All Superinterfaces:: AbstractModelComponent, AbstractModelComponent, Diagram, ReadOnlyInterface, WritableInterface

public interface Diagram
extends AbstractModelComponent, Diagram

Nested Class Summary

Nested Classes

Modifier and Type Interface Description

static class Diagram.NewNodePosition

Method Summary

Modifier and Type	Method	Description
`void`	`addItem(AbstractItem 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 `MetaboliteItem` or `Metabolite` to the diagram, a `MetaboliteType` is simultaneously added to the `Model`.
`void`	`addItem(Guideline item)`
`void`	`addItem(PatternItem item)`
`void`	`changePositionOfNodes(List<Diagram.NewNodePosition> newPositions)`	Set the positions of the items as specified in the NewNodePosition objects.
`boolean`	`clippingExists(String identifier)`
`List<? extends Clipping>`	`clippings()`
`List<? extends Comment>`	`comments()`
`List<? extends CompartmentItem>`	`compartments()`	Returns an unchangeable `List` of all compartment items.
`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.
`default 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.
`default BezierPoint`	`createBezierPoint(double x, double y)`	Create a bezier controlpoint.
`Clipping`	`createClipping(String identifier)`
`FluxEdgeItem`	`createCofactorEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, double coefficient, List<? extends AbstractCurvePoint> points)`	Creates a new cofactor edge between a source and destination node.
`default FluxEdgeItem`	`createCofactorEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, double coefficient, AbstractCurvePoint... points)`
`default FluxEdgeItem`	`createCofactorEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, List<? extends AbstractCurvePoint> points)`
`default FluxEdgeItem`	`createCofactorEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, AbstractCurvePoint... points)`
`LinkEdgeItem`	`createCofactorEdge(AbstractBioNodeItem src, LinkItem dst, double coefficient, List<? extends AbstractCurvePoint> points)`	Creates a new link edge with flux edge appearance between a source node and a link.
`default LinkEdgeItem`	`createCofactorEdge(AbstractBioNodeItem src, LinkItem dst, double coefficient, AbstractCurvePoint... points)`	Creates a new link edge with flux edge appearance between a source node and a link.
`default LinkEdgeItem`	`createCofactorEdge(AbstractBioNodeItem src, LinkItem dst, List<? extends AbstractCurvePoint> points)`	Creates a new link edge with flux edge appearance between a source node and a link.
`default LinkEdgeItem`	`createCofactorEdge(AbstractBioNodeItem src, LinkItem dst, AbstractCurvePoint... points)`	Creates a new link edge with flux edge appearance between a source node and a link.
`LinkEdgeItem`	`createCofactorEdge(LinkItem src, AbstractBioNodeItem dst, double coefficient, List<? extends AbstractCurvePoint> points)`	Creates a new link edge with flux edge appearance between a link and destination node.
`default LinkEdgeItem`	`createCofactorEdge(LinkItem src, AbstractBioNodeItem dst, double coefficient, AbstractCurvePoint... points)`	Creates a new link edge with flux edge appearance between a link and destination node.
`default LinkEdgeItem`	`createCofactorEdge(LinkItem src, AbstractBioNodeItem dst, List<? extends AbstractCurvePoint> points)`	Creates a new link edge with flux edge appearance between a link and destination node.
`default LinkEdgeItem`	`createCofactorEdge(LinkItem src, AbstractBioNodeItem dst, AbstractCurvePoint... points)`	Creates a new link edge with flux edge appearance between a link and destination node.
`CompartmentItem`	`createCompartment(String name)`	Create a new compartment item. After creating a new compartment, it must be explicitly added to the model by `addItem(AbstractItem)`.
`CompartmentItem`	`createCompartment(String namePlainText, String nameRichText)`	Create a new compartment item. After creating a new compartment, it must be explicitly added to the model by `addItem(AbstractItem)`.
`CompartmentItem`	`createCompartment(String namePlainText, String nameRichText, CompartmentItem outside)`	Create a new compartment item inside another compartment. After creating a new compartment, it must be explicitly added to the model by `addItem(AbstractItem)`.
`CompartmentItem`	`createCompartment(String name, CompartmentItem outside)`	Create a new compartment item inside another compartment. After creating a new compartment, it must be explicitly added to the model by `addItem(AbstractItem)`.
`CompartmentItem`	`createCompartmentItem(Compartment component)`
`CompartmentItem`	`createCompartmentItem(Compartment compartment, CompartmentItem outside)`
`Comment`	`createDiagramComment()`
`LinkEdgeItem`	`createEffectorEdge(LinkItem src, ReactionItem dst, double effect, List<? extends AbstractCurvePoint> points)`	Creates a new link edge with effector edge appearance between a link and destination node.
`default LinkEdgeItem`	`createEffectorEdge(LinkItem src, ReactionItem dst, double effect, AbstractCurvePoint... points)`	Creates a new link edge with effector edge appearance between a link and destination node.
`LinkEdgeItem`	`createEffectorEdge(MetaboliteItem src, LinkItem dst, double effect, List<? extends AbstractCurvePoint> points)`	Creates a new link edge with effector edge appearance between a source node and a link.
`default LinkEdgeItem`	`createEffectorEdge(MetaboliteItem src, LinkItem dst, double effect, AbstractCurvePoint... points)`	Creates a new link edge with effector edge appearance between a source node and a link.
`EffectorEdgeItem`	`createEffectorEdge(MetaboliteItem src, ReactionItem dst, double effect, List<? extends AbstractCurvePoint> points)`	Creates a new effector edge between a source and destination node with the given effect.
`default EffectorEdgeItem`	`createEffectorEdge(MetaboliteItem src, ReactionItem dst, double effect, AbstractCurvePoint... points)`	Creates a new effector edge between a source and destination node with the given effect.
`EffectorEdgeItem`	`createEffectorEdgeItem(EffectorEdge edge, MetaboliteItem src, ReactionItem dst, List<? extends AbstractCurvePoint> points)`
`default EffectorEdgeItem`	`createEffectorEdgeItem(EffectorEdge edge, MetaboliteItem src, ReactionItem dst, AbstractCurvePoint... points)`
`FluxEdgeItem`	`createFluxEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, double coefficient, List<? extends AbstractCurvePoint> points)`	Creates a new flux edge between a source and destination node.
`default FluxEdgeItem`	`createFluxEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, double coefficient, AbstractCurvePoint... points)`	Creates a new flux edge between a source and destination node.
`default FluxEdgeItem`	`createFluxEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, List<? extends AbstractCurvePoint> points)`
`default FluxEdgeItem`	`createFluxEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, AbstractCurvePoint... points)`	Creates a new flux edge between a source and destination node.
`LinkEdgeItem`	`createFluxEdge(AbstractBioNodeItem src, LinkItem dst, double coefficient, List<? extends AbstractCurvePoint> points)`	Creates a new link edge with flux edge appearance between a source node and a link.
