info.bioinfweb.libralign.model.factory

Class AbstractAlignmentModelFactory<T>

java.lang.Object

info.bioinfweb.libralign.model.factory.AbstractAlignmentModelFactory<T>

Type Parameters:

T - the token type of the alignment models to be created by this instance

All Implemented Interfaces:

AlignmentModelFactory<T>

Direct Known Subclasses:

BioPolymerCharAlignmentModelFactory, DoubleAlignmentModelFactory, FloatAlignmentModelFactory

public abstract class AbstractAlignmentModelFactory<T>
extends java.lang.Object
implements AlignmentModelFactory<T>

Implements shared functionality for alignment model factories.

Since:

0.4.0

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
AbstractAlignmentModelFactory() Creates a new instance of this class without an shared sequence ID manager.
AbstractAlignmentModelFactory(SequenceIDManager sharedIDManager, boolean reuseSequenceIDs, T defaultToken) Creates a new instance of this class using a shared sequence ID manager.
AbstractAlignmentModelFactory(T defaultToken) Creates a new instance of this class without an shared sequence ID manager.

Method Summary

Modifier and Type	Method and Description
AlignmentModel<T>	createNewModel(NewAlignmentModelParameterMap parameterMap) Creates a new instance of an alignment model according to the specified parameters.
T	createToken(AlignmentModel<T> alignmentModel, java.lang.String tokenRepresentation) Creates a token using TokenSet.tokenByRepresentation(String).
protected abstract AlignmentModel<T>	doCreateNewModel(NewAlignmentModelParameterMap parameterMap)
T	getDefaultToken() Returns the default token to be used if invalid token representations are passed to createToken(AlignmentModel, String).
SequenceIDManager	getSharedIDManager() Returns the sequence ID manager that is shared among all model instances created by this factory.
boolean	hasSharedIDManager() Determines whether this instance uses a shared sequence ID manager.
boolean	isReuseSequenceIDs() Determines whether models created by this factory should reuse IDs already present in their associated ID manager or should always create new IDs.

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractAlignmentModelFactory

public AbstractAlignmentModelFactory()

Creates a new instance of this class without an shared sequence ID manager. Each model instance, that will be created by this factory, will have its own sequence ID manager. No default token will be used.

AbstractAlignmentModelFactory

public AbstractAlignmentModelFactory(T defaultToken)

Creates a new instance of this class without an shared sequence ID manager. Each model instance, that will be created by this factory, will have its own sequence ID manager.

Parameters:

defaultToken - a default token to be used if invalid token representations are passed to createToken(AlignmentModel, String) (If null is specified here, createToken(AlignmentModel, String) will throw an exception instead in such cases.)

AbstractAlignmentModelFactory

public AbstractAlignmentModelFactory(SequenceIDManager sharedIDManager,
                                     boolean reuseSequenceIDs,
                                     T defaultToken)

Creates a new instance of this class using a shared sequence ID manager.

Parameters:

sharedIDManager - the sequence ID manager that will be shared by all model instances created by this factory

reuseSequenceIDs - Specify true if models created by this factory should reuse IDs already present in their associated ID manager or false if new IDs should always be created. (See the documentation of AbstractUndecoratedAlignmentModel.isReuseSequenceIDs() for details.)

defaultToken - a default token to be used if invalid token representations are passed to createToken(AlignmentModel, String) (If null is specified here, createToken(AlignmentModel, String) will throw an exception instead in such cases.)

Method Detail

getSharedIDManager

public SequenceIDManager getSharedIDManager()

Returns the sequence ID manager that is shared among all model instances created by this factory.

Returns:

the shared ID manager of null if no shared ID manager is used by this factory

See Also:

hasSharedIDManager()

isReuseSequenceIDs

public boolean isReuseSequenceIDs()

Determines whether models created by this factory should reuse IDs already present in their associated ID manager or should always create new IDs. (See the documentation of AbstractUndecoratedAlignmentModel.isReuseSequenceIDs() for details.)

Returns:

true if IDs should be reused, false otherwise

hasSharedIDManager

public boolean hasSharedIDManager()

Determines whether this instance uses a shared sequence ID manager.

Returns:

true if a shared ID manager is present, false otherwise

See Also:

getSharedIDManager()

getDefaultToken

public T getDefaultToken()

Returns the default token to be used if invalid token representations are passed to createToken(AlignmentModel, String).

Returns:

the default token or null if none is defined

createToken

public T createToken(AlignmentModel<T> alignmentModel,
                     java.lang.String tokenRepresentation)
              throws InvalidTokenRepresentationException

Creates a token using TokenSet.tokenByRepresentation(String).

Specified by:

createToken in interface AlignmentModelFactory<T>

Parameters:

alignmentModel - the alignment model which will hold the returned token

tokenRepresentation - the string representation of the token to be returned (e.g. read from an alignment file)

Returns:

the token or getDefaultToken() if no according representation was found in the set

Throws:

InvalidTokenRepresentationException - if a token representation is not found in the token set of alignmentModel and no default token was specified

See Also:

AlignmentModelFactory.createToken(info.bioinfweb.libralign.model.AlignmentModel, java.lang.String)

doCreateNewModel

protected abstract AlignmentModel<T> doCreateNewModel(NewAlignmentModelParameterMap parameterMap)

createNewModel

public AlignmentModel<T> createNewModel(NewAlignmentModelParameterMap parameterMap)

Description copied from interface: AlignmentModelFactory

Creates a new instance of an alignment model according to the specified parameters.

Specified by:

createNewModel in interface AlignmentModelFactory<T>

Parameters:

parameterMap - a map with parameters describing the requirements to be met by the returned instance

Returns:

a new instance of an alignment model or null if this factory is not able to create an object that meets the specified requirements