Module omix.api

Package omix.plugin.model

Interface Model

All Superinterfaces:

ReadOnlyInterface

All Known Subinterfaces:

Model

@OVLInaccessible
public interface Model
extends ReadOnlyInterface

This method represents the complete network model. A network model consists of multipls diagrams.

Since:

Omix 2.0

Author:

Dr. Peter Droste, Omix Visualization

Method Summary

Modifier and Type	Method	Description
boolean	accessoryExists(String namespace, String accessoryName)
void	addChangeListener(ChangeListener listener)	Adds a ChangeListener which is triggered when the composition of the network changes.
void	addChangeListener(ModelChangeListener listener)	Adds a ModelChangeListener which is triggered when the composition of the network changes.
void	addContextMenuEntryProvider(ContextMenuEntryProvider provider)
void	addPropertyChangeListener(PropertyChangeListener propertyChangeListener)
List<? extends Compartment>	allCompartments()	Returns an unchangeable List of all compartment items.
boolean	compartmentExists(String name)	Determines if compartment of certain name exists.
OVLObject	createOVLObject(OVLConstructorDefinition constructor, Object... params)	This method invokes the constructor and returns a new instance of the OVL class.
List<String>	customPropertyNames()	Returns a name list of all available custom properties.
List<? extends CustomShape>	customShapes()
boolean	diagramExists(String name)	Determines if diagram of certain identifier exists.
List<String>	diagramIdentifiers()
List<? extends Diagram>	diagrams()
List<? extends EffectorEdge>	effectorEdges()	Returns an unchangeable List of all effector edges.
boolean	fieldExists(String namespace, String fieldName)
List<? extends FluxEdge>	fluxEdges()	Returns an unchangeable List of all flux edges.
List<? extends Accessory>	getAccessories()	Returns all accessories of the submitted network object defined in the document embedded OVL script.
List<? extends Accessory>	getAccessories(String namespace)	Returns all accessories of the submitted network object defined in the namespace.
Accessory	getAccessory(String accessoryName)	Returns the accessory of the submitted network object defined in the document embedded OVL script.
Accessory	getAccessory(String namespace, String accessoryName)	Returns the accessory of the submitted network object defined in the namespace.
List<String>	getActivePlugins()	Returns a list of all acive plugins.
List<? extends Accessory>	getAllAccessories()	Returns all accessories of the submitted network object defined in the document embedded OVL script and all namespaces.
Diagram	getCurrentDiagram()
Object	getCustomProperty(String name)	Returns the value of the custom property or null if not available.
CustomShape	getCustomShape(String name)
DataSourceManager	getDataSourceManager()	Returns the DataSourceManager of the model.
Diagram	getDiagram(String identifier)
String	getDocumentSetting(String key)	Get a setting by key. A plugin program can read and write settings in order to realize an own document based settings management.
String	getDocumentSetting(String key, String defaultValue)	Get a setting by key. A plugin program can read and write settings in order to realize an own document based settings management.
Set<Map.Entry<String,String>>	getDocumentSettings()	Returns a set of all available settings of the document. A plugin program can read and write settings in order to realize an own document based settings management.
Field	getField(String fieldName)	Returns the field of the submitted network object defined in the document embedded OVL script.
Field	getField(String namespace, String fieldName)	Returns the field of the submitted network object defined in the give namespace.
GraphicsBox	getGraphicsBox(String identifier)	Returns the graphics box with the given identifier if available, otherwise null.