`default LinkEdgeItem`	`createFluxEdge(AbstractBioNodeItem src, LinkItem dst, double coefficient, AbstractCurvePoint... points)`	Creates a new link edge with flux edge appearance between a source node and a link.
`default LinkEdgeItem`	`createFluxEdge(AbstractBioNodeItem src, LinkItem dst, List<? extends AbstractCurvePoint> points)`	Creates a new link edge with flux edge appearance between a source node and a link.
`default LinkEdgeItem`	`createFluxEdge(AbstractBioNodeItem src, LinkItem dst, AbstractCurvePoint... points)`	Creates a new link edge with flux edge appearance between a source node and a link.
`LinkEdgeItem`	`createFluxEdge(LinkItem src, AbstractBioNodeItem dst, double coefficient, List<? extends AbstractCurvePoint> points)`	Creates a new link edge with flux edge appearance between a link and destination node.
`default LinkEdgeItem`	`createFluxEdge(LinkItem src, AbstractBioNodeItem dst, double coefficient, AbstractCurvePoint... points)`	Creates a new link edge with flux edge appearance between a link and destination node.
`default LinkEdgeItem`	`createFluxEdge(LinkItem src, AbstractBioNodeItem dst, List<? extends AbstractCurvePoint> points)`	Creates a new link edge with flux edge appearance between a link and destination node.
`default LinkEdgeItem`	`createFluxEdge(LinkItem src, AbstractBioNodeItem dst, AbstractCurvePoint... points)`	Creates a new link edge with flux edge appearance between a link and destination node.
`FluxEdgeItem`	`createFluxEdgeItem(FluxEdge edge, AbstractBioNodeItem src, AbstractBioNodeItem dst, List<? extends AbstractCurvePoint> points)`
`default FluxEdgeItem`	`createFluxEdgeItem(FluxEdge edge, AbstractBioNodeItem src, AbstractBioNodeItem dst, AbstractCurvePoint... points)`
`GraphicsBoxItem`	`createGraphicsBox()`	Create a new graphics box item with a generated random identifier. After creating a new box, it must be explicitly added to the model by `addItem(AbstractItem)`.
`GraphicsEdgeItem`	`createGraphicsEdge(AbstractNodeItem src, AbstractNodeItem dst, List<? extends AbstractCurvePoint> points)`	Creates a new graphics edge between a source and destination node.
`default GraphicsEdgeItem`	`createGraphicsEdge(AbstractNodeItem src, AbstractNodeItem dst, AbstractCurvePoint... points)`	Creates a new graphics edge between a source and destination node.
`LinkEdgeItem`	`createGraphicsEdge(AbstractNodeItem src, LinkItem dst, List<? extends AbstractCurvePoint> points)`	Creates a new link edge between a source node and a link.
`default LinkEdgeItem`	`createGraphicsEdge(AbstractNodeItem src, LinkItem dst, AbstractCurvePoint... points)`	Creates a new link edge between a source node and a link.
`LinkEdgeItem`	`createGraphicsEdge(LinkItem src, AbstractNodeItem dst, List<? extends AbstractCurvePoint> points)`	Creates a new link edge between a link and destination node.
`default LinkEdgeItem`	`createGraphicsEdge(LinkItem src, AbstractNodeItem dst, AbstractCurvePoint... points)`	Creates a new link edge between a link and destination node.
`GraphicsEdgeItem`	`createGraphicsEdgeItem(GraphicsEdge edge, AbstractNodeItem src, AbstractNodeItem dst, List<? extends AbstractCurvePoint> points)`
`default GraphicsEdgeItem`	`createGraphicsEdgeItem(GraphicsEdge edge, AbstractNodeItem src, AbstractNodeItem dst, AbstractCurvePoint... points)`
`GraphicsNodeItem`	`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 `addItem(AbstractItem)`.
`GraphicsNodeItem`	`createGraphicsNode(String text)`	Create a new graphics node item. After creating a new node, it must be explicitly added to the model by `addItem(AbstractItem)`.
`GraphicsNodeItem`	`createGraphicsNodeItem(GraphicsNode component)`
`GraphicsPathItem`	`createGraphicsPath(List<? extends AbstractCurvePoint> points)`
`default GraphicsPathItem`	`createGraphicsPath(AbstractCurvePoint... points)`	Create a new graphics path (free-form curve) item with a generated random identifier. After creating a new path, it must be explicitly added to the model by `addItem(AbstractItem)`.
`Group`	`createGroup(List<? extends Groupable> items)`	Groups submitted items to an item group.
`default Group`	`createGroup(Groupable item1, Groupable... items)`	Groups submitted items to an item group.
`Guideline`	`createGuideline(double x, double y, double angle)`
`default Guideline`	`createHorizontalGuideline(double y)`
`Comment`	`createItemComment(AbstractNodeItem item)`
`Comment`	`createItemComment(CompartmentItem item)`
`Comment`	`createItemComment(GraphicsBoxItem item)`
`Comment`	`createItemComment(GraphicsPathItem item)`
`Comment`	`createItemComment(PathwayItem item)`
`default LinkItem`	`createLink(File file)`
`LinkItem`	`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)`.
`LinkItem`	`createLink(String description)`	Create a new link item. After creating a new item, it must be explicitly added to the model by `addItem(AbstractItem)`.
`default LinkItem`	`createLink(Diagram diagram)`
`LinkItem`	`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)`.
`LinkItem`	`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)`.
`LinkEdgeItem`	`createLinkEdgeItem(LinkEdge edge, AbstractNodeItem src, LinkItem dst, List<? extends AbstractCurvePoint> points)`
`default LinkEdgeItem`	`createLinkEdgeItem(LinkEdge edge, AbstractNodeItem src, LinkItem dst, AbstractCurvePoint... points)`
`LinkEdgeItem`	`createLinkEdgeItem(LinkEdge edge, LinkItem src, AbstractNodeItem dst, List<? extends AbstractCurvePoint> points)`
`default LinkEdgeItem`	`createLinkEdgeItem(LinkEdge edge, LinkItem src, AbstractNodeItem dst, AbstractCurvePoint... points)`
`LinkItem`	`createLinkItem(Link component)`
`MetaboliteItem`	`createMetabolite(String name)`	Creates a new metabolite with the given unique name and returns a visible instance of the metabolite (`MetaboliteItem`).
`MetaboliteItem`	`createMetabolite(String namePlainText, String nameRichText)`	Creates a new metabolite with the given unique name and returns a visible instance of the metabolite (`MetaboliteItem`).
`MetaboliteItem`	`createMetabolite(String namePlainText, String nameRichText, CompartmentItem compartment)`	Creates a new metabolite with the given unique name lying in the given compartment.
`MetaboliteItem`	`createMetabolite(String namePlainText, String nameRichText, Compartment compartment)`
`MetaboliteItem`	`createMetabolite(String name, CompartmentItem compartment)`	Creates a new metabolite with the given unique name lying in the given compartment.
`MetaboliteItem`	`createMetabolite(String name, Compartment compartment)`
`MetaboliteItem`	`createMetaboliteItem(Metabolite metabolite)`	Creates another visible instance of the metabolite in the diagram (a duplicate node).
`MetaboliteItem`	`createMetaboliteItem(Metabolite metabolite, CompartmentItem compartment)`
`MetaboliteItem`	`createMetaboliteItem(MetaboliteType metaboliteType, CompartmentItem compartment)`
`MetaboliteItem`	`createMetaboliteItem(MetaboliteType metaboliteType, Compartment compartment)`
`PathwayItem`	`createPathway(String name)`	Create a new pathway item.
