Uses of Class
omix.plugin.util.IllegalComponentException

Packages that use IllegalComponentException

Package	Description
omix.plugin.diagram
omix.plugin.diagram.writable
omix.plugin.diagram.writable.pattern
omix.plugin.model.accessory
omix.plugin.model.accessory.annotation
omix.plugin.model.accessory.trigger
omix.plugin.model.writable
omix.plugin.model.writable.accessory
omix.plugin.model.writable.accessory.annotation
omix.plugin.model.writable.accessory.trigger
omix.plugin.motifstamp.writable
omix.util.io	This package contains classes for file input and output which can be used in plugin development.

Uses of IllegalComponentException in omix.plugin.diagram

Methods in omix.plugin.diagram that throw IllegalComponentException

Modifier and Type	Method	Description
List<? extends MetaboliteItem>	Diagram.getMetaboliteItems(CompartmentItem compartment, String name)

Uses of IllegalComponentException in omix.plugin.diagram.writable

Methods in omix.plugin.diagram.writable that throw IllegalComponentException

Modifier and Type	Method	Description
void	Diagram.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	Diagram.addItem(Guideline item)
void	Diagram.addItem(PatternItem item)
FluxEdgeItem	Diagram.createCofactorEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, double coefficient, List<? extends AbstractCurvePoint> points)	Creates a new cofactor edge between a source and destination node.
default FluxEdgeItem	Diagram.createCofactorEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, double coefficient, AbstractCurvePoint... points)
default FluxEdgeItem	Diagram.createCofactorEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, List<? extends AbstractCurvePoint> points)
default FluxEdgeItem	Diagram.createCofactorEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, AbstractCurvePoint... points)
LinkEdgeItem	Diagram.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	Diagram.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	Diagram.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	Diagram.createCofactorEdge(AbstractBioNodeItem src, LinkItem dst, AbstractCurvePoint... points)	Creates a new link edge with flux edge appearance between a source node and a link.
LinkEdgeItem	Diagram.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	Diagram.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	Diagram.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	Diagram.createCofactorEdge(LinkItem src, AbstractBioNodeItem dst, AbstractCurvePoint... points)	Creates a new link edge with flux edge appearance between a link and destination node.
CompartmentItem	Diagram.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 Diagram.addItem(AbstractItem).
CompartmentItem	Diagram.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 Diagram.addItem(AbstractItem).
CompartmentItem	Diagram.createCompartmentItem(Compartment component)
CompartmentItem	Diagram.createCompartmentItem(Compartment compartment, CompartmentItem outside)
LinkEdgeItem	Diagram.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	Diagram.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	Diagram.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	Diagram.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	Diagram.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	Diagram.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	Diagram.createEffectorEdgeItem(EffectorEdge edge, MetaboliteItem src, ReactionItem dst, List<? extends AbstractCurvePoint> points)
default EffectorEdgeItem	Diagram.createEffectorEdgeItem(EffectorEdge edge, MetaboliteItem src, ReactionItem dst, AbstractCurvePoint... points)
FluxEdgeItem	Diagram.createFluxEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, double coefficient, List<? extends AbstractCurvePoint> points)	Creates a new flux edge between a source and destination node.
default FluxEdgeItem	Diagram.createFluxEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, double coefficient, AbstractCurvePoint... points)	Creates a new flux edge between a source and destination node.
default FluxEdgeItem	Diagram.createFluxEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, List<? extends AbstractCurvePoint> points)
default FluxEdgeItem	Diagram.createFluxEdge(AbstractBioNodeItem src, AbstractBioNodeItem dst, AbstractCurvePoint... points)	Creates a new flux edge between a source and destination node.
