the metabolic network before taking any effect.
  OVL definitions do not become part of a diagram component until the item is added to the diagram.
  After adding a Metabolite or Metabolite to the diagram, a ModelMetaboliteType is simultaneously added to the Model.
  
  Parameters:
  
  item - the new component
  
  Throws:
  
  ComponentExistsException - when another item of the same type with the same name already exists or the component has already been added.
  
  IllegalComponentException - when the added item has not been created by using the Model but, for instance, is a plugin internal implementation.
  
  IllegalStateException
- addMotifStamp
  
  void addMotifStamp(MotifStamp motifStamp) throws ComponentExistsException, IllegalComponentException, IllegalStateException
  
  Throws:
  
  ComponentExistsException
  
  IllegalComponentException
  
  IllegalStateException
- addDiagram
  
  void addDiagram(Diagram diagram) throws ComponentExistsException, IllegalComponentException, IllegalStateException
  
  Throws:
  
  ComponentExistsException
  
  IllegalComponentException
  
  IllegalStateException
- removeComponent
  
  void removeComponent(AbstractModelComponent item) throws ComponentExistsException, IllegalComponentException, IllegalStateException
  
  Throws:
  
  ComponentExistsException
  
  IllegalComponentException
  
  IllegalStateException
- removeMotifStamp
  
  void removeMotifStamp(MotifStamp motifStamp) throws ComponentExistsException, IllegalComponentException, IllegalStateException
  
  Throws:
  
  ComponentExistsException
  
  IllegalComponentException
  
  IllegalStateException
- removeDiagram
  
  void removeDiagram(Diagram diagram) throws ComponentExistsException, IllegalComponentException, IllegalStateException
  
  Throws:
  
  ComponentExistsException
  
  IllegalComponentException
  
  IllegalStateException
- metaboliteTypes
  
  List<? extends MetaboliteType> metaboliteTypes()
  
  All metabolite types being part of the model.
  
  Specified by:
  
  metaboliteTypes in interface Model
  
  Returns:
  
  unmodifiable list of etabolite types
- getMetaboliteType
  
  MetaboliteType getMetaboliteType(String name)
  
  Get a metabolite type by name.
  
  Specified by:
  
  getMetaboliteType in interface Model
  
  Parameters:
  
  name -
  
  Returns:
  
  the metabolite type if exists or null
- metaboliteTypeExists
  
  boolean metaboliteTypeExists(String name)
  
  Determines if metabolite type of certain name exists.
  
  Specified by:
  
  metaboliteTypeExists in interface Model
  
  Parameters:
  
  name -
  
  Returns:
  
  metabolite type exists?
- getIdentifier
  
  String getIdentifier()
  
  Returns the name of the model
  
  Specified by:
  
  getIdentifier in interface Model
  
  See Also:
  
  omix.plugin.network.AbstractItem#getIdentifier()
- getDocumentSettings
  
  Set<Map.Entry<String,String>> getDocumentSettings()
  
  Returns a set of all available settings of the document.
  A plugin program can read and write settings in order to realize an own document based settings management.
  
  Specified by:
  
  getDocumentSettings in interface Model
  
  Returns:
  
  unmodifiable set of settings
- getDocumentSetting
  
  String getDocumentSetting(String key)
  
  Get a setting by key.
  A plugin program can read and write settings in order to realize an own document based settings management.
  
  Specified by:
  
  getDocumentSetting in interface Model
  
  Parameters:
  
  key -
  
  Returns:
  
  value of the setting if exists. null otherwise.
- getDocumentSetting
  
  String getDocumentSetting(String key, String defaultValue)
  
  Get a setting by key.
  A plugin program can read and write settings in order to realize an own document based settings management.
  
  Specified by:
  
  getDocumentSetting in interface Model
  
  Parameters:
  
  key -
  
  defaultValue -
  
  Returns:
  
  value of the setting if exists. defaultValue otherwise.
- getActivePlugins
  
  List<String> getActivePlugins()
  
  Returns a list of all acive plugins.
  