`PathwayItem`	`createPathway(String namePlainText, String nameRichText)`	Create a new pathway item.
`PathwayItem`	`createPathwayItem(Pathway component)`
`PatternBranch`	`createPatternBranch(double x, double y)`
`PatternPath`	`createPatternPath(PatternBranch startPoint, PatternBranch endPoint, List<? extends AbstractCurvePoint> points)`
`default PatternPath`	`createPatternPath(PatternBranch startPoint, PatternBranch endPoint, AbstractCurvePoint... points)`
`ReactionItem`	`createReaction(String name)`	Create a new reaction item.
`ReactionItem`	`createReaction(String name, String nameFormat)`	Create a new reaction item.
`ReactionItem`	`createReaction(String namePlainText, String nameRichText, PathwayItem 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 `addItem(omix.plugin.diagram.writable.AbstractItem)`.
`ReactionItem`	`createReaction(String name, PathwayItem 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 `addItem(omix.plugin.diagram.writable.AbstractItem)`.
`ReactionItem`	`createReactionItem(Reaction component)`
`ReactionItem`	`createReactionItem(Reaction component, PathwayItem pathway)`
`default Separator`	`createSeparator()`
`default SplinePoint`	`createSplinePoint(double x, double y)`	Create a spline point.
`default SplinePoint`	`createSplinePoint(double x, double y, Smoothness smoothness)`	Create a spline point with the given smoothness.
`default Guideline`	`createVerticalGuideline(double x)`
`Clipping`	`defaultClipping()`
`List<? extends EffectorEdgeItem>`	`effectorEdges()`	Returns an unchangeable `List` of all effector edges.
`List<? extends FluxEdgeItem>`	`fluxEdges()`	Returns an unchangeable `List` of all flux edges.
`default AccessoryItem`	`getAccessoryItem(String accessoryName)`	Returns the accessory item of the submitted name defined in the namespace.
`default <T extends AccessoryItem> T`	`getAccessoryItem(String accessoryName, Class<T> accessoryItemClass)`
`AccessoryItem`	`getAccessoryItem(String namespace, String accessoryName)`	Returns the accessory item of the submitted name defined in the namespace.
`default <T extends AccessoryItem> T`	`getAccessoryItem(String namespace, String accessoryName, Class<T> accessoryItemClass)`
`List<? extends AccessoryItem>`	`getAccessoryItems()`	Returns all accessory items defined in the document embedded OVL script.
`List<? extends AccessoryItem>`	`getAccessoryItems(String namespace)`	Returns all accessory items defined in the given namespace.
`List<? extends AccessoryItem>`	`getAllAccessoryItems()`	Returns all accessory items defined in the document embedded OVL script and all namespaces.
`Clipping`	`getClipping(String identifier)`
`Comment`	`getComment(String identifier)`
`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.
`List<? extends GraphicsBoxItem>`	`getGraphicsBoxItems(String name)`
`List<? extends GraphicsNodeItem>`	`getGraphicsNodeItems(String name)`
`List<? extends GraphicsPathItem>`	`getGraphicsPathItems(String name)`
`List<? extends LinkItem>`	`getLinkItems(String name)`
`List<? extends MetaboliteItem>`	`getMetaboliteItems(CompartmentItem compartment, String name)`
`List<? extends PathwayItem>`	`getPathwayItems(String name)`
`List<? extends AbstractItem>`	`getSelectedItems()`
`Thumbnails`	`getThumbnails()`	Returns thumbnails embedded in the model document file.
`List<? extends CompartmentItem>`	`getTopLevelCompartmentItems(String name)`
`List<? extends GraphicsBoxItem>`	`graphicsBoxes()`	Returns an unchangeable `List` of all graphical boxes.
`List<? extends GraphicsEdgeItem>`	`graphicsEdges()`	Returns an unchangeable `List` of all graphics edges (connection edges).
`List<? extends GraphicsNodeItem>`	`graphicsNodes()`	Returns an unchangeable `List` of all graphics nodes.
`List<? extends GraphicsPathItem>`	`graphicsPaths()`	Returns an unchangeable `List` of all graphical paths.
`List<? extends Group>`	`groups()`
`List<? extends Guideline>`	`guidelines()`
`boolean`	`isChangeable()`	Checks if the given element can be changed.
`List<? extends LinkEdgeItem>`	`linkEdges()`	Returns an unchangeable `List` of all link edges.
`List<? extends LinkItem>`	`links()`	Returns an unchangeable `List` of all links.
`List<? extends MetaboliteItem>`	`metabolites()`	Returns an unchangeable `List` of all metabolite nodes.
`Model`	`model()`	Reference to the model instance.
`List<? extends PathwayItem>`	`pathways()`	Returns an unchangeable `List` of all pathway items.
`List<? extends PatternBranch>`	`patternBranches()`
`List<? extends PatternPath>`	`patternPaths()`
`List<? extends ReactionItem>`	`reactions()`	Returns an unchangeable `List` of all reaction nodes.
`void`	`removeItem(AbstractItem item)`
`void`	`removeItem(Guideline item)`
`void`	`removeItem(PatternItem item)`
`Diagram`	`toReadOnly()`
`default AbstractBioNodeItem`	`toWritable(AbstractBioNodeItem type)`
`default AbstractEdgeItem`	`toWritable(AbstractEdgeItem type)`
`default AbstractItem`	`toWritable(AbstractItem type)`
`default AbstractModelItem`	`toWritable(AbstractModelItem type)`
`default AbstractNodeItem`	`toWritable(AbstractNodeItem type)`
`default AccessoryItem`	`toWritable(AccessoryItem type)`
`default AbstractSideBoxItem`	`toWritable(AbstractSideBoxItem type)`
`AnnotationArrayItem<?>`	`toWritable(AnnotationArrayItem<?> object)`
`ChartSideBoxItem`	`toWritable(ChartSideBoxItem object)`
`default DataAnnotationItem`	`toWritable(DataAnnotationItem type)`
`DoubleFieldItem`	`toWritable(DoubleFieldItem object)`
`ImageFieldItem`	`toWritable(ImageFieldItem object)`
`IntegerFieldItem`	`toWritable(IntegerFieldItem object)`
`ItemGroupItem`	`toWritable(ItemGroupItem object)`
`SideBoxItem`	`toWritable(SideBoxItem object)`
`default SimpleValueFieldItem`	`toWritable(SimpleValueFieldItem type)`
`TextFieldItem`	`toWritable(TextFieldItem object)`
`default ArrayItem<?>`	`toWritable(ArrayItem<?> type)`
`CheckButtonItem`	`toWritable(CheckButtonItem object)`
`DoublePlayerItem`	`toWritable(DoublePlayerItem object)`
`DoubleSliderItem`	`toWritable(DoubleSliderItem object)`
`DoubleSpinBoxItem`	`toWritable(DoubleSpinBoxItem object)`
`default DoubleTriggerItem`	`toWritable(DoubleTriggerItem type)`
`default IntegerTriggerItem`	`toWritable(IntegerTriggerItem type)`
`PlayerItem`	`toWritable(PlayerItem object)`
`PushButtonItem`	`toWritable(PushButtonItem object)`
`SliderItem`	`toWritable(SliderItem object)`
`SpinBoxItem`	`toWritable(SpinBoxItem object)`
`TriggerArrayItem<?>`	`toWritable(TriggerArrayItem<?> object)`
`default TriggerItem`	`toWritable(TriggerItem type)`
`Clipping`	`toWritable(Clipping clipping)`
`Comment`	`toWritable(Comment comment)`
`CompartmentItem`	`toWritable(CompartmentItem compartment)`
`EffectorEdgeItem`	`toWritable(EffectorEdgeItem edge)`
`FluxEdgeItem`	`toWritable(FluxEdgeItem edge)`
`GraphicsBoxItem`	`toWritable(GraphicsBoxItem item)`
`GraphicsEdgeItem`	`toWritable(GraphicsEdgeItem edge)`
`GraphicsNodeItem`	`toWritable(GraphicsNodeItem node)`
`Group`	`toWritable(Group group)`
`LinkEdgeItem`	`toWritable(LinkEdgeItem edge)`
`LinkItem`	`toWritable(LinkItem edge)`
`MetaboliteItem`	`toWritable(MetaboliteItem metabolite)`
`PathwayItem`	`toWritable(PathwayItem pathway)`
`ReactionItem`	`toWritable(ReactionItem reaction)`