LinkEdgeItem	Diagram.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	Diagram.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	Diagram.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	Diagram.createFluxEdge(AbstractBioNodeItem src, LinkItem dst, AbstractCurvePoint... points)	Creates a new link edge with flux edge appearance between a source node and a link.
LinkEdgeItem	Diagram.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	Diagram.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	Diagram.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	Diagram.createFluxEdge(LinkItem src, AbstractBioNodeItem dst, AbstractCurvePoint... points)	Creates a new link edge with flux edge appearance between a link and destination node.
FluxEdgeItem	Diagram.createFluxEdgeItem(FluxEdge edge, AbstractBioNodeItem src, AbstractBioNodeItem dst, List<? extends AbstractCurvePoint> points)
default FluxEdgeItem	Diagram.createFluxEdgeItem(FluxEdge edge, AbstractBioNodeItem src, AbstractBioNodeItem dst, AbstractCurvePoint... points)
GraphicsEdgeItem	Diagram.createGraphicsEdge(AbstractNodeItem src, AbstractNodeItem dst, List<? extends AbstractCurvePoint> points)	Creates a new graphics edge between a source and destination node.
default GraphicsEdgeItem	Diagram.createGraphicsEdge(AbstractNodeItem src, AbstractNodeItem dst, AbstractCurvePoint... points)	Creates a new graphics edge between a source and destination node.
LinkEdgeItem	Diagram.createGraphicsEdge(AbstractNodeItem src, LinkItem dst, List<? extends AbstractCurvePoint> points)	Creates a new link edge between a source node and a link.
default LinkEdgeItem	Diagram.createGraphicsEdge(AbstractNodeItem src, LinkItem dst, AbstractCurvePoint... points)	Creates a new link edge between a source node and a link.
LinkEdgeItem	Diagram.createGraphicsEdge(LinkItem src, AbstractNodeItem dst, List<? extends AbstractCurvePoint> points)	Creates a new link edge between a link and destination node.
default LinkEdgeItem	Diagram.createGraphicsEdge(LinkItem src, AbstractNodeItem dst, AbstractCurvePoint... points)	Creates a new link edge between a link and destination node.
GraphicsEdgeItem	Diagram.createGraphicsEdgeItem(GraphicsEdge edge, AbstractNodeItem src, AbstractNodeItem dst, List<? extends AbstractCurvePoint> points)
default GraphicsEdgeItem	Diagram.createGraphicsEdgeItem(GraphicsEdge edge, AbstractNodeItem src, AbstractNodeItem dst, AbstractCurvePoint... points)
GraphicsNodeItem	Diagram.createGraphicsNodeItem(GraphicsNode component)
GraphicsPathItem	Diagram.createGraphicsPath(List<? extends AbstractCurvePoint> points)
default GraphicsPathItem	Diagram.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 Diagram.addItem(AbstractItem).
Group	Diagram.createGroup(List<? extends Groupable> items)	Groups submitted items to an item group.
default Group	Diagram.createGroup(Groupable item1, Groupable... items)	Groups submitted items to an item group.
Comment	Diagram.createItemComment(AbstractNodeItem item)
Comment	Diagram.createItemComment(CompartmentItem item)
Comment	Diagram.createItemComment(GraphicsBoxItem item)
Comment	Diagram.createItemComment(GraphicsPathItem item)
Comment	Diagram.createItemComment(PathwayItem item)
default LinkItem	Diagram.createLink(Diagram diagram)
LinkItem	Diagram.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	Diagram.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	Diagram.createLinkEdgeItem(LinkEdge edge, AbstractNodeItem src, LinkItem dst, List<? extends AbstractCurvePoint> points)
default LinkEdgeItem	Diagram.createLinkEdgeItem(LinkEdge edge, AbstractNodeItem src, LinkItem dst, AbstractCurvePoint... points)
LinkEdgeItem	Diagram.createLinkEdgeItem(LinkEdge edge, LinkItem src, AbstractNodeItem dst, List<? extends AbstractCurvePoint> points)
default LinkEdgeItem	Diagram.createLinkEdgeItem(LinkEdge edge, LinkItem src, AbstractNodeItem dst, AbstractCurvePoint... points)
LinkItem	Diagram.createLinkItem(Link component)
MetaboliteItem	Diagram.createMetabolite(String namePlainText, String nameRichText, CompartmentItem compartment)	Creates a new metabolite with the given unique name lying in the given compartment.
MetaboliteItem	Diagram.createMetabolite(String namePlainText, String nameRichText, Compartment compartment)
MetaboliteItem	Diagram.createMetabolite(String name, CompartmentItem compartment)	Creates a new metabolite with the given unique name lying in the given compartment.
