All Superinterfaces:: AbstractModelComponent, AbstractModelComponent, AbstractVisibleComponent, AbstractVisibleComponent, Compartment, ReadOnlyInterface, WritableInterface

public interface Compartment
extends AbstractVisibleComponent, Compartment

Method Summary

Modifier and Type	Method	Description
`void`	`addPublicIdentifier(PublicIdentifier publicIdentifier)`	Adds a public identifier to the item.
`default void`	`addSynonym(String synonym)`	Adds a synonym to the item.
`void`	`addSynonym(String synonym, String htmlSynonym)`	Adds a synonym to the item.
`void`	`exchangeSynonyms(int index1, int index2)`	Exchanges the position of two synonyms.
`List<? extends CompartmentItem>`	`getDiagramItems()`
`List<? extends CompartmentItem>`	`getDiagramItems(Diagram diagram)`
`Metabolite`	`getMetabolite(String name)`	Returns the metabolite node of the given name if available in the compartment, otherwise null.
`Compartment`	`getSubCompartment(String name)`	Returns a sub compartment of the given name if available in the compartment, otherwise null.
`List<? extends Metabolite>`	`metabolites()`	Returns an unchangeable `List` of all metabolites that occur in this compartment.
`Compartment`	`outside()`	Returns the outside compartment if available otherwise null.
`void`	`removePublicIdentifier(PublicIdentifier publicIdentifier)`	Removes the public identifier from the item.
`void`	`removeSynonym(int synonymIndex)`	Removes the synonym from the item.
`void`	`removeSynonym(String synonym)`	Removes the synonym from the item.
`void`	`setBrushDefault()`	Sets the fill brush of the item's shape to default.
`void`	`setFont(Font font)`	Changes the font of the text label of the item.
`void`	`setFontDefault()`	Changes the font of the text label of the item.
`void`	`setFormattedLabel(String html)`	Set items visible label in html.
`void`	`setHidden(boolean hidden)`	Changes the visibility of the item in the diagram.
`void`	`setIdentifier(String identifier)`	Changes identifier of the item.
`void`	`setPaint(Paint paint)`	Sets the fill brush of the item's shape.
`void`	`setPublicIdentifiers(Collection<? extends PublicIdentifier> publicIdentifiers)`	Set the public identifiers of the item.
`void`	`setShape(Shape shape)`	Sets the item's shape.
`void`	`setShapeDefault()`	Sets the item's shape.
`void`	`setStrokeColor(Color strokeColor)`	Changes the color for the stroke of the item's shape.
`void`	`setStrokeColorDefault()`	Changes the color for the stroke of the item's shape.
`void`	`setStrokeStyle(StrokeStyle strokeStyle)`	Changes the paint style for the stroke of the item's shape.
`void`	`setStrokeStyleDefault()`	Changes the paint style for the stroke of the item's shape.
`void`	`setStrokeWidth(double strokeWidth)`	Changes the stroke width of the item's shape.
`void`	`setStrokeWidthDefault()`	Changes the stroke width of the item's shape.
`default void`	`setSynonym(int index, String synonymPlain)`	Sets the synonym at the given position.
`void`	`setSynonym(int index, String synonymPlain, String synonymRichText)`	Sets the synonym at the given position.
`void`	`setTextBrush(Brush textBrush)`	Changes the fill brush of the item's text label.
`void`	`setTextBrushDefault()`	Changes the fill brush of the item's text label.
`void`	`setTextStrokeColor(Color textStrokeColor)`	Changes the color for the stroke of the item's text label.
`void`	`setTextStrokeColorDefault()`	Changes the color for the stroke of the item's text label.
`void`	`setTextStrokeWidth(double textStrokeWidth)`	Changes the stroke width of the item's text label.
`void`	`setTextStrokeWidthDefault()`	Changes the stroke width of the item's text label.
`void`	`setTransparency(double transparency)`	Changes the transparency of the item's shape.
`void`	`setTransparencyDefault()`	Changes the transparency of the item's shape to default.
`List<? extends Compartment>`	`subCompartments()`	Returns an unchangeable `List` of all sub compartments.
`Compartment`	`toReadOnly()`