Methods inherited from interface omix.plugin.model.AbstractModelComponent

addPropertyChangeListener, fieldExists, removePropertyChangeListener

Methods inherited from interface omix.plugin.diagram.Diagram

addChangeListener, clearHighlight, commentExists, getIdentifier, highlight, highlight, highlight, highlight, highlight, highlight, removeChangeListener

Method Details
- model
  
  Model model()
  
  Description copied from interface: AbstractModelComponent
  
  Reference to the model instance.
  
  Specified by:
  
  model in interface AbstractModelComponent
  
  Specified by:
  
  model in interface AbstractModelComponent
  
  Specified by:
  
  model in interface Diagram
  
  Returns:
  
  model
- createReaction
  
  ReactionItem createReaction(String name)
  
  Create a new reaction item.
  
  Parameters:
  
  name - unique name (identifier) for the reaction in the diagram.
  
  Returns:
  
  reaction
- createReaction
  
  ReactionItem createReaction(String name, PathwayItem 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 addItem(omix.plugin.diagram.writable.AbstractItem).
  
  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 WritableMetabolicNetwork or WritableModel but, for instance, is a plugin internal implementation of Pathway.
- createReaction
  
  ReactionItem 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
  
  ReactionItem createReaction(String namePlainText, String nameRichText, PathwayItem 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 addItem(omix.plugin.diagram.writable.AbstractItem).
  
  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 WritableMetabolicNetwork or WritableModel but, for instance, is a plugin internal implementation of Pathway.
  
  Since:
  
  Omix 1.8.1
- createReactionItem
  
  ReactionItem createReactionItem(Reaction component) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createReactionItem
  
  ReactionItem createReactionItem(Reaction component, PathwayItem pathway) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createPathway
  
  PathwayItem createPathway(String name)
  
  Create a new pathway item.
  After creating a new pathway, it must be explicitly added to the model by addItem(AbstractItem).
  
  Parameters:
  
  name - unique name (identifier) for the pathway in the diagram.
  
  Returns:
  
  pathway
- createPathway
  
  PathwayItem createPathway(String namePlainText, String nameRichText)
  
  Create a new pathway item.
  After creating a new pathway, it must be explicitly added to the model by addItem(AbstractItem).
  
  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
- createPathwayItem
  
  PathwayItem createPathwayItem(Pathway component) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createMetabolite
  
  MetaboliteItem createMetabolite(String name)
  
  Creates a new metabolite with the given unique name and returns a visible instance of the metabolite (MetaboliteItem). Internally, a new MetaboliteItem object is the visible item of a Metabolite object.
  After creating a new metabolite instance, it must be explicitly added to the model by addItem(AbstractItem).
  
  Parameters:
  
  name - unique name of the new metabolite
  
  Returns:
  
  the visible instance of the new metabolite
  
  See Also:
  
  createMetabolite(String, Compartment)
- createMetabolite
  
  MetaboliteItem createMetabolite(String namePlainText, String nameRichText)
  
  Creates a new metabolite with the given unique name and returns a visible instance of the metabolite (MetaboliteItem). Internally, a new MetaboliteItem object is the visible item of a Metabolite object.
  After creating a new metabolite instance, it must be explicitly added to the model by addItem(AbstractItem).
  
  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
  
  MetaboliteItem createMetabolite(String name, CompartmentItem 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 (MetaboliteItem).
  After creating a new metabolite instance, it must be explicitly added to the model by addItem(AbstractItem).
  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 MetaboliteType. When the returned MetaboliteItem is added to the diagram, the according MetaboliteType 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 WritableMetabolicNetwork or WritableModel but, for instance, is a plugin internal implementation of Compartment.
- createMetabolite
  
  MetaboliteItem createMetabolite(String name, Compartment compartment) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createMetabolite
  
  MetaboliteItem createMetabolite(String namePlainText, String nameRichText, CompartmentItem 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 (MetaboliteItem).
  After creating a new metabolite instance, it must be explicitly added to the model by addItem(AbstractItem).
  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 MetaboliteType. When the returned MetaboliteItem is added to the diagram, the according MetaboliteType 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 WritableMetabolicNetwork or WritableModel but, for instance, is a plugin internal implementation of Compartment.
  
  Since:
  
  Omix 1.8.1
- createMetabolite
  
  MetaboliteItem createMetabolite(String namePlainText, String nameRichText, Compartment compartment) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createMetaboliteItem
  
  MetaboliteItem createMetaboliteItem(Metabolite metabolite) throws IllegalComponentException
  
  Creates another visible instance of the metabolite in the diagram (a duplicate node). The submitted metabolite must not necessarily be already added to the diagram. After creating the new instance, it has to be added to the diagram with addItem(AbstractItem).
  
  Parameters:
  
  metabolite - the metabolite which shall own a further duplicate in the diagram.
  
  Returns:
  
  a further instance of the given metabolite
  
  Throws:
  
  IllegalComponentException - when the submitted 'metabolite' object has not been created by using the WritableMetabolicNetwork or WritableModel but, for instance, is a plugin internal implementation of Metabolite.
- createMetaboliteItem
  
  MetaboliteItem createMetaboliteItem(MetaboliteType metaboliteType, CompartmentItem compartment) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createMetaboliteItem
  
  MetaboliteItem createMetaboliteItem(Metabolite metabolite, CompartmentItem compartment) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createMetaboliteItem
  
  MetaboliteItem createMetaboliteItem(MetaboliteType metaboliteType, Compartment compartment) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createCompartment
  
  CompartmentItem createCompartment(String name)
  
  Create a new compartment item.
  After creating a new compartment, it must be explicitly added to the model by addItem(AbstractItem).
  
  Parameters:
  
  name - unique name (identifier) for the compartment in the diagram.
  
  Returns:
  
  compartment
  
  See Also:
  
  WritableModel#createCompartment(String), WritableModel#createCompartment(String, Compartment)
- createCompartment
  
  CompartmentItem createCompartment(String namePlainText, String nameRichText)
  
  Create a new compartment item.
  After creating a new compartment, it must be explicitly added to the model by addItem(AbstractItem).
  
  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:
  
  WritableModel#createCompartment(String), WritableModel#createCompartment(String, Compartment)
- createCompartment
  
  CompartmentItem createCompartment(String name, CompartmentItem 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 addItem(AbstractItem).
  
  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 WritableMetabolicNetwork or WritableModel but, for instance, is a plugin internal implementation of Compartment.
  
  See Also:
  
  WritableModel#createCompartment(String), WritableModel#createCompartment(String, Compartment)
- createCompartment
  
  CompartmentItem createCompartment(String namePlainText, String nameRichText, CompartmentItem 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 addItem(AbstractItem).
  
  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 WritableMetabolicNetwork or WritableModel but, for instance, is a plugin internal implementation of Compartment.
  
  Since:
  
  Omix 1.8.1
  
  See Also:
  
  WritableModel#createCompartment(String), WritableModel#createCompartment(String, Compartment)
- createCompartmentItem
  
  CompartmentItem createCompartmentItem(Compartment component) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createCompartmentItem
  
  CompartmentItem createCompartmentItem(Compartment compartment, CompartmentItem outside) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createFluxEdge
  
  default FluxEdgeItem createFluxEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, double coefficient, AbstractCurvePoint... points) throws IllegalComponentException
  
  Creates a new flux edge between a source and destination node. Optionally, curve points can be submitted in order to define the shape of the curve. These curve points can be created by using the CurveFactory.
  
  Parameters:
  
  src - source node
  
  dst - destination node
  
  coefficient - stoichiometric coefficient
  
  points - (optional)
  
  Returns:
  
  a flux edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using the WritableMetabolicNetwork or WritableModel but, for instance, is a plugin internal implementation.
  
  See Also:
  
  CurveFactory
- createFluxEdge
  
  default FluxEdgeItem createFluxEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, AbstractCurvePoint... points) throws IllegalComponentException
  
  Creates a new flux edge between a source and destination node. Optionally, curve points can be submitted in order to define the shape of the curve. These curve points can be created by using the CurveFactory.
  
  Parameters:
  
  src - source node
  
  dst - destination node
  
  points - (optional)
  
  Returns:
  
  a flux edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using the WritableMetabolicNetwork or WritableModel but, for instance, is a plugin internal implementation.
  
  See Also:
  
  CurveFactory
- createFluxEdgeItem
  
  default FluxEdgeItem createFluxEdgeItem(FluxEdge edge, AbstractBioNodeItem src, AbstractBioNodeItem dst, AbstractCurvePoint... points) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createEffectorEdge
  
  default EffectorEdgeItem createEffectorEdge(MetaboliteItem src, ReactionItem dst, double effect, AbstractCurvePoint... points) throws IllegalComponentException
  
  Creates a new effector edge between a source and destination node with the given effect. Optionally, curve points can be submitted in order to define the shape of the curve. These curve points can be created by using the CurveFactory.
  
