public class PhyloDataReader extends TypedAtomicActor
Entity.ContainedObjectsIterator| Modifier and Type | Field and Description |
|---|---|
TypedIOPort |
inputNexusData
The phylogenetic data in Nexus format is passed to the PhyloDataReader
actor through this input port.
|
TypedIOPort |
outputDataMatrix
The data matrix information contained in the input data is parsed and
sent out through this output port.
|
TypedIOPort |
outputTaxaInfo
The taxa information contained in the input data is parsed and sent out
through this output port.
|
TypedIOPort |
outputTree
The tree information contained in the input data is parsed and sent out
through this output port.
|
_typesValid_actorFiringListeners, _initializables, _notifyingActorFiring, _stopRequested_changeListeners, _changeLock, _changeRequests, _debugging, _debugListeners, _deferChangeRequests, _elementName, _isPersistent, _verbose, _workspace, ATTRIBUTES, CLASSNAME, COMPLETE, CONTENTS, DEEP, FULLNAME, LINKSCOMPLETED, NOT_READY, STOP_ITERATING| Constructor and Description |
|---|
PhyloDataReader(CompositeEntity container,
java.lang.String name)
Construct a PhyloDataReader actor with the given container and name.
|
| Modifier and Type | Method and Description |
|---|---|
void |
fire()
Read and parse the Nexus data.
|
boolean |
postfire()
Post fire the actor.
|
_containedTypeConstraints, _customTypeConstraints, _defaultTypeConstraints, _fireAt, _fireAt, attributeTypeChanged, clone, clone, isBackwardTypeInferenceEnabled, newPort, typeConstraintList, typeConstraints_actorFiring, _actorFiring, _declareDelayDependency, addActorFiringListener, addInitializable, connectionsChanged, createReceivers, declareDelayDependency, getCausalityInterface, getDirector, getExecutiveDirector, getManager, initialize, inputPortList, isFireFunctional, isStrict, iterate, newReceiver, outputPortList, prefire, preinitialize, pruneDependencies, recordFiring, removeActorFiringListener, removeDependency, removeInitializable, setContainer, stop, stopFire, terminate, wrapup_adjustDeferrals, _checkContainer, _getContainedObject, _propagateExistence, getContainer, instantiate, isAtomic, isOpaque, moveDown, moveToFirst, moveToIndex, moveToLast, moveUp, propagateExistence, setName_addPort, _description, _exportMoMLContents, _removePort, _validateSettables, connectedPortList, connectedPorts, containedObjectsIterator, getAttribute, getPort, getPorts, linkedRelationList, linkedRelations, portList, removeAllPorts, setClassDefinition, uniqueName_setParent, exportMoML, getChildren, getElementName, getParent, getPrototypeList, isClassDefinition, isWithinClassDefinition_addAttribute, _adjustOverride, _attachText, _cloneFixAttributeFields, _containedDecorators, _copyChangeRequestList, _debug, _debug, _debug, _debug, _debug, _executeChangeRequests, _getIndentPrefix, _isMoMLSuppressed, _markContentsDerived, _notifyHierarchyListenersAfterChange, _notifyHierarchyListenersBeforeChange, _propagateValue, _removeAttribute, _splitName, _stripNumericSuffix, addChangeListener, addDebugListener, addHierarchyListener, attributeChanged, attributeDeleted, attributeList, attributeList, decorators, deepContains, depthInHierarchy, description, description, event, executeChangeRequests, exportMoML, exportMoML, exportMoML, exportMoML, exportMoMLPlain, getAttribute, getAttributes, getChangeListeners, getClassName, getDecoratorAttribute, getDecoratorAttributes, getDerivedLevel, getDerivedList, getDisplayName, getFullName, getModelErrorHandler, getName, getName, getSource, handleModelError, isDeferringChangeRequests, isOverridden, isPersistent, lazyContainedObjectsIterator, message, notifyOfNameChange, propagateValue, propagateValues, removeAttribute, removeChangeListener, removeDebugListener, removeHierarchyListener, requestChange, setClassName, setDeferringChangeRequests, setDerivedLevel, setDisplayName, setModelErrorHandler, setPersistent, setSource, sortContainedObjects, toplevel, toString, validateSettables, workspaceequals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, waitcreateReceivers, getCausalityInterface, getDirector, getExecutiveDirector, getManager, inputPortList, newReceiver, outputPortListisFireFunctional, isStrict, iterate, prefire, stop, stopFire, terminateaddInitializable, initialize, preinitialize, removeInitializable, wrapupdescription, getContainer, getDisplayName, getFullName, getName, getName, setNamegetDerivedLevel, getDerivedList, propagateValuepublic TypedIOPort inputNexusData
public TypedIOPort outputTree
public TypedIOPort outputDataMatrix
public TypedIOPort outputTaxaInfo
public PhyloDataReader(CompositeEntity container, java.lang.String name) throws NameDuplicationException, IllegalActionException
container - The container.name - The name of this actor.IllegalActionException - If the entity cannot be contained by the proposed
container.NameDuplicationException - If the container already has an actor with this name.public void fire() throws IllegalActionException
fire in interface Executablefire in class AtomicActor<TypedIOPort>IllegalActionException - If it is thrown by the send() method sending out the
token.public boolean postfire()
postfire in interface Executablepostfire in class AtomicActor<TypedIOPort>