Methods inherited from interface omix.plugin.model.AbstractModelComponent

addChangeListener, addPropertyChangeListener, fieldExists, removeChangeListener, removePropertyChangeListener

Methods inherited from interface omix.plugin.model.writable.AbstractModelComponent

getField, getField, isChangeable, model

Methods inherited from interface omix.plugin.model.AbstractVisibleComponent

accessoryExists, getAccessory, getAccessory, hasDiagramItems, hasDiagramItems

Methods inherited from interface omix.plugin.model.writable.AbstractVisibleComponent

getAccessories, getAccessories, getAccessory, getAccessory, getAllAccessories, getCustomProperty, getMethod, getMethod, getMethod, setCustomProperty, setTmpCustomProperty

Methods inherited from interface omix.plugin.model.Compartment

blur, font, getCustomProperty, getIdentifier, getPublicIdentifiers, hidden, name, paint, setCustomProperty, setTmpCustomProperty, shape, strokeColor, strokeStyle, strokeWidth, synonyms, textBlur, textBrush, textShadow, textStrokeColor, textStrokeWidth, textTransparency, transparency

Method Details
- setIdentifier
  
  void setIdentifier(String identifier) throws ComponentExistsException, IllegalChangeException
  
  Changes identifier of the item.
  
  Parameters:
  
  identifier - the new name of the item. CAUTION, the name must be unique in the network.
  
  Throws:
  
  ComponentExistsException
  
  IllegalChangeException
- setFormattedLabel
  
  void setFormattedLabel(String html) throws IllegalChangeException
  
  Set items visible label in html.
  
  Parameters:
  
  html - item's label in HTML
  
  Throws:
  
  IllegalChangeException
- setHidden
  
  void setHidden(boolean hidden) throws IllegalChangeException
  
  Changes the visibility of the item in the diagram.
  
  Parameters:
  
  hidden -
  
  Throws:
  
  IllegalChangeException
- setPaint
  
  void setPaint(@NonNull Paint paint) throws IllegalChangeException
  
  Sets the fill brush of the item's shape.
  
  Parameters:
  
  paint - the new paint
  
  Throws:
  
  IllegalChangeException
  
  See Also:
  
  Compartment.paint()
- setShape
  
  void setShape(@NonNull Shape shape) throws IllegalChangeException
  
  Sets the item's shape.
  
  Parameters:
  
  shape - the new shape
  
  Throws:
  
  IllegalChangeException
  
  See Also:
  
  Compartment.shape()
- setTextStrokeWidth
  
  void setTextStrokeWidth(double textStrokeWidth) throws IllegalChangeException
  
  Changes the stroke width of the item's text label. The text transparency of graphics nodes does not accept null.
  
  Parameters:
  
  textStrokeWidth -
  
  Throws:
  
  IllegalChangeException
  
  See Also:
  
  Compartment.textStrokeWidth()
- setStrokeWidth
  
  void setStrokeWidth(double strokeWidth) throws IllegalChangeException
  
  Changes the stroke width of the item's shape. The stroke width of graphics nodes does not accept null.
  
  Parameters:
  
  strokeWidth -
  
  Throws:
  
  IllegalChangeException
  
  See Also:
  
  Compartment.strokeWidth()
- setTextBrush
  
  void setTextBrush(@NonNull Brush textBrush) throws IllegalChangeException
  
  Changes the fill brush of the item's text label.
  
  Parameters:
  
  textBrush -
  
  Throws:
  
  IllegalChangeException
  
  See Also:
  
  Compartment.textBrush()
- setFont
  
  void setFont(@NonNull Font font) throws IllegalChangeException
  
  Changes the font of the text label of the item.
  
  Parameters:
  
  font -
  
  Throws:
  
  IllegalChangeException
  
  See Also:
  
  Compartment.font()
- setStrokeStyle
  
  void setStrokeStyle(@NonNull StrokeStyle strokeStyle) throws IllegalChangeException
  
  Changes the paint style for the stroke of the item's shape.
  
  Parameters:
  
  strokeStyle -
  
  Throws:
  
  IllegalChangeException
  
  See Also:
  
  Compartment.strokeStyle()
- setTextStrokeColor
  
  void setTextStrokeColor(@NonNull Color textStrokeColor) throws IllegalChangeException
  
  Changes the color for the stroke of the item's text label.
  