  Parameters:
  
  src - source node
  
  dst - destination node
  
  effect - -1.0 = inhibition, 1.0 = activation, 0.0 = unknown effect
  
  points - (optional)
  
  Returns:
  
  effector edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using the WritableMetabolicNetwork or WritableModel but, for instance, is a plugin internal implementation.
- createEffectorEdgeItem
  
  default EffectorEdgeItem createEffectorEdgeItem(EffectorEdge edge, MetaboliteItem src, ReactionItem dst, AbstractCurvePoint... points) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createFluxEdge
  
  FluxEdgeItem createFluxEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, double coefficient, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Creates a new flux edge between a source and destination node. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - source node
  
  dst - destination node
  
  coefficient - stoichiometric coefficient
  
  points - list of points describing the edge shape
  
  Returns:
  
  a flux edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using the WritableMetabolicNetwork or WritableModel but, for instance, is a plugin internal implementation.
  
  See Also:
  
  CurveFactory
- createFluxEdge
  
  default FluxEdgeItem createFluxEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createCofactorEdge
  
  FluxEdgeItem createCofactorEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, double coefficient, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Creates a new cofactor edge between a source and destination node. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - source node
  
  dst - destination node
  
  coefficient - stoichiometric coefficient
  
  points - list of points describing the edge shape
  
  Returns:
  
  a flux edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using the WritableMetabolicNetwork or WritableModel but, for instance, is a plugin internal implementation.
  
  See Also:
  
  CurveFactory
- createCofactorEdge
  
  default FluxEdgeItem createCofactorEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createCofactorEdge
  
  default FluxEdgeItem createCofactorEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, double coefficient, AbstractCurvePoint... points) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createCofactorEdge
  
  default FluxEdgeItem createCofactorEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, AbstractCurvePoint... points) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createFluxEdgeItem
  
  FluxEdgeItem createFluxEdgeItem(FluxEdge edge, AbstractBioNodeItem src, AbstractBioNodeItem dst, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createEffectorEdge
  
  EffectorEdgeItem createEffectorEdge(MetaboliteItem src, ReactionItem dst, double effect, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Creates a new effector edge between a source and destination node with the given effect. Optionally, curve points can be submitted in order to define the shape of the curve. These curve points can be created by using the CurveFactory.
  
  Parameters:
  
  src - source node
  
  dst - destination node
  
  effect - -1.0 = inhibition, 1.0 = activation, 0.0 = unknown effect
  
  points - list of points describing the edge shape
  
  Returns:
  
  effector edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using the WritableMetabolicNetwork or WritableModel but, for instance, is a plugin internal implementation.
- createEffectorEdgeItem
  
  EffectorEdgeItem createEffectorEdgeItem(EffectorEdge edge, MetaboliteItem src, ReactionItem dst, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createGraphicsNode
  
  GraphicsNodeItem createGraphicsNode(String text)
  
  Create a new graphics node item.
  After creating a new node, it must be explicitly added to the model by addItem(AbstractItem).
  
  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 1.8.0
- createGraphicsNodeItem
  
  GraphicsNodeItem createGraphicsNodeItem(GraphicsNode component) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createGraphicsNode
  
  GraphicsNodeItem 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 addItem(AbstractItem).
  
  Returns:
  
  graphics node
  
  Since:
  
  Omix 1.8.0
- createLink
  
  LinkItem createLink(String description)
  
  Create a new link item.
  After creating a new item, it must be explicitly added to the model by addItem(AbstractItem).
  
  Parameters:
  
  text - displayed text. the text is used as unique identifier for the link in the diagram if possible.
  
  Returns:
  
  link
  
  Since:
  
  Omix 2.0.0
- createLink
  
  LinkItem 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
  
  LinkItem 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 LinkItem createLink(File file)
- createLink
  
  LinkItem 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 LinkItem createLink(Diagram diagram) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createLinkItem
  
  LinkItem createLinkItem(Link component) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createGraphicsBox
  
  GraphicsBoxItem createGraphicsBox()
  
  Create a new graphics box item with a generated random identifier.
  After creating a new box, it must be explicitly added to the model by addItem(AbstractItem).
  
  Returns:
  
  graphics box
  
  Since:
  
  Omix 2.0.0
- createGraphicsPath
  
  default GraphicsPathItem createGraphicsPath(AbstractCurvePoint... points) throws IllegalComponentException, IllegalArgumentException
  
  Create a new graphics path (free-form curve) item with a generated random identifier.
  After creating a new path, it must be explicitly added to the model by addItem(AbstractItem).
  
  Returns:
  
  graphics path
  
  Throws:
  
  IllegalComponentException
  
  IllegalArgumentException
  
  Since:
  
  Omix 2.0.0
- createGraphicsPath
  
  GraphicsPathItem createGraphicsPath(List<? extends AbstractCurvePoint> points) throws IllegalComponentException, IllegalArgumentException
  
  Throws:
  
  IllegalComponentException
  
  IllegalArgumentException
- createGuideline
  
  Guideline createGuideline(double x, double y, double angle)
- createHorizontalGuideline
  
  default Guideline createHorizontalGuideline(double y)
- createVerticalGuideline
  
  default Guideline createVerticalGuideline(double x)
- createGroup
  
  Group createGroup(List<? extends Groupable> items) throws IllegalComponentException
  
  Groups submitted items to an item group. Additionally, groups can be parts of other groups.
  All components must be positioned in the diagram. If one of the submitted components does not have a position an exception is thrown. (see: AbstractNode#hasInvalidPosition(), AbstractEdge#hasInvalidPosition() and Compartment#hasInvalidPosition()). Pathways added to an item group must not be empty (Pathway#isEmpty()).
  
  Parameters:
  
  items - a list of items to be grouped
  
  Returns:
  
  an item group
  
  Throws:
  
  IllegalComponentException - when one of the submitted 'items' has not been created by using the WritableMetabolicNetwork or WritableModel but, for instance, is a plugin internal implementation. Is additionally thrown when one of the items is not positioned in the diagram of an empty pathway shall be grouped.
- createGraphicsEdge
  
  GraphicsEdgeItem createGraphicsEdge(AbstractNodeItem src, AbstractNodeItem dst, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Creates a new graphics edge between a source and destination node. Optionally, curve points can be submitted in order to define the shape of the curve. These curve points can be created by using the CurveFactory.
  
  Parameters:
  
  src - source node
  
  dst - destination node
  
  points - list of points describing the edge shape
  
  Returns:
  
  custom edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using the WritableMetabolicNetwork or WritableModel but, for instance, is a plugin internal implementation.
  
  Since:
  
  Omix 1.8.0
- createGraphicsEdgeItem
  
  GraphicsEdgeItem createGraphicsEdgeItem(GraphicsEdge edge, AbstractNodeItem src, AbstractNodeItem dst, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createGraphicsEdge
  
  default GraphicsEdgeItem createGraphicsEdge(AbstractNodeItem src, AbstractNodeItem dst, AbstractCurvePoint... points) throws IllegalComponentException
  
  Creates a new graphics edge between a source and destination node. Optionally, curve points can be submitted in order to define the shape of the curve. These curve points can be created by using the CurveFactory.
  
  Parameters:
  
  src - source node
  
  dst - destination node
  
  points - (optional)
  
  Returns:
  
  custom edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using the WritableMetabolicNetwork or WritableModel but, for instance, is a plugin internal implementation.
  