  Specified by:
  
  getActivePlugins in interface Model
  
  Returns:
  
  active plugins
- isPluginActive
  
  boolean isPluginActive(String id)
  
  Asks if a plugin is active on the network model.
  
  Specified by:
  
  isPluginActive in interface Model
  
  Parameters:
  
  id - plugin ID
  
  Returns:
  
  plugin active
- getPublicIdentifiers
  
  Set<? extends PublicIdentifier> getPublicIdentifiers()
  
  Returns the components public identifiers
  
  Specified by:
  
  getPublicIdentifiers in interface Model
  
  Returns:
  
  set of public identifiers
  
  Since:
  
  Omix 1.9.0
- reactions
  
  List<? extends Reaction> reactions()
  
  Returns an unchangeable List of all reaction nodes.
  
  Specified by:
  
  reactions in interface Model
  
  Returns:
  
  list of reactions
- metabolites
  
  List<? extends Metabolite> metabolites()
  
  Returns an unchangeable List of all metabolite nodes.
  
  Specified by:
  
  metabolites in interface Model
  
  Returns:
  
  list of metabolites
- pathways
  
  List<? extends Pathway> pathways()
  
  Returns an unchangeable List of all pathway items.
  
  Specified by:
  
  pathways in interface Model
  
  Returns:
  
  list of pathways
- allCompartments
  
  List<? extends Compartment> allCompartments()
  
  Returns an unchangeable List of all compartment items.
  
  Specified by:
  
  allCompartments in interface Model
  
  Returns:
  
  list of compartments
- graphicsEdges
  
  List<? extends GraphicsEdge> graphicsEdges()
  
  Returns an unchangeable List of all graphics edges (connection edges).
  
  Specified by:
  
  graphicsEdges in interface Model
  
  Returns:
  
  list of graphics edges
  
  Since:
  
  Omix 1.8.0
- linkEdges
  
  List<? extends LinkEdge> linkEdges()
  
  Returns an unchangeable List of all link edges.
  
  Specified by:
  
  linkEdges in interface Model
  
  Returns:
  
  list of link edges
  
  Since:
  
  Omix 2.0.0
- graphicsNodes
  
  List<? extends GraphicsNode> graphicsNodes()
  
  Returns an unchangeable List of all graphics nodes.
  
  Specified by:
  
  graphicsNodes in interface Model
  
  Returns:
  
  list of graphics nodes
  
  Since:
  
  Omix 1.8.0
- links
  
  List<? extends Link> links()
  
  Returns an unchangeable List of all links.
  
  Specified by:
  
  links in interface Model
  
  Returns:
  
  list of links
  
  Since:
  
  Omix 2.0.0
- effectorEdges
  
  List<? extends EffectorEdge> effectorEdges()
  
  Returns an unchangeable List of all effector edges.
  
  Specified by:
  
  effectorEdges in interface Model
  
  Returns:
  
  list of effector edges
- fluxEdges
  
  List<? extends FluxEdge> fluxEdges()
  
  Returns an unchangeable List of all flux edges.
  
  Specified by:
  
  fluxEdges in interface Model
  
  Returns:
  
  list of flux edges
- graphicsBoxes
  
  List<? extends GraphicsBox> graphicsBoxes()
  
  Returns an unchangeable List of all graphical boxes.
  
  Specified by:
  
  graphicsBoxes in interface Model
  
  Returns:
  
  list of graphical boxes
  
  Since:
  
  Omix 2.0.0
- graphicsPaths
  
  List<? extends GraphicsPath> graphicsPaths()
  
  Returns an unchangeable List of all graphical paths.
  
  Specified by:
  
  graphicsPaths in interface Model
  
  Returns:
  
  list of graphical paths
  
  Since:
  
  Omix 2.0.0
- getReaction
  
  Reaction getReaction(String name)
  
  Returns the reaction nodes of the given name if available, otherwise null.
  
  Specified by:
  
  getReaction in interface Model
  
  Parameters:
  
  name - of the reaction
  
  Returns:
  
  found reaction
- 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).
  
