All Superinterfaces:: AbstractModelComponent, ReadOnlyInterface

All Known Subinterfaces:: Diagram

public interface Diagram
extends AbstractModelComponent

Method Summary

Modifier and Type	Method	Description
`void`	`addChangeListener(ChangeListener changeListener)`
`void`	`clearHighlight()`
`boolean`	`clippingExists(String identifier)`
`List<? extends Clipping>`	`clippings()`
`boolean`	`commentExists(String identifier)`
`List<? extends Comment>`	`comments()`
`List<? extends CompartmentItem>`	`compartments()`	Returns an unchangeable `List` of all compartment items.
`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.
`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 identifier)`
`List<? extends GraphicsPathItem>`	`getGraphicsPathItems(String name)`
`String`	`getIdentifier()`
`List<? extends LinkItem>`	`getLinkItems(String identifier)`
`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()`
`default void`	`highlight(List<? extends AbstractItem> items)`
`default void`	`highlight(List<? extends AbstractItem> items, double blur)`
`default void`	`highlight(List<? extends AbstractItem> items, double width, double blur)`
`default void`	`highlight(List<? extends AbstractItem> items, Color color)`
`default void`	`highlight(List<? extends AbstractItem> items, Color color, double width)`
`void`	`highlight(List<? extends AbstractItem> items, Color color, double width, double blur)`
`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`	`removeChangeListener(ChangeListener changeListener)`

Methods inherited from interface omix.plugin.model.AbstractModelComponent

addPropertyChangeListener, fieldExists, removePropertyChangeListener

Method Details
- model
  
  Model model()
  
  Description copied from interface: AbstractModelComponent
  
  Reference to the model instance.
  
  Specified by:
  
  model in interface AbstractModelComponent
  
  Returns:
  
  model
- reactions
  
  List<? extends ReactionItem> reactions()
  
  Returns an unchangeable List of all reaction nodes.
  
  Returns:
  
  list of reactions
- metabolites
  
  List<? extends MetaboliteItem> metabolites()
  
  Returns an unchangeable List of all metabolite nodes.
  
  Returns:
  
  list of metabolites
- getMetaboliteItems
  
  List<? extends MetaboliteItem> getMetaboliteItems(CompartmentItem compartment, String name) throws IllegalComponentException
  
  Throws:
  
  IllegalComponentException
- pathways
  
  List<? extends PathwayItem> pathways()
  
  Returns an unchangeable List of all pathway items.
  
  Returns:
  
  list of pathways
- getPathwayItems
  
  List<? extends PathwayItem> getPathwayItems(String name)
- compartments
  
  List<? extends CompartmentItem> compartments()
  
  Returns an unchangeable List of all compartment items.
  
  Returns:
  
  list of compartments
- getTopLevelCompartmentItems
  
  List<? extends CompartmentItem> getTopLevelCompartmentItems(String name)
- graphicsEdges
  
  List<? extends GraphicsEdgeItem> graphicsEdges()
  
  Returns an unchangeable List of all graphics edges (connection edges).
  
  Returns:
  
  list of graphics edges
  
  Since:
  
  Omix 1.8.0
- graphicsNodes
  
  List<? extends GraphicsNodeItem> graphicsNodes()
  
  Returns an unchangeable List of all graphics nodes.
  
  Returns:
  
  list of graphics nodes
  
  Since:
  
  Omix 1.8.0
- getGraphicsNodeItems
  
  List<? extends GraphicsNodeItem> getGraphicsNodeItems(String identifier)
- linkEdges
  
  List<? extends LinkEdgeItem> linkEdges()
  
  Returns an unchangeable List of all link edges.
  
  Returns:
  
  list of link edges
  
  Since:
  
  Omix 2.0.0
- links
  
  List<? extends LinkItem> links()
  
  Returns an unchangeable List of all links.
  
  Returns:
  
  list of links
  
  Since:
  
  Omix 2.0.0
- getLinkItems
  
  List<? extends LinkItem> getLinkItems(String identifier)
- effectorEdges
  
  List<? extends EffectorEdgeItem> effectorEdges()
  
  Returns an unchangeable List of all effector edges.
  
  Returns:
  
  list of effector edges
- fluxEdges
  
  List<? extends FluxEdgeItem> fluxEdges()
  
  Returns an unchangeable List of all flux edges.
  
  Returns:
  
  list of flux edges
- graphicsBoxes
  
  List<? extends GraphicsBoxItem> graphicsBoxes()
  
  Returns an unchangeable List of all graphical boxes.
  
  Returns:
  
  list of graphical boxes
  
  Since:
  
  Omix 2.0.0
- getGraphicsBoxItems
  
  List<? extends GraphicsBoxItem> getGraphicsBoxItems(String name)
- graphicsPaths
  
  List<? extends GraphicsPathItem> graphicsPaths()
  
  Returns an unchangeable List of all graphical paths.
  
  Returns:
  
  list of graphical paths
  
  Since:
  
  Omix 2.0.0
- getGraphicsPathItems
  
  List<? extends GraphicsPathItem> getGraphicsPathItems(String name)
- groups
  
  List<? extends Group> groups()
- comments
  
  List<? extends Comment> comments()
- commentExists
  
  boolean commentExists(String identifier)
- getComment
  
  Comment getComment(String identifier)
- clippings
  
  List<? extends Clipping> clippings()
- clippingExists
  
  boolean clippingExists(String identifier)
- getClipping
  
  Clipping getClipping(String identifier)
- defaultClipping
  
  Clipping defaultClipping()
- getIdentifier
  
  String getIdentifier()
  
  Specified by:
  
  getIdentifier in interface AbstractModelComponent
- patternPaths
  
  List<? extends PatternPath> patternPaths()
- patternBranches
  
  List<? extends PatternBranch> patternBranches()
- getThumbnails
  
  Thumbnails getThumbnails()
  
  Returns thumbnails embedded in the model document file.
  
  Returns:
  
  thumbnails
- 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
  
  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
  
  Parameters:
  
  namespace -
  
  fieldName -
  
  Returns:
  
  reference object representing the field
  
  Throws:
  
  IllegalAccessException - if field is protected
  
  NoSuchFieldException - if field does not exist
- highlight
  
  void highlight(List<? extends AbstractItem> items, Color color, double width, double blur)
- highlight
  
  default void highlight(List<? extends AbstractItem> items)
- highlight
  
  default void highlight(List<? extends AbstractItem> items, Color color)
- highlight
  
  default void highlight(List<? extends AbstractItem> items, Color color, double width)
- highlight
  
  default void highlight(List<? extends AbstractItem> items, double width, double blur)
- highlight
  
  default void highlight(List<? extends AbstractItem> items, double blur)
- clearHighlight
  
  void clearHighlight()
- getSelectedItems
  
  List<? extends AbstractItem> getSelectedItems()
- addChangeListener
  
  void addChangeListener(ChangeListener changeListener)
  
  Specified by:
  
  addChangeListener in interface AbstractModelComponent
- removeChangeListener
  
  void removeChangeListener(ChangeListener changeListener)
  
  Specified by:
  
  removeChangeListener in interface AbstractModelComponent

Interface Diagram

Method Summary

Methods inherited from interface omix.plugin.model.AbstractModelComponent

Method Details