MetaboliteItem	Diagram.createMetabolite(String name, Compartment compartment)
MetaboliteItem	Diagram.createMetaboliteItem(Metabolite metabolite)	Creates another visible instance of the metabolite in the diagram (a duplicate node).
MetaboliteItem	Diagram.createMetaboliteItem(Metabolite metabolite, CompartmentItem compartment)
MetaboliteItem	Diagram.createMetaboliteItem(MetaboliteType metaboliteType, CompartmentItem compartment)
MetaboliteItem	Diagram.createMetaboliteItem(MetaboliteType metaboliteType, Compartment compartment)
PathwayItem	Diagram.createPathwayItem(Pathway component)
PatternPath	Diagram.createPatternPath(PatternBranch startPoint, PatternBranch endPoint, List<? extends AbstractCurvePoint> points)
default PatternPath	Diagram.createPatternPath(PatternBranch startPoint, PatternBranch endPoint, AbstractCurvePoint... points)
ReactionItem	Diagram.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 Diagram.addItem(omix.plugin.diagram.writable.AbstractItem).
ReactionItem	Diagram.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 Diagram.addItem(omix.plugin.diagram.writable.AbstractItem).
ReactionItem	Diagram.createReactionItem(Reaction component)
ReactionItem	Diagram.createReactionItem(Reaction component, PathwayItem pathway)
List<? extends MetaboliteItem>	Diagram.getMetaboliteItems(CompartmentItem compartment, String name)
void	Diagram.removeItem(AbstractItem item)
void	Diagram.removeItem(Guideline item)
void	Diagram.removeItem(PatternItem item)
void	AbstractEdgeItem.setPoints(List<? extends AbstractCurvePoint> points)
default void	AbstractEdgeItem.setPoints(AbstractCurvePoint... points)
void	GraphicsPathItem.setPoints(List<? extends AbstractCurvePoint> points)
default void	GraphicsPathItem.setPoints(AbstractCurvePoint... points)
default AbstractBioNodeItem	Diagram.toWritable(AbstractBioNodeItem type)
default AbstractEdgeItem	Diagram.toWritable(AbstractEdgeItem type)
default AbstractItem	Diagram.toWritable(AbstractItem type)
default AbstractModelItem	Diagram.toWritable(AbstractModelItem type)
default AbstractNodeItem	Diagram.toWritable(AbstractNodeItem type)
default AccessoryItem	Diagram.toWritable(AccessoryItem type)
default AbstractSideBoxItem	Diagram.toWritable(AbstractSideBoxItem type)
AnnotationArrayItem<?>	Diagram.toWritable(AnnotationArrayItem<?> object)
ChartSideBoxItem	Diagram.toWritable(ChartSideBoxItem object)
default DataAnnotationItem	Diagram.toWritable(DataAnnotationItem type)
DoubleFieldItem	Diagram.toWritable(DoubleFieldItem object)
ImageFieldItem	Diagram.toWritable(ImageFieldItem object)
IntegerFieldItem	Diagram.toWritable(IntegerFieldItem object)
ItemGroupItem	Diagram.toWritable(ItemGroupItem object)
SideBoxItem	Diagram.toWritable(SideBoxItem object)
default SimpleValueFieldItem	Diagram.toWritable(SimpleValueFieldItem type)
TextFieldItem	Diagram.toWritable(TextFieldItem object)
default ArrayItem<?>	Diagram.toWritable(ArrayItem<?> type)
CheckButtonItem	Diagram.toWritable(CheckButtonItem object)
DoublePlayerItem	Diagram.toWritable(DoublePlayerItem object)
DoubleSliderItem	Diagram.toWritable(DoubleSliderItem object)
DoubleSpinBoxItem	Diagram.toWritable(DoubleSpinBoxItem object)
default DoubleTriggerItem	Diagram.toWritable(DoubleTriggerItem type)
default IntegerTriggerItem	Diagram.toWritable(IntegerTriggerItem type)
PlayerItem	Diagram.toWritable(PlayerItem object)
PushButtonItem	Diagram.toWritable(PushButtonItem object)
SliderItem	Diagram.toWritable(SliderItem object)
SpinBoxItem	Diagram.toWritable(SpinBoxItem object)
TriggerArrayItem<?>	Diagram.toWritable(TriggerArrayItem<?> object)
default TriggerItem	Diagram.toWritable(TriggerItem type)
Clipping	Diagram.toWritable(Clipping clipping)
Comment	Diagram.toWritable(Comment comment)
CompartmentItem	Diagram.toWritable(CompartmentItem compartment)
EffectorEdgeItem	Diagram.toWritable(EffectorEdgeItem edge)
FluxEdgeItem	Diagram.toWritable(FluxEdgeItem edge)
GraphicsBoxItem	Diagram.toWritable(GraphicsBoxItem item)
GraphicsEdgeItem	Diagram.toWritable(GraphicsEdgeItem edge)
GraphicsNodeItem	Diagram.toWritable(GraphicsNodeItem node)
Group	Diagram.toWritable(Group group)
LinkEdgeItem	Diagram.toWritable(LinkEdgeItem edge)
LinkItem	Diagram.toWritable(LinkItem edge)
MetaboliteItem	Diagram.toWritable(MetaboliteItem metabolite)
PathwayItem	Diagram.toWritable(PathwayItem pathway)
ReactionItem	Diagram.toWritable(ReactionItem reaction)