  Specified by:
  
  getMetabolite in interface Model
  
  Parameters:
  
  name - of metabolite
  
  Returns:
  
  found metabolite
- getPathway
  
  Pathway getPathway(String name)
  
  Returns the pathway of the given name if available, otherwise null.
  
  Specified by:
  
  getPathway in interface Model
  
  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).
  
  Specified by:
  
  getTopLevelCompartment in interface Model
  
  Parameters:
  
  name - of the compartment
  
  Returns:
  
  found compartment
- getGraphicsNode
  
  GraphicsNode getGraphicsNode(String identifier)
  
  Returns the graphics node by identifier if available, otherwise null.
  
  Specified by:
  
  getGraphicsNode in interface Model
  
  Parameters:
  
  identifier - of the GraphicsNode
  
  Returns:
  
  found GraphicsNode
  
  Since:
  
  Omix 1.8.0
- getLink
  
  Link getLink(String identifier)
  
  Returns the link by identifier if available, otherwise null.
  
  Specified by:
  
  getLink in interface Model
  
  Parameters:
  
  identifier - of the link
  
  Returns:
  
  found link
  
  Since:
  
  Omix 2.0.0
- getGraphicsBox
  
  GraphicsBox getGraphicsBox(String identifier)
  
  Returns the graphics item with the given identifier if available, otherwise null.
  
  Specified by:
  
  getGraphicsBox in interface Model
  
  Parameters:
  
  identifier - of the graphics item
  
  Returns:
  
  found graphics item
- reactionExists
  
  boolean reactionExists(String name)
  
  Determines if reaction of certain name exists.
  
  Specified by:
  
  reactionExists in interface Model
  
  Parameters:
  
  name -
  
  Returns:
  
  reaction exist?
- pathwayExists
  
  boolean pathwayExists(String name)
  
  Determines if pathway of certain name exists.
  
  Specified by:
  
  pathwayExists in interface Model
  
  Parameters:
  
  name -
  
  Returns:
  
  pathway exist?
- compartmentExists
  
  boolean compartmentExists(String name)
  
  Determines if compartment of certain name exists.
  
  Specified by:
  
  compartmentExists in interface Model
  
  Parameters:
  
  name -
  
  Returns:
  
  compartment exist?
- graphicsNodeExists
  
  boolean graphicsNodeExists(String identifier)
  
  Determines if graphics node item of certain name exists.
  
  Specified by:
  
  graphicsNodeExists in interface Model
  
  Parameters:
  
  identifier -
  
  Returns:
  
  custom node exist?
  
  Since:
  
  Omix 1.8.0
- graphicsBoxExists
  
  boolean graphicsBoxExists(String identifier)
  
  Determines if graphics box of certain name exists.
  
  Specified by:
  
  graphicsBoxExists in interface Model
  
  Parameters:
  
  identifier -
  
  Returns:
  
  graphics box exist?
  
  Since:
  
  Omix 2.0.0
- graphicsPathExists
  
  boolean graphicsPathExists(String identifier)
  
  Determines if graphics path (free-form curve) of certain name exists.
  
  Specified by:
  
  graphicsPathExists in interface Model
  
  Parameters:
  
  identifier -
  
  Returns:
  
  graphics path exist?
  
  Since:
  
  Omix 2.0.0
- addChangeListener
  
  @OVLInaccessible void addChangeListener(ModelChangeListener listener)
  
  Adds a NetworkChangeListener which is triggered when the composition of the network changes.
  
  Specified by:
  
  addChangeListener in interface Model
  
  Parameters:
  
  listener - to be added
- removeChangeListener
  
  @OVLInaccessible void removeChangeListener(ModelChangeListener listener)
  
  Removes the listener which is therefore no longer triggered.
  
  Specified by:
  
  removeChangeListener in interface Model
  
  Parameters:
  
  listener - to be removed
- addPublicIdentifier
  
  void addPublicIdentifier(PublicIdentifier publicIdentifier) throws IllegalChangeException
  
  Adds a public identifier to the model.
  