GraphicsNode	getGraphicsNode(String identifier)	Returns the graphics node item by identifier if available, otherwise null.
GraphicsPath	getGraphicsPath(String identifier)	Returns the graphics path (free-form curve) with the given identifier if available, otherwise null.
String	getIdentifier()	Returns the name of the model
Link	getLink(String identifier)	Returns the link by identifier if available, otherwise null.
Metabolite	getMetabolite(String name)	Returns the (compartment free) metabolite node of the given name if available, otherwise null.
MetaboliteType	getMetaboliteType(String name)	Get a metabolite type by name.
MotifStamp	getMotifStamp(String name)
OVLProgram	getOVLProgram()	Returns the document embedded OVL program.
OVLProgram	getOVLProgram(String namespace)	Returns the OVL program matching the given namespace if available
Pathway	getPathway(String name)	Returns the pathway of the given name if available, otherwise null.
Set<? extends PublicIdentifier>	getPublicIdentifiers()	Returns the components public identifiers
Reaction	getReaction(String name)	Returns the reaction nodes of the given name if available, otherwise null.
Compartment	getTopLevelCompartment(String name)	Returns a toplevel compartment of the given name if available, otherwise null.
List<? extends GraphicsBox>	graphicsBoxes()	Returns an unchangeable List of all graphical boxes.
boolean	graphicsBoxExists(String identifier)	Determines if graphics box of certain identifier exists.
List<? extends GraphicsEdge>	graphicsEdges()	Returns an unchangeable List of all graphics edges (connection edges).
boolean	graphicsNodeExists(String identifier)	Determines if graphics node item of certain identifier exists.
List<? extends GraphicsNode>	graphicsNodes()	Returns an unchangeable List of all graphics nodes.
boolean	graphicsPathExists(String identifier)	Determines if graphics path (free-form curve) of certain identifier exists.
List<? extends GraphicsPath>	graphicsPaths()	Returns an unchangeable List of all graphical paths.
boolean	isNamespaceAvailable(String namespace)	Returns true if the given namespace is activated on the model.
boolean	isPluginActive(String id)	Asks if a plugin is active on the network model.
List<? extends LinkEdge>	linkEdges()	Returns an unchangeable List of all link edges.
boolean	linkExists(String identifier)	Determines if link of certain identifier exists.
List<? extends Link>	links()	Returns an unchangeable List of all links.
List<? extends Metabolite>	metabolites()	Returns an unchangeable List of all metabolite nodes.
boolean	metaboliteTypeExists(String name)	Determines if metabolite type of certain name exists.
List<? extends MetaboliteType>	metaboliteTypes()	All metabolite types being part of the model.
boolean	motifStampExists(String name)
List<? extends MotifStamp>	motifStamps()
boolean	pathwayExists(String name)	Determines if pathway of certain name exists.
List<? extends Pathway>	pathways()	Returns an unchangeable List of all pathway items.
boolean	reactionExists(String name)	Determines if reaction of certain name exists.
List<? extends Reaction>	reactions()	Returns an unchangeable List of all reaction nodes.
void	removeChangeListener(ChangeListener listener)	Removes the listener which is therefore no longer triggered.
void	removeChangeListener(ModelChangeListener listener)	Removes the listener which is therefore no longer triggered.
void	removeContextMenuEntryProvider(ContextMenuEntryProvider provider)
void	removePropertyChangeListener(PropertyChangeListener propertyChangeListener)
void	setCustomProperty(String name, Object value)	Adds a custom property to the network item.
void	setTmpCustomProperty(String name, Object value)	Adds a temporary custom property to the network item.
StyleSheet	styleSheet()