Uses of IllegalComponentException in omix.plugin.diagram.writable.pattern

Methods in omix.plugin.diagram.writable.pattern that throw IllegalComponentException

Modifier and Type	Method	Description
void	PatternPath.setElements(List<Double> keys, List<? extends AbstractNodeItem> nodes, List<? extends AbstractEdgeItem> edges)
void	PatternBranch.setNode(AbstractNodeItem node)

Uses of IllegalComponentException in omix.plugin.model.accessory

Methods in omix.plugin.model.accessory that throw IllegalComponentException

Modifier and Type	Method	Description
List<? extends AccessoryItem>	Accessory.getDiagramItems(Diagram diagram)
List<? extends ArrayItem<?>>	Array.getDiagramItems(Diagram diagram)

Uses of IllegalComponentException in omix.plugin.model.accessory.annotation

Methods in omix.plugin.model.accessory.annotation that throw IllegalComponentException

Modifier and Type	Method	Description
List<? extends AbstractSideBoxItem>	AbstractSideBox.getDiagramItems(Diagram diagram)
List<? extends AnnotationArrayItem<?>>	AnnotationArray.getDiagramItems(Diagram diagram)
List<? extends ChartSideBoxItem>	ChartSideBox.getDiagramItems(Diagram diagram)
List<? extends DataAnnotationItem>	DataAnnotation.getDiagramItems(Diagram diagram)
List<? extends DoubleFieldItem>	DoubleField.getDiagramItems(Diagram diagram)
List<? extends ImageFieldItem>	ImageField.getDiagramItems(Diagram diagram)
List<? extends IntegerFieldItem>	IntegerField.getDiagramItems(Diagram diagram)
List<? extends ItemGroupItem>	ItemGroup.getDiagramItems(Diagram diagram)
List<? extends ObjectFieldItem<T>>	ObjectField.getDiagramItems(Diagram diagram)
List<? extends SideBoxItem>	SideBox.getDiagramItems(Diagram diagram)
List<? extends SimpleValueFieldItem>	SimpleValueField.getDiagramItems(Diagram diagram)
List<? extends TextFieldItem>	TextField.getDiagramItems(Diagram diagram)

