Deprecated API

Contents

• Methods
• Constructors
• Enum Constants

Deprecated Methods

Method	Description
org.biopax.paxtools.controller.Cloner.clone(Model, Set<BioPAXElement>)	use Cloner.clone(Set) instead ('source' model was not used in previous versions)
org.biopax.paxtools.controller.Completer.complete(Collection<BioPAXElement>, Model)	use Completer.complete(Collection) instead (- model is never explicitly used there)
org.biopax.paxtools.controller.ModelUtils.getAllChildren(BioPAXElement, Filter<PropertyEditor>...)	use Fetcher.fetch(BioPAXElement, Model) instead (with Fetcher.nextStepFilter or without)
org.biopax.paxtools.model.level3.Control.addControlled(Process)	violates OWL functional property restriction; should be: setControlled(process)
org.biopax.paxtools.model.level3.Control.getControlled()	should return one Process or null; see also deprecated Control.addControlled(Process)
org.biopax.paxtools.model.level3.Control.removeControlled(Process)	was a mistake; see also deprecated Control.addControlled(Process)

Deprecated Constructors

Constructor	Description
org.biopax.paxtools.controller.ShallowCopy(EditorMap)	use Level based constructor instead.

Deprecated Enum Constants

Enum Constant	Description
org.biopax.paxtools.model.level3.ControlType.ACTIVATION_UNKMECH	LEVEL 1 workaround
org.biopax.paxtools.model.level3.ControlType.INHIBITION_UNKMECH	LEVEL 1 workaround