Module omix.api

Package omix.plugin.model

Interface MetaboliteType

All Superinterfaces:

AbstractModelComponent, ReadOnlyInterface

All Known Subinterfaces:

MetaboliteType

@OVLInaccessible
public interface MetaboliteType
extends AbstractModelComponent

This class represents metabolite types of a biochamical model. A metabolite type can be available in different pools subdivided by different compartments.

Author:

Dr. Peter Droste, Omix Visualization

Method Summary

Modifier and Type	Method	Description
Object	getCustomProperty(String name)	Returns the value of the custom property or null if not available.
List<? extends Metabolite>	getExistingMetabolites()
List<? extends Metabolite>	getExistingMetabolites(Diagram diagram)
String	getIdentifier()
Metabolite	getMetabolite(Compartment compartment)	Returns the metabolite pool inside the given compartment.
default Metabolite	getNonCompartmentalizedMetabolite()
Set<? extends PublicIdentifier>	getPublicIdentifiers()	Returns the components public identifiers
List<? extends Metabolite>	metabolites()	Returns all metabolite pools of different compartments.
FormattedName	name()
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.
Synonyms	synonyms()	Returns the synonyms of the item.

Methods inherited from interface omix.plugin.model.AbstractModelComponent

addChangeListener, addPropertyChangeListener, fieldExists, getField, getField, model, removeChangeListener, removePropertyChangeListener

Method Details

getMetabolite

Metabolite getMetabolite(Compartment compartment)

Returns the metabolite pool inside the given compartment.

Parameters:

compartment -

Returns:

metabolite

getNonCompartmentalizedMetabolite

default Metabolite getNonCompartmentalizedMetabolite()

metabolites

List<? extends Metabolite> metabolites()

Returns all metabolite pools of different compartments.

Returns:

list of all metabolite pools

getIdentifier

String getIdentifier()

Specified by:

getIdentifier in interface AbstractModelComponent

name

FormattedName name()

synonyms

Synonyms synonyms()

Returns the synonyms of the item.

Returns:

synonyms

Since:

Omix 1.9.0

getPublicIdentifiers

Set<? extends PublicIdentifier> getPublicIdentifiers()

Returns the components public identifiers

Returns:

set of public identifiers

Since:

Omix 1.9.0

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

getExistingMetabolites

List<? extends Metabolite> getExistingMetabolites()

getExistingMetabolites

List<? extends Metabolite> getExistingMetabolites(Diagram diagram)