Uses of IllegalComponentException in omix.plugin.model.accessory.trigger

Methods in omix.plugin.model.accessory.trigger that throw IllegalComponentException

Modifier and Type	Method	Description
List<? extends CheckButtonItem>	CheckButton.getDiagramItems(Diagram diagram)
List<? extends DoublePlayerItem>	DoublePlayer.getDiagramItems(Diagram diagram)
List<? extends DoubleSliderItem>	DoubleSlider.getDiagramItems(Diagram diagram)
List<? extends DoubleSpinBoxItem>	DoubleSpinBox.getDiagramItems(Diagram diagram)
List<? extends DoubleTriggerItem>	DoubleTrigger.getDiagramItems(Diagram diagram)
List<? extends IntegerTriggerItem>	IntegerTrigger.getDiagramItems(Diagram diagram)
List<? extends PlayerItem>	Player.getDiagramItems(Diagram diagram)
List<? extends PushButtonItem>	PushButton.getDiagramItems(Diagram diagram)
List<? extends SliderItem>	Slider.getDiagramItems(Diagram diagram)
List<? extends SpinBoxItem>	SpinBox.getDiagramItems(Diagram diagram)
List<? extends TriggerItem>	Trigger.getDiagramItems(Diagram diagram)
List<? extends TriggerArrayItem<?>>	TriggerArray.getDiagramItems(Diagram diagram)