  Since:
  
  Omix 1.8.0
- createGraphicsEdgeItem
  
  default GraphicsEdgeItem createGraphicsEdgeItem(GraphicsEdge edge, AbstractNodeItem src, AbstractNodeItem dst, AbstractCurvePoint... points) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createGraphicsEdge
  
  LinkEdgeItem createGraphicsEdge(LinkItem src, AbstractNodeItem dst, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Creates a new link edge between a link and destination node. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - link
  
  dst - destination node
  
  points - list of points describing the edge shape
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createGraphicsEdge
  
  default LinkEdgeItem createGraphicsEdge(LinkItem src, AbstractNodeItem dst, AbstractCurvePoint... points) throws IllegalComponentException
  
  Creates a new link edge between a link and destination node. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - link
  
  dst - destination node
  
  points - (optional)
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createGraphicsEdge
  
  LinkEdgeItem createGraphicsEdge(AbstractNodeItem src, LinkItem dst, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Creates a new link edge between a source node and a link. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - source node
  
  dst - link
  
  points - list of points describing the edge shape
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createGraphicsEdge
  
  default LinkEdgeItem createGraphicsEdge(AbstractNodeItem src, LinkItem dst, AbstractCurvePoint... points) throws IllegalComponentException
  
  Creates a new link edge between a source node and a link. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - source node
  
  dst - link
  
  points - (optional)
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createFluxEdge
  
  default LinkEdgeItem createFluxEdge(LinkItem src, AbstractBioNodeItem dst, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Creates a new link edge with flux edge appearance between a link and destination node. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - link
  
  dst - destination node
  
  points - list of points describing the edge shape
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createFluxEdge
  
  default LinkEdgeItem createFluxEdge(LinkItem src, AbstractBioNodeItem dst, AbstractCurvePoint... points) throws IllegalComponentException
  
  Creates a new link edge with flux edge appearance between a link and destination node. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - link
  
  dst - destination node
  
  points - (optional)
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createFluxEdge
  
  default LinkEdgeItem createFluxEdge(AbstractBioNodeItem src, LinkItem dst, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Creates a new link edge with flux edge appearance between a source node and a link. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - source node
  
  dst - link
  
  points - list of points describing the edge shape
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createFluxEdge
  
  default LinkEdgeItem createFluxEdge(AbstractBioNodeItem src, LinkItem dst, AbstractCurvePoint... points) throws IllegalComponentException
  
  Creates a new link edge with flux edge appearance between a source node and a link. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - source node
  
  dst - link
  
  points - (optional)
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createFluxEdge
  
  LinkEdgeItem createFluxEdge(LinkItem src, AbstractBioNodeItem dst, double coefficient, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Creates a new link edge with flux edge appearance between a link and destination node. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - link
  
  dst - destination node
  
  points - list of points describing the edge shape
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createFluxEdge
  
  default LinkEdgeItem createFluxEdge(LinkItem src, AbstractBioNodeItem dst, double coefficient, AbstractCurvePoint... points) throws IllegalComponentException
  
  Creates a new link edge with flux edge appearance between a link and destination node. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - link
  
  dst - destination node
  
  points - (optional)
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createFluxEdge
  
  LinkEdgeItem createFluxEdge(AbstractBioNodeItem src, LinkItem dst, double coefficient, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Creates a new link edge with flux edge appearance between a source node and a link. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - source node
  
  dst - link
  
  points - list of points describing the edge shape
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createFluxEdge
  
  default LinkEdgeItem createFluxEdge(AbstractBioNodeItem src, LinkItem dst, double coefficient, AbstractCurvePoint... points) throws IllegalComponentException
  
  Creates a new link edge with flux edge appearance between a source node and a link. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - source node
  
  dst - link
  
  points - (optional)
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createCofactorEdge
  
  default LinkEdgeItem createCofactorEdge(LinkItem src, AbstractBioNodeItem dst, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Creates a new link edge with flux edge appearance between a link and destination node. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - link
  
  dst - destination node
  
  points - list of points describing the edge shape
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createCofactorEdge
  
  default LinkEdgeItem createCofactorEdge(LinkItem src, AbstractBioNodeItem dst, AbstractCurvePoint... points) throws IllegalComponentException
  
  Creates a new link edge with flux edge appearance between a link and destination node. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - link
  
  dst - destination node
  
  points - (optional)
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createCofactorEdge
  
  default LinkEdgeItem createCofactorEdge(AbstractBioNodeItem src, LinkItem dst, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Creates a new link edge with flux edge appearance between a source node and a link. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - source node
  
  dst - link
  
  points - list of points describing the edge shape
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createCofactorEdge
  
  default LinkEdgeItem createCofactorEdge(AbstractBioNodeItem src, LinkItem dst, AbstractCurvePoint... points) throws IllegalComponentException
  
  Creates a new link edge with flux edge appearance between a source node and a link. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - source node
  
  dst - link
  
  points - (optional)
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createCofactorEdge
  
  LinkEdgeItem createCofactorEdge(LinkItem src, AbstractBioNodeItem dst, double coefficient, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Creates a new link edge with flux edge appearance between a link and destination node. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - link
  
  dst - destination node
  
  points - list of points describing the edge shape
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createCofactorEdge
  
  default LinkEdgeItem createCofactorEdge(LinkItem src, AbstractBioNodeItem dst, double coefficient, AbstractCurvePoint... points) throws IllegalComponentException
  
  Creates a new link edge with flux edge appearance between a link and destination node. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - link
  
  dst - destination node
  
  points - (optional)
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createCofactorEdge
  
  LinkEdgeItem createCofactorEdge(AbstractBioNodeItem src, LinkItem dst, double coefficient, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Creates a new link edge with flux edge appearance between a source node and a link. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - source node
  
  dst - link
  
  points - list of points describing the edge shape
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createCofactorEdge
  
  default LinkEdgeItem createCofactorEdge(AbstractBioNodeItem src, LinkItem dst, double coefficient, AbstractCurvePoint... points) throws IllegalComponentException
  
  Creates a new link edge with flux edge appearance between a source node and a link. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - source node
  
  dst - link
  
  points - (optional)
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createEffectorEdge
  
  LinkEdgeItem createEffectorEdge(LinkItem src, ReactionItem dst, double effect, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Creates a new link edge with effector edge appearance between a link and destination node. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - link
  
  dst - destination node
  
  points - list of points describing the edge shape
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createEffectorEdge
  
  default LinkEdgeItem createEffectorEdge(LinkItem src, ReactionItem dst, double effect, AbstractCurvePoint... points) throws IllegalComponentException
  
  Creates a new link edge with effector edge appearance between a link and destination node. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - link
  
  dst - destination node
  
  points - (optional)
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createEffectorEdge
  
  LinkEdgeItem createEffectorEdge(MetaboliteItem src, LinkItem dst, double effect, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Creates a new link edge with effector edge appearance between a source node and a link. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - source node
  
  dst - link
  
  points - list of points describing the edge shape
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createEffectorEdge
  
  default LinkEdgeItem createEffectorEdge(MetaboliteItem src, LinkItem dst, double effect, AbstractCurvePoint... points) throws IllegalComponentException
  
  Creates a new link edge with effector edge appearance between a source node and a link. Optionally, curve points can be submitted in order to define the shape of the curve.
  
  Parameters:
  
  src - source node
  
  dst - link
  
  points - (optional)
  
  Returns:
  
  link edge
  
  Throws:
  
  IllegalComponentException - when 'src' or 'dst' has not been created by using this Diagram.
  
  Since:
  
  Omix 2.0.0
- createLinkEdgeItem
  
  LinkEdgeItem createLinkEdgeItem(LinkEdge edge, LinkItem src, AbstractNodeItem dst, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createLinkEdgeItem
  
  LinkEdgeItem createLinkEdgeItem(LinkEdge edge, AbstractNodeItem src, LinkItem dst, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createLinkEdgeItem
  
  default LinkEdgeItem createLinkEdgeItem(LinkEdge edge, LinkItem src, AbstractNodeItem dst, AbstractCurvePoint... points) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createLinkEdgeItem
  
  default LinkEdgeItem createLinkEdgeItem(LinkEdge edge, AbstractNodeItem src, LinkItem dst, AbstractCurvePoint... points) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createGroup
  
  default Group createGroup(Groupable item1, Groupable... items) throws IllegalComponentException
  
  Groups submitted items to an item group. Additionally, groups can be parts of other groups.
  All components must be positioned in the diagram. If one of the submitted components does not have a position an exception is thrown. (see: AbstractNode#hasInvalidPosition(), AbstractEdge#hasInvalidPosition() and Compartment#hasInvalidPosition()). Pathways added to an item group must not be empty (Pathway#isEmpty()).
  
