Deprecated API

Contents

• Deprecated Methods
• Deprecated Constructors
• Deprecated Enum Constants

Deprecated Methods

Method and Description
org.biopax.paxtools.model.level3.Control.addControlled(Process) violates OWL functional property restriction; should be: setControlled(process)
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.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 and Description
org.biopax.paxtools.controller.ShallowCopy(EditorMap) use Level based constructor instead.

Deprecated Enum Constants

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