info.bioinfweb.libralign.model.implementations

Class AbstractMapBasedAlignmentModel<S,T>

java.lang.Object

info.bioinfweb.libralign.model.implementations.AbstractAlignmentModel<T>

info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel<T>

info.bioinfweb.libralign.model.implementations.AbstractMapBasedAlignmentModel<S,T>

Type Parameters:

S - the type of the sequence objects (e.g. a List implementation or a BioJava sequence type)

T - the type of sequence elements (tokens) the implementing provider object works with

All Implemented Interfaces:

AlignmentModel<T>

Direct Known Subclasses:

AbstractListAlignmentModel, AbstractUnmodifyableAlignmentModel

public abstract class AbstractMapBasedAlignmentModel<S,T>
extends AbstractUndecoratedAlignmentModel<T>

Implements all methods dealing with the organization of the sequence set using some implementation of Map to identify the sequence object belonging to a sequence ID. The ordering of the sequences is implemented using an additional list storing the IDs. Inherited classes have the option to provide a custom map implementation instead of HashMap which is the default.

Sequences are sorted by the order they are added to the model. This ordering in independent to the SequenceOrder object used in an associated AlignmentArea.

Author:

Ben Stöver

See Also:

SequenceAccessAlignmentModel, SequenceOrder, AlignmentArea

Constructor Summary

Constructors

Constructor and Description
AbstractMapBasedAlignmentModel(TokenSet<T> tokenSet, SequenceIDManager idManager, boolean reuseSequenceIDs) Creates a new instance of this class relying on a HashMap.
AbstractMapBasedAlignmentModel(TokenSet<T> tokenSet, SequenceIDManager idManager, boolean reuseSequenceIDs, java.util.Map<java.lang.String,S> sequenceMap) Creates a new instance of this class with a custom map implementation.
AbstractMapBasedAlignmentModel(TokenSet<T> tokenSet, SequenceIDManager idManager, boolean reuseSequenceIDs, java.util.Map<java.lang.String,S> sequenceMap, java.util.List<java.lang.String> sequenceOrder) Creates a new instance of this class with a custom map and list implementation.

Method Summary

Modifier and Type	Method and Description
boolean	containsSequence(java.lang.String sequenceID) Checks if a sequence associated with the specified unique identifier is contained in this model.
protected abstract S	createNewSequence(java.lang.String sequenceID, java.lang.String sequenceName) Implementing classes must offer a way to create their custom instances of sequence objects overwriting this method.
protected void	doAddSequence(java.lang.String sequenceID, java.lang.String sequenceName) This method is called by AbstractUndecoratedAlignmentModel.addSequence(String) if #isReadOnly() returns false.
protected void	doRemoveSequence(java.lang.String sequenceID) This method is called by #removeSequence(int) if #isReadOnly() returns false.
int	getSequenceCount() Returns the number of sequences in the underlying data source.
protected java.util.Map<java.lang.String,S>	getSequenceMap() Returns the underlying map object used to assign sequences to their IDs.
protected java.util.List<java.lang.String>	getSequenceOrder() Returns the list object used to determine the order of the sequences.
java.util.Iterator<java.lang.String>	sequenceIDIterator() Returns an iterator returned the IDs of the stored sequences in the order they were added to this model.

Methods inherited from class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel

addSequence, addSequence, appendToken, appendTokens, doRenameSequence, fireAfterSequenceChange, fireAfterTokenChange, getApproxMaxSequenceLength, getIDManager, getMaxSequenceLength, getTokenSet, isReuseSequenceIDs, isSequencesReadOnly, isTokensReadOnly, removeSequence, renameSequence, sequenceIDsByName, sequenceNameByID, setMaxSequeceLengthRecalculte, setReuseSequenceIDs, setTokenSet

Methods inherited from class info.bioinfweb.libralign.model.implementations.AbstractAlignmentModel

fireAfterSequenceRenamed, getChangeListeners, getID, getLabel, setID, setLabel

Methods inherited from class java.lang.Object

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

Methods inherited from interface info.bioinfweb.libralign.model.AlignmentModel

getSequenceLength, getTokenAt, getWriteType, insertTokenAt, insertTokensAt, removeTokenAt, removeTokensAt, setTokenAt, setTokensAt

Constructor Detail

AbstractMapBasedAlignmentModel

public AbstractMapBasedAlignmentModel(TokenSet<T> tokenSet,
                                      SequenceIDManager idManager,
                                      boolean reuseSequenceIDs,
                                      java.util.Map<java.lang.String,S> sequenceMap,
                                      java.util.List<java.lang.String> sequenceOrder)

Creates a new instance of this class with a custom map and list implementation.