  Parameters:
  
  publicIdentifier -
  
  Throws:
  
  IllegalChangeException
- setPublicIdentifiers
  
  void setPublicIdentifiers(Collection<? extends PublicIdentifier> publicIdentifiers) throws IllegalChangeException
  
  Set the public identifiers of the model.
  
  Parameters:
  
  publicIdentifiers -
  
  Throws:
  
  IllegalChangeException
- removePublicIdentifier
  
  void removePublicIdentifier(PublicIdentifier publicIdentifier) throws IllegalChangeException
  
  Removes the public identifier from the model.
  
  Parameters:
  
  publicIdentifier -
  
  Throws:
  
  IllegalChangeException
- setName
  
  void setName(String name) throws IllegalChangeException
  
  Changes name of the model.
  
  Parameters:
  
  name - the new name
  
  Throws:
  
  IllegalChangeException
- isChangeable
  
  boolean isChangeable()
  
  Checks if the given element can be changed.
  
  Returns:
  
  is changeable
- motifStamps
  
  List<? extends MotifStamp> motifStamps()
  
  Specified by:
  
  motifStamps in interface Model
- getMotifStamp
  
  MotifStamp getMotifStamp(String name)
  
  Specified by:
  
  getMotifStamp in interface Model
- createSeparator
  
  Separator createSeparator()
- createBezierPoint
  
  BezierPoint createBezierPoint(double x, double y)
  
  Create a bezier controlpoint.
  
  Parameters:
  
  x -
  
  y -
  
  Returns:
  
  bezier controlpoint.
- createSplinePoint
  
  default SplinePoint createSplinePoint(double x, double y)
  
  Create a spline point.
  
  Parameters:
  
  x -
  
  y -
  
  Returns:
  
  spline point
- createSplinePoint
  
  SplinePoint createSplinePoint(double x, double y, Smoothness smoothness)
  
  Create a spline point with the given smoothness.
  
  Parameters:
  
  x -
  
  y -
  
  smoothness -
  
  Returns:
  
  spline point
- createArc
  
  default Arc createArc(double x, double y, double radius, double startAngle, double length)
  
  Create an arc with the given center, radius, start angle and length.
  
  Parameters:
  
  x -
  
  y -
  
  radius - (must not be 0)
  
  startAngle - in degrees
  
  length - in degrees (must not be 0)
  
  Returns:
  
  arc
- createArc
  
  Arc createArc(double x, double y, double radiusX, double radiusY, double startAngle, double length)
  
  Create an arc with the given center, radiusX, radiusY, start angle and length.
  
  Parameters:
  
  x -
  
  y -
  
  radiusX - (must not be 0)
  
  radiusY - (must not be 0)
  
  startAngle - in degrees
  
  length - in degrees (must not be 0)
  
  Returns:
  
  arc
- getAccessories
  
  List<? extends Accessory> getAccessories()
  
  Returns all accessories of the submitted network object defined in the document embedded OVL script.
  
  Specified by:
  
  getAccessories in interface Model
  
  Returns:
  
  unmodifiable list of accessories
- getAccessories
  
  List<? extends Accessory> getAccessories(String namespace)
  
  Returns all accessories of the submitted network object defined in the namespace.
  
  Specified by:
  
  getAccessories in interface Model
  
  Parameters:
  
  namespace -
  
  Returns:
  
  unmodifiable list of accessories
- getAllAccessories
  
  List<? extends Accessory> getAllAccessories()
  
  Returns all accessories of the submitted network object defined in the document embedded OVL script and all namespaces.
  
  Specified by:
  
  getAllAccessories in interface Model
  
  Returns:
  
  unmodifiable list of accessories
- getAccessory
  
  Accessory getAccessory(String namespace, String accessoryName) throws IllegalAccessException, NoSuchFieldException
  
  Returns the accessory of the submitted network object defined in the namespace.
  
