info.bioinfweb.jphyloio.dataadapters

Interface ObjectListDataAdapter<E extends JPhyloIOEvent>

Type Parameters:

E - the event type of start events representing elements of this list

All Known Subinterfaces:

OTUListDataAdapter

All Known Implementing Classes:

EmptyObjectListDataAdapter, StoreObjectListDataAdapter, StoreOTUListDataAdapter, UndefinedOTUListDataAdapter

public interface ObjectListDataAdapter<E extends JPhyloIOEvent>

Allows to provide data for a list of phylogenetic objects. All objects need to be identified by unique IDs, provided by getIDIterator(ReadWriteParameterMap). The start event of each object will be requested by separate calls of getObjectStartEvent(ReadWriteParameterMap, String) and the event sequence by separate calls of writeContentData(ReadWriteParameterMap, JPhyloIOEventReceiver, String).

Such objects may e.g. be OTUs, token sets or character sets, depending on where instances of this interface are used.

Applications implementing this adapter may consider to inherit their implementation from EmptyAnnotatedDataAdapter. EmptyObjectListDataAdapter allows to directly define an empty list.

Author:

Ben Stöver

Method Summary

Modifier and Type	Method and Description
long	getCount(ReadWriteParameterMap parameters) Returns the number of objects to be returned by getIDIterator(ReadWriteParameterMap).
java.util.Iterator<java.lang.String>	getIDIterator(ReadWriteParameterMap parameters) Returns an iterator returning the IDs of all objects contained in the list modeled by this instance.
E	getObjectStartEvent(ReadWriteParameterMap parameters, java.lang.String id) Returns the start event of an object determined by the specified object ID.
void	writeContentData(ReadWriteParameterMap parameters, JPhyloIOEventReceiver receiver, java.lang.String id) Writes the nested events in the specified object describing its contents.

Method Detail

getObjectStartEvent

E getObjectStartEvent(ReadWriteParameterMap parameters,
                      java.lang.String id)
               throws java.lang.IllegalArgumentException

Returns the start event of an object determined by the specified object ID.

Parameters:

parameters - the parameter map of the calling writer that provides context information for the data request

id - the ID of the requested object

Returns:

an instance of a labeled ID event that describes the specified object

Throws:

java.lang.IllegalArgumentException - if no to object for the specified ID is present

getCount

long getCount(ReadWriteParameterMap parameters)

Returns the number of objects to be returned by getIDIterator(ReadWriteParameterMap).

Parameters:

parameters - the parameter map of the calling writer that provides context information for the data request

Returns:

the number of objects in the list modeled by this instance

getIDIterator

java.util.Iterator<java.lang.String> getIDIterator(ReadWriteParameterMap parameters)

Returns an iterator returning the IDs of all objects contained in the list modeled by this instance.

Parameters:

parameters - the parameter map of the calling writer that provides context information for the data request

Returns:

an iterator returning the IDs (Depending in the usage of this object, the returned iterator must return at least one element or can be empty, but it may never be null.)

writeContentData

void writeContentData(ReadWriteParameterMap parameters,
                      JPhyloIOEventReceiver receiver,
                      java.lang.String id)
               throws java.io.IOException,
                      java.lang.IllegalArgumentException

Writes the nested events in the specified object describing its contents.

Parameters:

parameters - the parameter map of the calling writer that provides context information for the data request

receiver - the receiver for the events

nodeID - the ID of the requested node

Throws:

java.io.IOException - if a I/O error occurs while writing the data

java.lang.IllegalArgumentException - if an unknown ID was specified