  Parameters:
  
  textStrokeColor -
  
  Throws:
  
  IllegalChangeException
  
  See Also:
  
  Compartment.textStrokeColor()
- setStrokeColor
  
  void setStrokeColor(@NonNull Color strokeColor) throws IllegalChangeException
  
  Changes the color for the stroke of the item's shape.
  
  Parameters:
  
  strokeColor -
  
  Throws:
  
  IllegalChangeException
  
  See Also:
  
  Compartment.strokeColor()
- setTransparency
  
  void setTransparency(double transparency) throws IllegalChangeException
  
  Changes the transparency of the item's shape.
  
  Parameters:
  
  transparency -
  
  Throws:
  
  IllegalChangeException
  
  See Also:
  
  Compartment.transparency()
- setBrushDefault
  
  void setBrushDefault() throws IllegalChangeException
  
  Sets the fill brush of the item's shape to default.
  
  Parameters:
  
  brush - the new brush
  
  Throws:
  
  IllegalChangeException
  
  See Also:
  
  Compartment.brush()
- setShapeDefault
  
  void setShapeDefault() throws IllegalChangeException
  
  Sets the item's shape.
  
  Throws:
  
  IllegalChangeException
  
  See Also:
  
  Compartment.shape()
- setTextStrokeWidthDefault
  
  void setTextStrokeWidthDefault() throws IllegalChangeException
  
  Changes the stroke width of the item's text label.
  
  Throws:
  
  IllegalChangeException
  
  See Also:
  
  Compartment.textStrokeWidth()
- setStrokeWidthDefault
  
  void setStrokeWidthDefault() throws IllegalChangeException
  
  Changes the stroke width of the item's shape.
  
  Throws:
  
  IllegalChangeException
  
  See Also:
  
  Compartment.strokeWidth()
- setTextBrushDefault
  
  void setTextBrushDefault() throws IllegalChangeException
  
  Changes the fill brush of the item's text label.
  
  Throws:
  
  IllegalChangeException
  
  See Also:
  
  Compartment.textBrush()
- setFontDefault
  
  void setFontDefault() throws IllegalChangeException
  
  Changes the font of the text label of the item.
  
  Throws:
  
  IllegalChangeException
  
  See Also:
  
  Compartment.font()
- setStrokeStyleDefault
  
  void setStrokeStyleDefault() throws IllegalChangeException
  
  Changes the paint style for the stroke of the item's shape.
  
  Throws:
  
  IllegalChangeException
  
  See Also:
  
  Compartment.strokeStyle()
- setTextStrokeColorDefault
  
  void setTextStrokeColorDefault() throws IllegalChangeException
  
  Changes the color for the stroke of the item's text label.
  
  Throws:
  
  IllegalChangeException
  
  See Also:
  
  Compartment.textStrokeColor()
- setStrokeColorDefault
  
  void setStrokeColorDefault() throws IllegalChangeException
  
  Changes the color for the stroke of the item's shape.
  
  Throws:
  
  IllegalChangeException
  
  See Also:
  
  Compartment.strokeColor()
- setTransparencyDefault
  
  void setTransparencyDefault() throws IllegalChangeException
  
  Changes the transparency of the item's shape to default.
  
  Throws:
  
  IllegalChangeException
  
  See Also:
  
  Compartment.transparency()
- addSynonym
  
  default void addSynonym(String synonym) throws IllegalChangeException
  
  Adds a synonym to the item.
  
  Parameters:
  
  synonym -
  
  Throws:
  
  IllegalChangeException
- addSynonym
  
  void addSynonym(String synonym, String htmlSynonym) throws IllegalChangeException
  
  Adds a synonym to the item.
  
  Parameters:
  
  synonym -
  
  html -
  
  Throws:
  
  IllegalChangeException
- removeSynonym
  
  void removeSynonym(String synonym) throws IllegalChangeException
  
  Removes the synonym from the item.
  