Uses of IllegalComponentException in omix.plugin.model.writable

Methods in omix.plugin.model.writable that throw IllegalComponentException

Modifier and Type	Method	Description
void	Model.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	Model.addCustomShape(String name, List<? extends AbstractCurvePoint> points)	Creates a new custom shape available for nodes or edge markers.
void	Model.addDiagram(Diagram diagram)
void	Model.addMotifStamp(MotifStamp motifStamp)
default FluxEdge	Model.createCofactorEdge(AbstractBioNode src, AbstractBioNode dst)
FluxEdge	Model.createCofactorEdge(AbstractBioNode src, AbstractBioNode dst, double coefficient)	Creates a new cofactor edge between a source and destination node.
default LinkEdge	Model.createCofactorEdge(AbstractBioNode src, Link dst)
LinkEdge	Model.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	Model.createCofactorEdge(Link src, AbstractBioNode dst)
LinkEdge	Model.createCofactorEdge(Link src, AbstractBioNode dst, double coefficient)	Creates a new link edge with flux edge appearance between a source link and destination node.
Compartment	Model.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 Model.addComponent(AbstractModelComponent).
Compartment	Model.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 Model.addComponent(AbstractModelComponent).
LinkEdge	Model.createEffectorEdge(Link src, Reaction dst, double effect)	Creates a new link edge with effector edge appearance between a source link and destination node.
LinkEdge	Model.createEffectorEdge(Metabolite src, Link dst, double effect)	Creates a new link edge with effector edge appearance between a source node and destination link.
EffectorEdge	Model.createEffectorEdge(Metabolite src, Reaction dst, double effect)	Creates a new effector edge between a source and destination node with the given effect.
default FluxEdge	Model.createFluxEdge(AbstractBioNode src, AbstractBioNode dst)
FluxEdge	Model.createFluxEdge(AbstractBioNode src, AbstractBioNode dst, double coefficient)	Creates a new flux edge between a source and destination node.
default LinkEdge	Model.createFluxEdge(AbstractBioNode src, Link dst)
LinkEdge	Model.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	Model.createFluxEdge(Link src, AbstractBioNode dst)
LinkEdge	Model.createFluxEdge(Link src, AbstractBioNode dst, double coefficient)	Creates a new link edge with flux edge appearance between a source link and destination node.
GraphicsEdge	Model.createGraphicsEdge(AbstractNode src, AbstractNode dst)	Creates a new graphics edge between a source and destination node.
LinkEdge	Model.createGraphicsEdge(AbstractNode src, Link dst)	Creates a new link edge between a source node and destination link.
LinkEdge	Model.createGraphicsEdge(Link src, AbstractNode dst)	Creates a new link edge between a source link and destination node.
default Link	Model.createLink(Diagram diagram)
Link	Model.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 Model.addComponent(AbstractModelComponent).
Link	Model.createLink(Pathway pathway)	Create a new link to given pathway. After creating a new link, it must be explicitly added to the model by Model.addComponent(AbstractModelComponent).
Metabolite	Model.createMetabolite(String namePlainText, String nameRichText, Compartment compartment)	Creates a new metabolite with the given unique name lying in the given compartment.
Metabolite	Model.createMetabolite(String name, Compartment compartment)	Creates a new metabolite with the given unique name lying in the given compartment.
Reaction	Model.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 Model.addComponent(AbstractModelComponent).
Reaction	Model.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 Model.addComponent(AbstractModelComponent).
void	Model.removeComponent(AbstractModelComponent item)
void	Model.removeDiagram(Diagram diagram)
void	Model.removeMotifStamp(MotifStamp motifStamp)
void	Model.setCurrentDiagram(Diagram diagram)
Diagram	Model.toWritable(Diagram type)
default AbstractBioNode	Model.toWritable(AbstractBioNode type)
default AbstractEdge	Model.toWritable(AbstractEdge type)
default AbstractModelComponent	Model.toWritable(AbstractModelComponent type)
default AbstractNode	Model.toWritable(AbstractNode type)
default AbstractVisibleComponent	Model.toWritable(AbstractVisibleComponent type)
default Accessory	Model.toWritable(Accessory type)
default AbstractSideBox	Model.toWritable(AbstractSideBox type)
AnnotationArray<?>	Model.toWritable(AnnotationArray<?> type)
ChartSideBox	Model.toWritable(ChartSideBox type)
default DataAnnotation	Model.toWritable(DataAnnotation type)
DoubleField	Model.toWritable(DoubleField type)
ImageField	Model.toWritable(ImageField type)
IntegerField	Model.toWritable(IntegerField type)
ItemGroup	Model.toWritable(ItemGroup type)
SideBox	Model.toWritable(SideBox type)
default SimpleValueField	Model.toWritable(SimpleValueField type)
TextField	Model.toWritable(TextField type)
default Array<?>	Model.toWritable(Array<?> type)
CheckButton	Model.toWritable(CheckButton type)
DoublePlayer	Model.toWritable(DoublePlayer type)
DoubleSlider	Model.toWritable(DoubleSlider type)
DoubleSpinBox	Model.toWritable(DoubleSpinBox type)
default DoubleTrigger	Model.toWritable(DoubleTrigger type)
default IntegerTrigger	Model.toWritable(IntegerTrigger type)
Player	Model.toWritable(Player type)
PushButton	Model.toWritable(PushButton type)
Slider	Model.toWritable(Slider type)
SpinBox	Model.toWritable(SpinBox type)
default Trigger	Model.toWritable(Trigger type)
TriggerArray<?>	Model.toWritable(TriggerArray<?> type)
Compartment	Model.toWritable(Compartment compartment)
EffectorEdge	Model.toWritable(EffectorEdge edge)
FluxEdge	Model.toWritable(FluxEdge edge)
GraphicsBox	Model.toWritable(GraphicsBox item)
GraphicsEdge	Model.toWritable(GraphicsEdge edge)
GraphicsNode	Model.toWritable(GraphicsNode node)
Link	Model.toWritable(Link node)
LinkEdge	Model.toWritable(LinkEdge edge)
Metabolite	Model.toWritable(Metabolite metabolite)
MetaboliteType	Model.toWritable(MetaboliteType type)
default Model	Model.toWritable(Model model)
OVLObject	Model.toWritable(OVLObject ovlObject)
Pathway	Model.toWritable(Pathway pathway)
Reaction	Model.toWritable(Reaction reaction)
default WritableInterface	Model.toWritable(ReadOnlyInterface type)