  Specified by:
  
  getAccessory in interface Model
  
  Parameters:
  
  namespace -
  
  accessoryName -
  
  Returns:
  
  accessory
  
  Throws:
  
  IllegalAccessException - if accessory is protected
  
  NoSuchFieldException - if accessory does not exist
- getAccessory
  
  default <T extends Accessory> T getAccessory(String namespace, String accessoryName, Class<T> accessoryItemClass) throws IllegalAccessException, NoSuchFieldException
  
  Throws:
  
  IllegalAccessException
  
  NoSuchFieldException
- getAccessory
  
  Accessory getAccessory(String accessoryName) throws IllegalAccessException, NoSuchFieldException
  
  Returns the accessory of the submitted network object defined in the document embedded OVL script.
  
  Specified by:
  
  getAccessory in interface Model
  
  Parameters:
  
  accessoryName -
  
  Returns:
  
  accessory
  
  Throws:
  
  IllegalAccessException - if accessory is protected
  
  NoSuchFieldException - if accessory does not exist
- getAccessory
  
  default <T extends Accessory> T getAccessory(String accessoryName, Class<T> accessoryItemClass) throws IllegalAccessException, NoSuchFieldException
  
  Throws:
  
  IllegalAccessException
  
  NoSuchFieldException
- getField
  
  Field getField(String fieldName) throws IllegalAccessException, NoSuchFieldException
  
  Returns the field of the submitted network object defined in the document embedded OVL script.
  
  Specified by:
  
  getField in interface Model
  
  Parameters:
  
  fieldName -
  
  Returns:
  
  reference object representing the field
  
  Throws:
  
  IllegalAccessException - if field is protected
  
  NoSuchFieldException - if field does not exist
- getField
  
  Field getField(String namespace, String fieldName) throws IllegalAccessException, NoSuchFieldException
  
  Returns the field of the submitted network object defined in the give namespace.
  
  Specified by:
  
  getField in interface Model
  
  Parameters:
  
  namespace -
  
  fieldName -
  
  Returns:
  
  reference object representing the field
  
  Throws:
  
  IllegalAccessException - if field is protected
  
  NoSuchFieldException - if field does not exist
- getMethod
  
  Method getMethod(String methodName, Class<?>... params) throws IllegalAccessException, NoSuchMethodException
  
  Returns the method of the submitted network object defined in the document embedded OVL script.
  
  Parameters:
  
  methodName -
  
  params - list of classes of the method parameters
  
  Returns:
  
  reference object representing the method
  
  Throws:
  
  IllegalAccessException - if method is protected
  
  NoSuchMethodException - if method does not exist
  
  See Also:
  
  #getMethod(String, Object, String, Class...)
- getMethod
  
  Method getMethod(String namespace, String methodName, Class<?>... params) throws IllegalAccessException, NoSuchMethodException
  Returns the method of the submitted network object defined in the given namespace.
  Example code:
  OVL:
  extend Model{ void myMethod(String strg, int i){...} }
  can be called by:
  
  getMethod("myMethod", String.class, int.class) or
  
  getMethod("myMethod(java.lang.String,int)")
  Parameters:
  
  namespace -
  
  methodName -
  
  params - list of classes of the method parameters
  
  Returns:
  
  reference object representing the method
  
  Throws:
  
  IllegalAccessException - if method is protected
  
  NoSuchMethodException - if method does not exist
- getMethod
  
  default Method getMethod(OVLMethodDefinition methodDefinition) throws IllegalAccessException, NoSuchMethodException
  
  Returns the method of the submitted network object defined in the document embedded OVL script.
  
  Parameters:
  
  methodDefinition - the method definition object from the OVLProgram
  
  Returns:
  
  reference object representing the method
  
  Throws:
  
  IllegalAccessException - if method is protected
  
  NoSuchMethodException - if method does not exist
- attach
  
  void attach(OVLEnvironment environment) throws IllegalArgumentException
  
  Attaches this writable model to the OVL environment. Thus, all changes performed by this writable model are managed by the OVL engine.
  
  Parameters:
  
  environment -
  
  Throws:
  
  IllegalArgumentException - if environment has wrong type
  
  See Also:
  
  detach(OVLEnvironment)
- detach
  
  void detach(OVLEnvironment environment) throws IllegalArgumentException
  
  Detaches this writable model from the OVL environment.
  