  Parameters:
  
  synonym -
  
  Throws:
  
  IllegalChangeException
- removeSynonym
  
  void removeSynonym(int synonymIndex) throws IllegalChangeException
  
  Removes the synonym from the item.
  
  Parameters:
  
  synonym - index
  
  Throws:
  
  IllegalChangeException
- exchangeSynonyms
  
  void exchangeSynonyms(int index1, int index2) throws IllegalChangeException
  
  Exchanges the position of two synonyms.
  
  Parameters:
  
  index1 -
  
  index2 -
  
  Throws:
  
  IllegalChangeException
- setSynonym
  
  default void setSynonym(int index, String synonymPlain) throws IllegalChangeException
  
  Sets the synonym at the given position.
  
  Parameters:
  
  index -
  
  synonymPlain - plain text
  
  Throws:
  
  IllegalChangeException
- setSynonym
  
  void setSynonym(int index, String synonymPlain, String synonymRichText) throws IllegalChangeException
  
  Sets the synonym at the given position.
  
  Parameters:
  
  index -
  
  synonymPlain - plain text
  
  synonymRichText - rich text
  
  Throws:
  
  IllegalChangeException
- addPublicIdentifier
  
  void addPublicIdentifier(PublicIdentifier publicIdentifier) throws IllegalChangeException
  
  Adds a public identifier to the item.
  
  Parameters:
  
  publicIdentifier -
  
  Throws:
  
  IllegalChangeException
- setPublicIdentifiers
  
  void setPublicIdentifiers(Collection<? extends PublicIdentifier> publicIdentifiers) throws IllegalChangeException
  
  Set the public identifiers of the item.
  
  Parameters:
  
  publicIdentifiers -
  
  Throws:
  
  IllegalChangeException
- removePublicIdentifier
  
  void removePublicIdentifier(PublicIdentifier publicIdentifier) throws IllegalChangeException
  
  Removes the public identifier from the item.
  
  Parameters:
  
  publicIdentifier -
  
  Throws:
  
  IllegalChangeException
- subCompartments
  
  List<? extends Compartment> subCompartments()
  
  Returns an unchangeable List of all sub compartments.
  
  Specified by:
  
  subCompartments in interface Compartment
  
  Returns:
  
  sub compartments
- outside
  
  Compartment outside()
  
  Returns the outside compartment if available otherwise null.
  
  Specified by:
  
  outside in interface Compartment
  
  Returns:
  
  outside compartment
- metabolites
  
  List<? extends Metabolite> metabolites()
  
  Returns an unchangeable List of all metabolites that occur in this compartment.
  
  Specified by:
  
  metabolites in interface Compartment
  
  Returns:
  
  all metabolites
- getMetabolite
  
  Metabolite getMetabolite(String name)
  
  Returns the metabolite node of the given name if available in the compartment, otherwise null.
  
  Specified by:
  
  getMetabolite in interface Compartment
  
  Parameters:
  
  name - of metabolite node
  
  Returns:
  
  found metabolite node
- getSubCompartment
  
  Compartment getSubCompartment(String name)
  
  Returns a sub compartment of the given name if available in the compartment, otherwise null.
  
  Specified by:
  
  getSubCompartment in interface Compartment
  
  Parameters:
  
  name - of sub compartment
  
  Returns:
  
  found sub compartment
- getDiagramItems
  
  List<? extends CompartmentItem> getDiagramItems()
  
  Specified by:
  
  getDiagramItems in interface AbstractVisibleComponent
  
  Specified by:
  
  getDiagramItems in interface AbstractVisibleComponent
  
  Specified by:
  
  getDiagramItems in interface Compartment
- getDiagramItems
  
  List<? extends CompartmentItem> getDiagramItems(Diagram diagram)
  
  Specified by:
  
  getDiagramItems in interface AbstractVisibleComponent
  
  Specified by:
  
  getDiagramItems in interface AbstractVisibleComponent
  
  Specified by:
  
  getDiagramItems in interface Compartment
- toReadOnly
  
  Compartment toReadOnly()
  
  Specified by:
  
  toReadOnly in interface AbstractModelComponent
  
  Specified by:
  
  toReadOnly in interface AbstractVisibleComponent
  
  Specified by:
  
  toReadOnly in interface WritableInterface