Uses of IllegalComponentException in omix.plugin.model.writable.accessory

Methods in omix.plugin.model.writable.accessory that throw IllegalComponentException

Modifier and Type	Method	Description
List<? extends AccessoryItem>	Accessory.getDiagramItems(Diagram diagram)
List<? extends ArrayItem<?>>	Array.getDiagramItems(Diagram diagram)

Uses of IllegalComponentException in omix.plugin.model.writable.accessory.annotation

Methods in omix.plugin.model.writable.accessory.annotation that throw IllegalComponentException

Modifier and Type	Method	Description
List<? extends AbstractSideBoxItem>	AbstractSideBox.getDiagramItems(Diagram diagram)
List<? extends AnnotationArrayItem<?>>	AnnotationArray.getDiagramItems(Diagram diagram)
List<? extends ChartSideBoxItem>	ChartSideBox.getDiagramItems(Diagram diagram)
List<? extends DataAnnotationItem>	DataAnnotation.getDiagramItems(Diagram diagram)
List<? extends DoubleFieldItem>	DoubleField.getDiagramItems(Diagram diagram)
List<? extends ImageFieldItem>	ImageField.getDiagramItems(Diagram diagram)
List<? extends IntegerFieldItem>	IntegerField.getDiagramItems(Diagram diagram)
List<? extends ItemGroupItem>	ItemGroup.getDiagramItems(Diagram diagram)
List<? extends ObjectFieldItem<T>>	ObjectField.getDiagramItems(Diagram diagram)
List<? extends SideBoxItem>	SideBox.getDiagramItems(Diagram diagram)
List<? extends SimpleValueFieldItem>	SimpleValueField.getDiagramItems(Diagram diagram)
List<? extends TextFieldItem>	TextField.getDiagramItems(Diagram diagram)

Uses of IllegalComponentException in omix.plugin.model.writable.accessory.trigger

Methods in omix.plugin.model.writable.accessory.trigger that throw IllegalComponentException

Modifier and Type	Method	Description
List<? extends CheckButtonItem>	CheckButton.getDiagramItems(Diagram diagram)
List<? extends DoublePlayerItem>	DoublePlayer.getDiagramItems(Diagram diagram)
List<? extends DoubleSliderItem>	DoubleSlider.getDiagramItems(Diagram diagram)
List<? extends DoubleSpinBoxItem>	DoubleSpinBox.getDiagramItems(Diagram diagram)
List<? extends DoubleTriggerItem>	DoubleTrigger.getDiagramItems(Diagram diagram)
List<? extends IntegerTriggerItem>	IntegerTrigger.getDiagramItems(Diagram diagram)
List<? extends PlayerItem>	Player.getDiagramItems(Diagram diagram)
List<? extends PushButtonItem>	PushButton.getDiagramItems(Diagram diagram)
List<? extends SliderItem>	Slider.getDiagramItems(Diagram diagram)
List<? extends SpinBoxItem>	SpinBox.getDiagramItems(Diagram diagram)
List<? extends TriggerItem>	Trigger.getDiagramItems(Diagram diagram)
List<? extends TriggerArrayItem<?>>	TriggerArray.getDiagramItems(Diagram diagram)