Parameters:

tokenSet - the token set which is supported by the implementation

idManager - the ID manager to be used by the new instance (maybe shared among multiple instances)

reuseSequenceIDs - Specifies whether unused IDs of the underlying ID manager should be reused by this model. (See the documentation of AbstractUndecoratedAlignmentModel.isReuseSequenceIDs() for details. Specify false, if you are unsure what this property does.)

sequenceMap - the map instance used to assign sequences to their IDs (must be empty)

sequenceOrder - the list object defining the order of the sequences

AbstractMapBasedAlignmentModel

public AbstractMapBasedAlignmentModel(TokenSet<T> tokenSet,
                                      SequenceIDManager idManager,
                                      boolean reuseSequenceIDs,
                                      java.util.Map<java.lang.String,S> sequenceMap)

Creates a new instance of this class with a custom map implementation.

Parameters:

tokenSet - the token set which is supported by the implementation

idManager - the ID manager to be used by the new instance (maybe shared among multiple instances)

reuseSequenceIDs - Specifies whether unused IDs of the underlying ID manager should be reused by this model. (See the documentation of AbstractUndecoratedAlignmentModel.isReuseSequenceIDs() for details. Specify false, if you are unsure what this property does.)

sequenceMap - the map instance used to assign sequences to their IDs

AbstractMapBasedAlignmentModel

public AbstractMapBasedAlignmentModel(TokenSet<T> tokenSet,
                                      SequenceIDManager idManager,
                                      boolean reuseSequenceIDs)

Creates a new instance of this class relying on a HashMap.

Parameters:

tokenSet - the token set which is supported by the implementation

idManager - the ID manager to be used by the new instance (maybe shared among multiple instances)

reuseSequenceIDs - Specifies whether unused IDs of the underlying ID manager should be reused by this model. (See the documentation of AbstractUndecoratedAlignmentModel.isReuseSequenceIDs() for details. Specify false, if you are unsure what this property does.)

Method Detail

getSequenceMap

protected java.util.Map<java.lang.String,S> getSequenceMap()

Returns the underlying map object used to assign sequences to their IDs. Note that you must fire the according events if your implementation modifies this map.

Returns:

the instance of a map implementation provided in the constructor

getSequenceOrder

protected java.util.List<java.lang.String> getSequenceOrder()

Returns the list object used to determine the order of the sequences. Note that you must fire the according events if your implementation modifies this list.

Returns:

an instance of ArrayList in the current implementation (Note that the implementing class might change in future releases of LibrAlign.)

containsSequence

public boolean containsSequence(java.lang.String sequenceID)

Description copied from interface: AlignmentModel

Checks if a sequence associated with the specified unique identifier is contained in this model.

Parameters:

sequenceID - the ID of the sequence to checked on

Returns:

true if an according sequence was found, false otherwise

sequenceIDIterator

public java.util.Iterator<java.lang.String> sequenceIDIterator()

Returns an iterator returned the IDs of the stored sequences in the order they were added to this model.

Returns:

an iterator over the IDs

See Also:

AlignmentModel.sequenceIDIterator()

getSequenceCount

public int getSequenceCount()

Description copied from interface: AlignmentModel

Returns the number of sequences in the underlying data source.

createNewSequence

protected abstract S createNewSequence(java.lang.String sequenceID,
                                       java.lang.String sequenceName)

Implementing classes must offer a way to create their custom instances of sequence objects overwriting this method. This method is called in #doAddSequence(int, String) before adding the new sequences to map and the oder list.

Parameters:

sequenceID - the ID the new sequence must have

sequenceName - the name the new sequence will have

Returns:

the new sequence object

doAddSequence

protected void doAddSequence(java.lang.String sequenceID,
                             java.lang.String sequenceName)

Description copied from class: AbstractUndecoratedAlignmentModel

This method is called by AbstractUndecoratedAlignmentModel.addSequence(String) if #isReadOnly() returns false. Implementing classes should add the specified new sequence to their underlying data source in this method. The according events or exceptions are already created by this class if necessary, therefore this does not need to be done in the implementation of this method.

Specified by:

doAddSequence in class AbstractUndecoratedAlignmentModel<T>

Parameters:

sequenceID - the unique identifier for the new sequence which has been generated before the call of this method

sequenceName - the initial name the new sequence shall have

doRemoveSequence

protected void doRemoveSequence(java.lang.String sequenceID)

Description copied from class: AbstractUndecoratedAlignmentModel

This method is called by #removeSequence(int) if #isReadOnly() returns false. Implementing classes should remove the specified sequence from their underlying data source in this method. The according events or exceptions are already created by this class if necessary, therefore this does not need to be done in the implementation of this method.

Specified by:

doRemoveSequence in class AbstractUndecoratedAlignmentModel<T>

Parameters:

sequenceID - the unique identifier of the sequence to be removed