  Parameters:
  
  environment -
  
  Throws:
  
  IllegalArgumentException - if environment has wrong type
  
  See Also:
  
  attach(OVLEnvironment)
- getNamespaces
  
  List<String> getNamespaces()
  
  Returns a list of all available namespaces.
  
  Returns:
  
  list of namespaces
- beginUndoMacro
  
  UndoMacro beginUndoMacro(Supplier<String> description) throws IllegalAccessException
  
  Throws:
  
  IllegalAccessException
- performAction
  
  void performAction(UndoableAction change) throws IllegalAccessException
  
  Throws:
  
  IllegalAccessException
- toWritable
  
  default WritableInterface toWritable(ReadOnlyInterface type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default AbstractModelComponent toWritable(AbstractModelComponent type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default AbstractVisibleComponent toWritable(AbstractVisibleComponent type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default AbstractNode toWritable(AbstractNode type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default AbstractBioNode toWritable(AbstractBioNode type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default AbstractEdge toWritable(AbstractEdge type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default Accessory toWritable(Accessory type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default Array<?> toWritable(Array<?> type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default DataAnnotation toWritable(DataAnnotation type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default SimpleValueField toWritable(SimpleValueField type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default AbstractSideBox toWritable(AbstractSideBox type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default Trigger toWritable(Trigger type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default IntegerTrigger toWritable(IntegerTrigger type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default DoubleTrigger toWritable(DoubleTrigger type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  DoublePlayer toWritable(DoublePlayer type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  DoubleSlider toWritable(DoubleSlider type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  DoubleSpinBox toWritable(DoubleSpinBox type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  Player toWritable(Player type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  Slider toWritable(Slider type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  SpinBox toWritable(SpinBox type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  CheckButton toWritable(CheckButton type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  PushButton toWritable(PushButton type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  TextField toWritable(TextField type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  DoubleField toWritable(DoubleField type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  IntegerField toWritable(IntegerField type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  ImageField toWritable(ImageField type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  ItemGroup toWritable(ItemGroup type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  ChartSideBox toWritable(ChartSideBox type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  SideBox toWritable(SideBox type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  AnnotationArray<?> toWritable(AnnotationArray<?> type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  TriggerArray<?> toWritable(TriggerArray<?> type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  Diagram toWritable(Diagram type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  MetaboliteType toWritable(MetaboliteType type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  Metabolite toWritable(Metabolite metabolite) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  Reaction toWritable(Reaction reaction) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  GraphicsNode toWritable(GraphicsNode node) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  Link toWritable(Link node) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  GraphicsBox toWritable(GraphicsBox item) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  GraphicsEdge toWritable(GraphicsEdge edge) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  LinkEdge toWritable(LinkEdge edge) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  FluxEdge toWritable(FluxEdge edge) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  EffectorEdge toWritable(EffectorEdge edge) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  Pathway toWritable(Pathway pathway) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  Compartment toWritable(Compartment compartment) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  OVLObject toWritable(OVLObject ovlObject) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default Model toWritable(Model model) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- styleSheet
  
  StyleSheet styleSheet()
  
  Specified by:
  
  styleSheet in interface Model
- setCapabilities
  
  default void setCapabilities(ModelCapability... capabilities) throws IllegalAccessException
  
  Throws:
  
  IllegalAccessException
- setCapabilities
  
  void setCapabilities(ModelCapabilities capabilities) throws IllegalAccessException
  
  Throws:
  
  IllegalAccessException
- clearCapabilities
  
  default void clearCapabilities(ModelCapability... capabilities) throws IllegalAccessException
  
  Throws:
  
  IllegalAccessException
- clearCapabilities
  
  void clearCapabilities(ModelCapabilities capabilities) throws IllegalAccessException
  
  Throws:
  
  IllegalAccessException
- capabilities
  
  ModelCapabilities capabilities()

Interface Model

Method Summary

Methods inherited from interface omix.plugin.model.Model

Method Details