Method Details

metaboliteTypes

List<? extends MetaboliteType> metaboliteTypes()

All metabolite types being part of the model.

Returns:

unmodifiable list of etabolite types

getMetaboliteType

MetaboliteType getMetaboliteType(String name)

Get a metabolite type by name.

Parameters:

name -

Returns:

the metabolite type if exists or null

metaboliteTypeExists

boolean metaboliteTypeExists(String name)

Determines if metabolite type of certain name exists.

Parameters:

name -

Returns:

metabolite type exists?

getIdentifier

String getIdentifier()

Returns the name of the model

See Also:

omix.plugin.network.AbstractItem#getIdentifier()

getDocumentSettings

Set<Map.Entry<String,String>> getDocumentSettings()

Returns a set of all available settings of the document.
A plugin program can read and write settings in order to realize an own document based settings management.

Returns:

unmodifiable set of settings

getDocumentSetting

String getDocumentSetting(String key)

Get a setting by key.
A plugin program can read and write settings in order to realize an own document based settings management.

Parameters:

key -

Returns:

value of the setting if exists. null otherwise.

getDocumentSetting

String getDocumentSetting(String key, String defaultValue)

Get a setting by key.
A plugin program can read and write settings in order to realize an own document based settings management.

Parameters:

key -

defaultValue -

Returns:

value of the setting if exists. defaultValue otherwise.

getActivePlugins

List<String> getActivePlugins()

Returns a list of all acive plugins.

Returns:

active plugins

isPluginActive

boolean isPluginActive(String id)

Asks if a plugin is active on the network model.

Parameters:

id - plugin ID

Returns:

plugin active

getPublicIdentifiers

Set<? extends PublicIdentifier> getPublicIdentifiers()

Returns the components public identifiers

Returns:

set of public identifiers

Since:

Omix 1.9.0

getDataSourceManager

DataSourceManager getDataSourceManager()

Returns the DataSourceManager of the model.

Returns:

DataSourceManager

reactions

List<? extends Reaction> reactions()

Returns an unchangeable List of all reaction nodes.

Returns:

list of reactions

metabolites

List<? extends Metabolite> metabolites()

Returns an unchangeable List of all metabolite nodes.

Returns:

list of metabolites

pathways

List<? extends Pathway> pathways()

Returns an unchangeable List of all pathway items.

Returns:

list of pathways

allCompartments

List<? extends Compartment> allCompartments()

Returns an unchangeable List of all compartment items.

Returns:

list of compartments

graphicsEdges

List<? extends GraphicsEdge> graphicsEdges()

Returns an unchangeable List of all graphics edges (connection edges).

Returns:

list of graphics edges

Since:

Omix 1.8.0

graphicsNodes

List<? extends GraphicsNode> graphicsNodes()

Returns an unchangeable List of all graphics nodes.

Returns:

list of graphics nodes

Since:

Omix 1.8.0

linkEdges

List<? extends LinkEdge> linkEdges()

Returns an unchangeable List of all link edges.

Returns:

list of link edges

Since:

Omix 2.0.0

links

List<? extends Link> links()

Returns an unchangeable List of all links.

Returns:

list of links

Since:

Omix 2.0.0

effectorEdges

List<? extends EffectorEdge> effectorEdges()

Returns an unchangeable List of all effector edges.

Returns:

list of effector edges

fluxEdges

List<? extends FluxEdge> fluxEdges()

Returns an unchangeable List of all flux edges.

Returns:

list of flux edges

graphicsBoxes

List<? extends GraphicsBox> graphicsBoxes()

Returns an unchangeable List of all graphical boxes.

Returns:

list of graphical boxes

Since:

Omix 2.0.0

graphicsPaths

List<? extends GraphicsPath> graphicsPaths()

Returns an unchangeable List of all graphical paths.

Returns:

list of graphical paths

Since:

Omix 2.0.0

diagrams

List<? extends Diagram> diagrams()

diagramIdentifiers

List<String> diagramIdentifiers()

getDiagram

Diagram getDiagram(String identifier)

getCurrentDiagram

Diagram getCurrentDiagram()

getReaction

Reaction getReaction(String name)

Returns the reaction nodes of the given name if available, otherwise null.

Parameters:

name - of the reaction

Returns:

found reaction

getMetabolite

Metabolite getMetabolite(String name)

Returns the (compartment free) metabolite node of the given name if available, otherwise null. In order to get access to metabolites contained in a compartment call Compartment.getMetabolite(String).

Parameters:

name - of metabolite

Returns:

found metabolite

getPathway

Pathway getPathway(String name)

Returns the pathway of the given name if available, otherwise null.

Parameters:

name - of the pathway

Returns:

found pathway

getTopLevelCompartment

Compartment getTopLevelCompartment(String name)

Returns a toplevel compartment of the given name if available, otherwise null. In order to get access to a sub compartment call Compartment.getSubCompartment(String).

