info.bioinfweb.libralign.model.io

Class AlignmentModelEventReader

java.lang.Object

info.bioinfweb.libralign.model.io.AlignmentModelEventReader

All Implemented Interfaces:

info.bioinfweb.jphyloio.push.JPhyloIOEventListener

public class AlignmentModelEventReader
extends java.lang.Object
implements info.bioinfweb.jphyloio.push.JPhyloIOEventListener

Reads alignment models from a JPhyloIO event stream. Usually instances of this class will not be used directly in application code, but an instance of AlignmentDataReader would be used instead.

Since:

0.4.0

Author:

Ben Stöver

See Also:

AlignmentDataReader

Module:

info.bioinfweb.libralign.io

Constructor Summary

Constructors

Constructor and Description
AlignmentModelEventReader() Creates a new instance of this class using StringAlignmentModelFactory as the default factory and DoubleAlignmentModelFactory as the factory for continuous data.
AlignmentModelEventReader(AlignmentModelFactory<?> defaultFactory) Creates a new instance of this class with an empty factory map.
AlignmentModelEventReader(AlignmentModelFactory<?> defaultFactory, java.util.Map<CharacterStateSetType,AlignmentModelFactory> factoryMap) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
java.util.List<AlignmentModel<?>>	getCompletedModels() Returns the list of alignment models that have been completely read from the underlying JPhyloIO event stream until now.
java.lang.String	getCurrentAlignmentID() Returns the JPhyloIO ID of the alignment model that is currently read and returned by getCurrentModel().
ConcatenatedAlignmentModel	getCurrentConcatenatedModel() Returns the concatenated model that is currently read by this instance.
AlignmentModel<?>	getCurrentModel() Returns the alignment model that is currently read.
AlignmentModelFactory<?>	getDefaultFactory() Returns the alignment model factory that is used to create new model instances for character state (token) set types which are not defined in the factory map.
java.util.Map<CharacterStateSetType,AlignmentModelFactory>	getFactoryMap() Returns the map of alignment model factories for different character state (token) set types.
AlignmentModel<?>	getModelByJPhyloIOID(java.lang.String id) Returns the alignment model associated with the specified JPhyloIO ID.
boolean	hasCurrentConcatenatedModel() Checks if a concatenated alignment model is currently read by this instance.
boolean	hasCurrentModel() Checks whether an alignment model that is currently filled with data from the stream is present.
void	processEvent(info.bioinfweb.jphyloio.JPhyloIOEventReader source, info.bioinfweb.jphyloio.events.JPhyloIOEvent event)
void	setNucleotideFactories(AlignmentModelFactory<?> factory) Sets the specified map for all nucleotide factories (identified with the keys CharacterStateSetType.NUCLEOTIDE, CharacterStateSetType.DNA, CharacterStateSetType.RNA).

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AlignmentModelEventReader

public AlignmentModelEventReader()

Creates a new instance of this class using StringAlignmentModelFactory as the default factory and DoubleAlignmentModelFactory as the factory for continuous data.

AlignmentModelEventReader

public AlignmentModelEventReader(AlignmentModelFactory<?> defaultFactory)

Creates a new instance of this class with an empty factory map. The map can be populated later on using getFactoryMap().

Parameters:

defaultFactory - the factory to use to create new model instances for character state (token) set types which are not defined in the factory map

AlignmentModelEventReader

public AlignmentModelEventReader(AlignmentModelFactory<?> defaultFactory,
                                 java.util.Map<CharacterStateSetType,AlignmentModelFactory> factoryMap)

Creates a new instance of this class.

Parameters:

defaultFactory - the factory to use to create new model instances for character state (token) set types which are not defined in the factory map

factoryMap - a map of alignment model factories for different character state (token) set types

Method Detail

getDefaultFactory

public AlignmentModelFactory<?> getDefaultFactory()

Returns the alignment model factory that is used to create new model instances for character state (token) set types which are not defined in the factory map.

Returns:

the default alignment model factory

See Also:

getFactoryMap()

getFactoryMap

public java.util.Map<CharacterStateSetType,AlignmentModelFactory> getFactoryMap()

Returns the map of alignment model factories for different character state (token) set types.

Returns:

the map of factories

See Also:

getDefaultFactory()

setNucleotideFactories

public void setNucleotideFactories(AlignmentModelFactory<?> factory)

Sets the specified map for all nucleotide factories (identified with the keys CharacterStateSetType.NUCLEOTIDE, CharacterStateSetType.DNA, CharacterStateSetType.RNA).

Previously defined factories for the according types are replaced by this operation.

Parameters:

factory - the alignment model factory to be used for all nucleotide token set types

getCurrentModel

public AlignmentModel<?> getCurrentModel()

Returns the alignment model that is currently read. Note that this model might not yet contain all data, because this data is currently read from the underlying JPhyloIO event stream. As soon as a model is read completely (an alignment end event if reached) it is added to getCompletedModels() and this method will return null until the next alignment is reached in the stream.

Returns:

the current alignment model or null if the current stream position is not between an alignment start and end event

getCurrentAlignmentID

public java.lang.String getCurrentAlignmentID()

Returns the JPhyloIO ID of the alignment model that is currently read and returned by getCurrentModel().

Returns:

the ID or null if no model is currently read

getCurrentConcatenatedModel

public ConcatenatedAlignmentModel getCurrentConcatenatedModel()

Returns the concatenated model that is currently read by this instance.

Returns:

the concatenated model or null if the model currently read is not an concatenated model or not model currently is read

See Also:

hasCurrentConcatenatedModel(), getCurrentModel()

hasCurrentConcatenatedModel

public boolean hasCurrentConcatenatedModel()

Checks if a concatenated alignment model is currently read by this instance.

Returns:

true if a concatenated model is currently read, false if no model is read or the current model is not a concatenated instance

hasCurrentModel

public boolean hasCurrentModel()

Checks whether an alignment model that is currently filled with data from the stream is present. That would be the case every time the reader is positioned between an alignment start and end event.

Returns:

true if an alignment model is currently present, false otherwise.

getCompletedModels

public java.util.List<AlignmentModel<?>> getCompletedModels()

Returns the list of alignment models that have been completely read from the underlying JPhyloIO event stream until now.

Returns:

the list of models (may be empty, but is never null)

getModelByJPhyloIOID

public AlignmentModel<?> getModelByJPhyloIOID(java.lang.String id)

Returns the alignment model associated with the specified JPhyloIO ID. (The ID of the alignment start event in JPhyloIO.) This method will first test if the currently loading model is associated with this ID and return it. Otherwise a completed model associated with this ID will be returned. (Note that the model that is currently loading might not yet be complete.)

Parameters:

id - the JPhyloIO of the alignment model

Returns:

the alignment model or null is no model associated with the specified ID has yet been started to be loaded

processEvent

public void processEvent(info.bioinfweb.jphyloio.JPhyloIOEventReader source,
                         info.bioinfweb.jphyloio.events.JPhyloIOEvent event)

Specified by:

processEvent in interface info.bioinfweb.jphyloio.push.JPhyloIOEventListener