  Parameters:
  
  item1 - the first item in the group
  
  items - an arbitrary number of additional items to be grouped
  
  Returns:
  
  an item group
  
  Throws:
  
  IllegalComponentException - if 'item1' one of the submitted 'items' has not been created by using the WritableMetabolicNetwork or WritableModel but, for instance, is a plugin internal implementation. Is additionally thrown when one of the items is not positioned in the diagram of an empty pathway shall be grouped.
- createClipping
  
  Clipping createClipping(String identifier)
- createDiagramComment
  
  Comment createDiagramComment()
- createItemComment
  
  Comment createItemComment(CompartmentItem item) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createItemComment
  
  Comment createItemComment(PathwayItem item) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createItemComment
  
  Comment createItemComment(AbstractNodeItem item) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createItemComment
  
  Comment createItemComment(GraphicsBoxItem item) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createItemComment
  
  Comment createItemComment(GraphicsPathItem item) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- addItem
  
  void addItem(AbstractItem 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 MetaboliteItem or Metabolite to the diagram, a MetaboliteType 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 WritableMetabolicNetwork or WritableModel but, for instance, is a plugin internal implementation.
  
  IllegalStateException
- addItem
  
  void addItem(Guideline item) throws ComponentExistsException, IllegalComponentException, IllegalStateException
  
  Throws:
  
  ComponentExistsException
  
  IllegalComponentException
  
  IllegalStateException
- addItem
  
  void addItem(PatternItem item) throws ComponentExistsException, IllegalComponentException
  
  Throws:
  
  ComponentExistsException
  
  IllegalComponentException
- removeItem
  
  void removeItem(AbstractItem item) throws ComponentExistsException, IllegalComponentException, IllegalStateException
  
  Throws:
  
  ComponentExistsException
  
  IllegalComponentException
  
  IllegalStateException
- removeItem
  
  void removeItem(Guideline item) throws ComponentExistsException, IllegalComponentException, IllegalStateException
  
  Throws:
  
  ComponentExistsException
  
  IllegalComponentException
  
  IllegalStateException
- removeItem
  
  void removeItem(PatternItem item) throws ComponentExistsException, IllegalComponentException
  
  Throws:
  
  ComponentExistsException
  
  IllegalComponentException
- isChangeable
  
  boolean isChangeable()
  
  Checks if the given element can be changed.
  
  Specified by:
  
  isChangeable in interface AbstractModelComponent
  
  Returns:
  
  is changeable
- reactions
  
  List<? extends ReactionItem> reactions()
  
  Returns an unchangeable List of all reaction nodes.
  
  Specified by:
  
  reactions in interface Diagram
  
  Returns:
  
  list of reactions
- metabolites
  
  List<? extends MetaboliteItem> metabolites()
  
  Returns an unchangeable List of all metabolite nodes.
  
  Specified by:
  
  metabolites in interface Diagram
  
  Returns:
  
  list of metabolites
- getMetaboliteItems
  
  List<? extends MetaboliteItem> getMetaboliteItems(CompartmentItem compartment, String name) throws IllegalComponentException
  
  Specified by:
  
  getMetaboliteItems in interface Diagram
  
  Throws:
  
  IllegalComponentException
- pathways
  
  List<? extends PathwayItem> pathways()
  
  Returns an unchangeable List of all pathway items.
  
  Specified by:
  
  pathways in interface Diagram
  
  Returns:
  
  list of pathways
- getPathwayItems
  
  List<? extends PathwayItem> getPathwayItems(String name)
  
  Specified by:
  
  getPathwayItems in interface Diagram
- compartments
  
  List<? extends CompartmentItem> compartments()
  
  Returns an unchangeable List of all compartment items.
  
  Specified by:
  
  compartments in interface Diagram
  
  Returns:
  
  list of compartments
- getTopLevelCompartmentItems
  
  List<? extends CompartmentItem> getTopLevelCompartmentItems(String name)
  
  Specified by:
  
  getTopLevelCompartmentItems in interface Diagram
- graphicsEdges
  
  List<? extends GraphicsEdgeItem> graphicsEdges()
  
  Returns an unchangeable List of all graphics edges (connection edges).
  
  Specified by:
  
  graphicsEdges in interface Diagram
  
  Returns:
  
  list of graphics edges
  
  Since:
  
  Omix 1.8.0
- graphicsNodes
  
  List<? extends GraphicsNodeItem> graphicsNodes()
  
  Returns an unchangeable List of all graphics nodes.
  
  Specified by:
  
  graphicsNodes in interface Diagram
  
  Returns:
  
  list of graphics nodes
  
  Since:
  
  Omix 1.8.0
- getGraphicsNodeItems
  
  List<? extends GraphicsNodeItem> getGraphicsNodeItems(String name)
  
  Specified by:
  
  getGraphicsNodeItems in interface Diagram
- linkEdges
  
  List<? extends LinkEdgeItem> linkEdges()
  
  Returns an unchangeable List of all link edges.
  
  Specified by:
  
  linkEdges in interface Diagram
  
  Returns:
  
  list of link edges
  
  Since:
  
  Omix 2.0.0
- links
  
  List<? extends LinkItem> links()
  
  Returns an unchangeable List of all links.
  
  Specified by:
  
  links in interface Diagram
  
  Returns:
  
  list of links
  
  Since:
  
  Omix 2.0.0
- getLinkItems
  
  List<? extends LinkItem> getLinkItems(String name)
  
  Specified by:
  
  getLinkItems in interface Diagram
- effectorEdges
  
  List<? extends EffectorEdgeItem> effectorEdges()
  
  Returns an unchangeable List of all effector edges.
  
  Specified by:
  
  effectorEdges in interface Diagram
  
  Returns:
  
  list of effector edges
- fluxEdges
  
  List<? extends FluxEdgeItem> fluxEdges()
  
  Returns an unchangeable List of all flux edges.
  
  Specified by:
  
  fluxEdges in interface Diagram
  
  Returns:
  
  list of flux edges
- graphicsBoxes
  
  List<? extends GraphicsBoxItem> graphicsBoxes()
  
  Returns an unchangeable List of all graphical boxes.
  
  Specified by:
  
  graphicsBoxes in interface Diagram
  
  Returns:
  
  list of graphical boxes
  
  Since:
  
  Omix 2.0.0
- getGraphicsBoxItems
  
  List<? extends GraphicsBoxItem> getGraphicsBoxItems(String name)
  
  Specified by:
  
  getGraphicsBoxItems in interface Diagram
- graphicsPaths
  
  List<? extends GraphicsPathItem> graphicsPaths()
  
  Returns an unchangeable List of all graphical paths.
  
  Specified by:
  
  graphicsPaths in interface Diagram
  
  Returns:
  
  list of graphical paths
  
  Since:
  
  Omix 2.0.0
- getGraphicsPathItems
  
  List<? extends GraphicsPathItem> getGraphicsPathItems(String name)
  
  Specified by:
  
  getGraphicsPathItems in interface Diagram
- groups
  
  List<? extends Group> groups()
  
  Specified by:
  
  groups in interface Diagram
- comments
  
  List<? extends Comment> comments()
  
  Specified by:
  
  comments in interface Diagram
- getComment
  
  Comment getComment(String identifier)
  
  Specified by:
  
  getComment in interface Diagram
- clippings
  
  List<? extends Clipping> clippings()
  
  Specified by:
  
  clippings in interface Diagram
- guidelines
  
  List<? extends Guideline> guidelines()
- clippingExists
  
  boolean clippingExists(String identifier)
  
  Specified by:
  
  clippingExists in interface Diagram
- getClipping
  
  Clipping getClipping(String identifier)
  
  Specified by:
  
  getClipping in interface Diagram
- defaultClipping
  
  Clipping defaultClipping()
  
  Specified by:
  
  defaultClipping in interface Diagram
- createSeparator
  
  default Separator createSeparator()
- createBezierPoint
  
  default 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
  
  default 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
  
  default 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
- getAccessoryItem
  
  AccessoryItem getAccessoryItem(String namespace, String accessoryName) throws IllegalAccessException, NoSuchFieldException
  
  Returns the accessory item of the submitted name defined in the namespace.
  