Uses of IllegalComponentException in omix.plugin.motifstamp.writable

Methods in omix.plugin.motifstamp.writable that throw IllegalComponentException

Modifier and Type	Method	Description
void	MotifStamp.addItem(AbstractItem item)
FluxEdge	MotifStamp.createCofactorEdgeFrom(Metabolite src, double coefficient, List<AbstractCurvePoint> points)
default FluxEdge	MotifStamp.createCofactorEdgeFrom(Metabolite src, double coefficient, AbstractCurvePoint... points)
default FluxEdge	MotifStamp.createCofactorEdgeFrom(Metabolite src, List<AbstractCurvePoint> points)
default FluxEdge	MotifStamp.createCofactorEdgeFrom(Metabolite src, AbstractCurvePoint... points)
FluxEdge	MotifStamp.createCofactorEdgeTo(Metabolite dst, double coefficient, List<AbstractCurvePoint> points)
default FluxEdge	MotifStamp.createCofactorEdgeTo(Metabolite dst, double coefficient, AbstractCurvePoint... points)
default FluxEdge	MotifStamp.createCofactorEdgeTo(Metabolite dst, List<AbstractCurvePoint> points)
default FluxEdge	MotifStamp.createCofactorEdgeTo(Metabolite dst, AbstractCurvePoint... points)
EffectorEdge	MotifStamp.createEffectorEdge(Metabolite src, double effect, List<AbstractCurvePoint> points)
default EffectorEdge	MotifStamp.createEffectorEdge(Metabolite src, double effect, AbstractCurvePoint... points)
FluxEdge	MotifStamp.createFluxEdgeFrom(Metabolite src, double coefficient, List<AbstractCurvePoint> points)
default FluxEdge	MotifStamp.createFluxEdgeFrom(Metabolite src, double coefficient, AbstractCurvePoint... points)
default FluxEdge	MotifStamp.createFluxEdgeFrom(Metabolite src, List<AbstractCurvePoint> points)
default FluxEdge	MotifStamp.createFluxEdgeFrom(Metabolite src, AbstractCurvePoint... points)
FluxEdge	MotifStamp.createFluxEdgeTo(Metabolite dst, double coefficient, List<AbstractCurvePoint> points)
default FluxEdge	MotifStamp.createFluxEdgeTo(Metabolite dst, double coefficient, AbstractCurvePoint... points)
default FluxEdge	MotifStamp.createFluxEdgeTo(Metabolite dst, List<AbstractCurvePoint> points)
default FluxEdge	MotifStamp.createFluxEdgeTo(Metabolite dst, AbstractCurvePoint... points)
GraphicsEdge	MotifStamp.createGraphicsEdgeFrom(GraphicsNode src, List<AbstractCurvePoint> points)
default GraphicsEdge	MotifStamp.createGraphicsEdgeFrom(GraphicsNode src, AbstractCurvePoint... points)
GraphicsEdge	MotifStamp.createGraphicsEdgeFrom(Metabolite src, List<AbstractCurvePoint> points)
default GraphicsEdge	MotifStamp.createGraphicsEdgeFrom(Metabolite src, AbstractCurvePoint... points)
GraphicsEdge	MotifStamp.createGraphicsEdgeTo(GraphicsNode src, List<AbstractCurvePoint> points)
default GraphicsEdge	MotifStamp.createGraphicsEdgeTo(GraphicsNode dst, AbstractCurvePoint... points)
GraphicsEdge	MotifStamp.createGraphicsEdgeTo(Metabolite src, List<AbstractCurvePoint> points)
default GraphicsEdge	MotifStamp.createGraphicsEdgeTo(Metabolite dst, AbstractCurvePoint... points)

Uses of IllegalComponentException in omix.util.io

Methods in omix.util.io that throw IllegalComponentException

Modifier and Type	Method	Description
protected abstract void	AbstractModelIODomHandler.readFromDom(String suffix, URLConnection connection, Model model, InputUtilities utilities)	Reads an XML file by using DOM.
protected void	StandardModelIODomHandler.readFromDom(String suffix, URLConnection connection, Model model, InputUtilities utilities)	Manages the parsing of a XML file into a Document.
protected abstract void	AbstractDomReader.readOmixModel(Model model, Element domElement)	This method assembles the model according the content inside the given DOM element.