Module omix.api

Package omix.plugin.model.writable

Interface MetaboliteType

All Superinterfaces:

AbstractModelComponent, AbstractModelComponent, MetaboliteType, ReadOnlyInterface, WritableInterface

public interface MetaboliteType
extends AbstractModelComponent, MetaboliteType

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 Metabolite>	getExistingMetabolites()
List<? extends Metabolite>	getExistingMetabolites(Diagram diagram)
Metabolite	getMetabolite(Compartment compartment)	Returns the metabolite pool inside the given compartment.
default Metabolite	getNonCompartmentalizedMetabolite()
List<? extends Metabolite>	metabolites()	Returns all metabolite pools of different compartments.
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	setFormattedLabel(String html)	Set items visible label in html.
void	setIdentifier(String identifier)	Changes identifier of the item.
void	setPublicIdentifiers(Collection<? extends PublicIdentifier> publicIdentifiers)	Set the public identifiers of the item.
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.
MetaboliteType	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.MetaboliteType

getCustomProperty, getIdentifier, getPublicIdentifiers, name, setCustomProperty, setTmpCustomProperty, synonyms

Method Details

getMetabolite

Metabolite getMetabolite(Compartment compartment)

Returns the metabolite pool inside the given compartment.

Specified by:

getMetabolite in interface MetaboliteType

Parameters:

compartment -

Returns:

metabolite

getNonCompartmentalizedMetabolite

default Metabolite getNonCompartmentalizedMetabolite()

Specified by:

getNonCompartmentalizedMetabolite in interface MetaboliteType

metabolites

List<? extends Metabolite> metabolites()

Returns all metabolite pools of different compartments.

Specified by:

metabolites in interface MetaboliteType

Returns:

list of all metabolite pools

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

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

toReadOnly

MetaboliteType toReadOnly()

Specified by:

toReadOnly in interface AbstractModelComponent

Specified by:

toReadOnly in interface WritableInterface

getExistingMetabolites

List<? extends Metabolite> getExistingMetabolites()

Specified by:

getExistingMetabolites in interface MetaboliteType

getExistingMetabolites

List<? extends Metabolite> getExistingMetabolites(Diagram diagram)

Specified by:

getExistingMetabolites in interface MetaboliteType