  Parameters:
  
  namespace -
  
  accessoryName -
  
  Returns:
  
  accessory item
  
  Throws:
  
  IllegalAccessException - if accessory item is protected
  
  NoSuchFieldException - if accessory item does not exist
- getAccessoryItem
  
  default <T extends AccessoryItem> T getAccessoryItem(String namespace, String accessoryName, Class<T> accessoryItemClass) throws IllegalAccessException, NoSuchFieldException
  
  Throws:
  
  IllegalAccessException
  
  NoSuchFieldException
- getAccessoryItem
  
  default AccessoryItem getAccessoryItem(String accessoryName) throws IllegalAccessException, NoSuchFieldException
  
  Returns the accessory item of the submitted name defined in the namespace.
  
  Parameters:
  
  accessoryName -
  
  Returns:
  
  accessory item
  
  Throws:
  
  IllegalAccessException - if accessory is protected
  
  NoSuchFieldException - if accessory does not exist
- getAccessoryItem
  
  default <T extends AccessoryItem> T getAccessoryItem(String accessoryName, Class<T> accessoryItemClass) throws IllegalAccessException, NoSuchFieldException
  
  Throws:
  
  IllegalAccessException
  
  NoSuchFieldException
- getAllAccessoryItems
  
  List<? extends AccessoryItem> getAllAccessoryItems()
  
  Returns all accessory items defined in the document embedded OVL script and all namespaces.
  
  Returns:
  
  unmodifiable list of accessory items
- getAccessoryItems
  
  List<? extends AccessoryItem> getAccessoryItems()
  
  Returns all accessory items defined in the document embedded OVL script.
  
  Returns:
  
  unmodifiable list of accessory items
  
  Throws:
  
  IllegalArgumentException - if object is not a network item
- getAccessoryItems
  
  List<? extends AccessoryItem> getAccessoryItems(String namespace)
  
  Returns all accessory items defined in the given namespace.
  
  Parameters:
  
  namespace -
  
  Returns:
  
  unmodifiable list of accessory items
  
  Throws:
  
  IllegalArgumentException - if object is not a network item
- 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 AbstractModelComponent
  
  Specified by:
  
  getField in interface AbstractModelComponent
  
  Specified by:
  
  getField in interface Diagram
  
  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 AbstractModelComponent
  
  Specified by:
  
  getField in interface AbstractModelComponent
  
  Specified by:
  
  getField in interface Diagram
  
  Parameters:
  
  namespace -
  
  fieldName -
  
  Returns:
  
  reference object representing the field
  
  Throws:
  
  IllegalAccessException - if field is protected
  
  NoSuchFieldException - if field does not exist
- getThumbnails
  
  Thumbnails getThumbnails()
  
  Returns thumbnails embedded in the model document file.
  
  Specified by:
  
  getThumbnails in interface Diagram
  
  Returns:
  
  thumbnails
- changePositionOfNodes
  
  void changePositionOfNodes(List<Diagram.NewNodePosition> newPositions) throws IllegalChangeException
  
  Set the positions of the items as specified in the NewNodePosition objects.
  
  Parameters:
  
  newPositions -
  
  Throws:
  
  IllegalChangeException
- toReadOnly
  
  Diagram toReadOnly()
  
  Specified by:
  
  toReadOnly in interface AbstractModelComponent
  
  Specified by:
  
  toReadOnly in interface WritableInterface
- toWritable
  
  default AbstractItem toWritable(AbstractItem type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default AbstractModelItem toWritable(AbstractModelItem type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default AbstractNodeItem toWritable(AbstractNodeItem type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default AbstractBioNodeItem toWritable(AbstractBioNodeItem type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default AbstractEdgeItem toWritable(AbstractEdgeItem type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default AccessoryItem toWritable(AccessoryItem type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default ArrayItem<?> toWritable(ArrayItem<?> type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default DataAnnotationItem toWritable(DataAnnotationItem type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default SimpleValueFieldItem toWritable(SimpleValueFieldItem type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default AbstractSideBoxItem toWritable(AbstractSideBoxItem type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default TriggerItem toWritable(TriggerItem type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default IntegerTriggerItem toWritable(IntegerTriggerItem type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  default DoubleTriggerItem toWritable(DoubleTriggerItem type) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  DoublePlayerItem toWritable(DoublePlayerItem object) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  DoubleSliderItem toWritable(DoubleSliderItem object) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  DoubleSpinBoxItem toWritable(DoubleSpinBoxItem object) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  PlayerItem toWritable(PlayerItem object) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  SliderItem toWritable(SliderItem object) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  SpinBoxItem toWritable(SpinBoxItem object) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  CheckButtonItem toWritable(CheckButtonItem object) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  PushButtonItem toWritable(PushButtonItem object) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  TextFieldItem toWritable(TextFieldItem object) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  DoubleFieldItem toWritable(DoubleFieldItem object) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  IntegerFieldItem toWritable(IntegerFieldItem object) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  ImageFieldItem toWritable(ImageFieldItem object) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  ItemGroupItem toWritable(ItemGroupItem object) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  ChartSideBoxItem toWritable(ChartSideBoxItem object) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  SideBoxItem toWritable(SideBoxItem object) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  AnnotationArrayItem<?> toWritable(AnnotationArrayItem<?> object) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  TriggerArrayItem<?> toWritable(TriggerArrayItem<?> object) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  Clipping toWritable(Clipping clipping) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  Group toWritable(Group group) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  Comment toWritable(Comment comment) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  MetaboliteItem toWritable(MetaboliteItem metabolite) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  ReactionItem toWritable(ReactionItem reaction) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  GraphicsNodeItem toWritable(GraphicsNodeItem node) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  GraphicsBoxItem toWritable(GraphicsBoxItem item) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  GraphicsEdgeItem toWritable(GraphicsEdgeItem edge) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  LinkItem toWritable(LinkItem edge) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  LinkEdgeItem toWritable(LinkEdgeItem edge) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  FluxEdgeItem toWritable(FluxEdgeItem edge) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  EffectorEdgeItem toWritable(EffectorEdgeItem edge) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  PathwayItem toWritable(PathwayItem pathway) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- toWritable
  
  CompartmentItem toWritable(CompartmentItem compartment) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- getSelectedItems
  
  List<? extends AbstractItem> getSelectedItems()
  
  Specified by:
  
  getSelectedItems in interface Diagram
- patternPaths
  
  List<? extends PatternPath> patternPaths()
  
  Specified by:
  
  patternPaths in interface Diagram
- patternBranches
  
  List<? extends PatternBranch> patternBranches()
  
  Specified by:
  
  patternBranches in interface Diagram
- createPatternBranch
  
  PatternBranch createPatternBranch(double x, double y)
- createPatternPath
  
  default PatternPath createPatternPath(PatternBranch startPoint, PatternBranch endPoint, AbstractCurvePoint... points) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- createPatternPath
  
  PatternPath createPatternPath(PatternBranch startPoint, PatternBranch endPoint, List<? extends AbstractCurvePoint> points) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException

Interface Diagram

Nested Class Summary

Method Summary

Methods inherited from interface omix.plugin.model.AbstractModelComponent

Methods inherited from interface omix.plugin.diagram.Diagram

Method Details