Parameters:

name - of the compartment

Returns:

found compartment

getGraphicsNode

GraphicsNode getGraphicsNode(String identifier)

Returns the graphics node item by identifier if available, otherwise null.

Parameters:

identifier - of the GraphicsNode

Returns:

found GraphicsNode

Since:

Omix 1.8.0

getLink

Link getLink(String identifier)

Returns the link by identifier if available, otherwise null.

Parameters:

identifier - of the Link

Returns:

found Link

Since:

Omix 2.0.0

getGraphicsBox

GraphicsBox getGraphicsBox(String identifier)

Returns the graphics box with the given identifier if available, otherwise null.

Parameters:

identifier - of the graphics box

Returns:

found graphics path

getGraphicsPath

GraphicsPath getGraphicsPath(String identifier)

Returns the graphics path (free-form curve) with the given identifier if available, otherwise null.

Parameters:

identifier - of the graphics path

Returns:

found graphics path

reactionExists

boolean reactionExists(String name)

Determines if reaction of certain name exists.

Parameters:

name -

Returns:

reaction exist?

pathwayExists

boolean pathwayExists(String name)

Determines if pathway of certain name exists.

Parameters:

name -

Returns:

pathway exist?

compartmentExists

boolean compartmentExists(String name)

Determines if compartment of certain name exists.

Parameters:

name -

Returns:

compartment exist?

graphicsNodeExists

boolean graphicsNodeExists(String identifier)

Determines if graphics node item of certain identifier exists.

Parameters:

identifier -

Returns:

graphics node exist?

Since:

Omix 1.8.0

linkExists

boolean linkExists(String identifier)

Determines if link of certain identifier exists.

Parameters:

identifier -

Returns:

link exist?

Since:

Omix 2.0.0

graphicsBoxExists

boolean graphicsBoxExists(String identifier)

Determines if graphics box of certain identifier exists.

Parameters:

identifier -

Returns:

graphics box exist?

Since:

Omix 2.0.0

graphicsPathExists

boolean graphicsPathExists(String identifier)

Determines if graphics path (free-form curve) of certain identifier exists.

Parameters:

identifier -

Returns:

graphics path exist?

Since:

Omix 2.0.0

diagramExists

boolean diagramExists(String name)

Determines if diagram of certain identifier exists.

Parameters:

identifier -

Returns:

diagram exist?

addChangeListener

@OVLInaccessible void addChangeListener(ModelChangeListener listener)

Adds a ModelChangeListener which is triggered when the composition of the network changes.

Parameters:

listener - to be added

removeChangeListener

@OVLInaccessible void removeChangeListener(ModelChangeListener listener)

Removes the listener which is therefore no longer triggered.

Parameters:

listener - to be removed

addChangeListener

@OVLInaccessible void addChangeListener(ChangeListener listener)

Adds a ChangeListener which is triggered when the composition of the network changes.

Parameters:

listener - to be added

removeChangeListener

@OVLInaccessible void removeChangeListener(ChangeListener listener)

Removes the listener which is therefore no longer triggered.

Parameters:

listener - to be removed

motifStampExists

boolean motifStampExists(String name)

motifStamps

List<? extends MotifStamp> motifStamps()

getMotifStamp

MotifStamp getMotifStamp(String name)

setCustomProperty

void setCustomProperty(String name, Object value) throws IllegalAccessException

Adds a custom property to the network item. Each item can carry arbitrary values as custom property. The property content is stored to the document file as far as possible. If the value cannot be saved to file, the property is removed after relaunch. Custom properties can be accessed from all namespaces. Set null to remove property. Setting custom properties in OVL is undoable.

Parameters:

name -

value -

Throws:

IllegalAccessException

See Also:

setTmpCustomProperty(String, Object), getCustomProperty(String), customPropertyNames()

setTmpCustomProperty

void setTmpCustomProperty(String name, Object value) throws IllegalAccessException

Adds a temporary custom property to the network item. Each item can carry arbitrary values as custom property. The property content is not stored to the document file. Instead, the property is removed after relaunch. Custom properties can be accessed from all namespaces. Set null to remove property. Setting custom properties in OVL is undoable.

Parameters:

name -

value -

Throws:

IllegalAccessException

See Also:

setCustomProperty(String, Object), getCustomProperty(String), customPropertyNames()

getCustomProperty

Object getCustomProperty(String name)

Returns the value of the custom property or null if not available.

Parameters:

name -

Returns:

value

customPropertyNames

List<String> customPropertyNames()

Returns a name list of all available custom properties.

Returns:

name list

customShapes

List<? extends CustomShape> customShapes()

getCustomShape

CustomShape getCustomShape(String name)

getAccessories

List<? extends Accessory> getAccessories()

Returns all accessories of the submitted network object defined in the document embedded OVL script.

Returns:

unmodifiable list of accessories

getAccessories

List<? extends Accessory> getAccessories(String namespace)

Returns all accessories of the submitted network object defined in the namespace.

Parameters:

namespace -

Returns:

unmodifiable list of accessories

getAllAccessories

List<? extends Accessory> getAllAccessories()

Returns all accessories of the submitted network object defined in the document embedded OVL script and all namespaces.

Returns:

unmodifiable list of accessories

getAccessory

Accessory getAccessory(String namespace, String accessoryName) throws IllegalAccessException, NoSuchFieldException

Returns the accessory of the submitted network object defined in the namespace.

Parameters:

namespace -

accessoryName -

Returns:

accessory

Throws:

IllegalAccessException - if accessory is protected

NoSuchFieldException - if accessory does not exist

getAccessory

Accessory getAccessory(String accessoryName) throws IllegalAccessException, NoSuchFieldException

Returns the accessory of the submitted network object defined in the document embedded OVL script.

Parameters:

accessoryName -

Returns:

accessory

Throws:

IllegalAccessException - if accessory is protected

NoSuchFieldException - if accessory does not exist

accessoryExists

boolean accessoryExists(String namespace, String accessoryName)

fieldExists

boolean fieldExists(String namespace, String fieldName)

getField

Field getField(String fieldName) throws IllegalAccessException, NoSuchFieldException

Returns the field of the submitted network object defined in the document embedded OVL script.

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.

Parameters:

namespace -

fieldName -

Returns:

reference object representing the field

Throws:

IllegalAccessException - if field is protected

NoSuchFieldException - if field does not exist

getOVLProgram

OVLProgram getOVLProgram()

Returns the document embedded OVL program.

Returns:

reference object representing the OVL program

getOVLProgram

OVLProgram getOVLProgram(String namespace)

Returns the OVL program matching the given namespace if available

Returns:

reference object representing the OVL program if available or null.

isNamespaceAvailable

boolean isNamespaceAvailable(String namespace)

Returns true if the given namespace is activated on the model.

Parameters:

namespace -

Returns:

namespace available?

addContextMenuEntryProvider

void addContextMenuEntryProvider(ContextMenuEntryProvider provider)

removeContextMenuEntryProvider

void removeContextMenuEntryProvider(ContextMenuEntryProvider provider)

addPropertyChangeListener

void addPropertyChangeListener(PropertyChangeListener propertyChangeListener)

removePropertyChangeListener

void removePropertyChangeListener(PropertyChangeListener propertyChangeListener)

styleSheet

StyleSheet styleSheet()

createOVLObject

OVLObject createOVLObject(OVLConstructorDefinition constructor, Object... params) throws IllegalAccessException, IllegalArgumentException, InvocationTargetException

This method invokes the constructor and returns a new instance of the OVL class.

Parameters:

params - a list of parameters matching to OVLAbstractInvokableDefinition.getParameterTypes()

Returns:

the new OVL object

Throws:

IllegalAccessException - if this constructor is inaccessible

IllegalArgumentException - if the number or type of arguments is invalid

InvocationTargetException - nesting one of OVLAbstractInvokableDefinition.getExceptionTypes()