info.bioinfweb.libralign.model.implementations

Class ArrayListAlignmentModel<T>

java.lang.Object

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

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

info.bioinfweb.libralign.model.implementations.AbstractMapBasedAlignmentModel<java.util.List<T>,T>

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

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

Type Parameters:

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

All Implemented Interfaces:

AlignmentModel<T>

public class ArrayListAlignmentModel<T>
extends AbstractListAlignmentModel<T>

An implementation of AlignmentModel using a map of array lists to store alignment data. The constructors offer different options to specify the initial capacity a new ArrayList instance.

Since:

0.1.0

Author:

Ben Stöever

Field Summary

Fields inherited from class info.bioinfweb.libralign.model.implementations.AbstractListAlignmentModel

DEFAULT_INITIAL_CAPACITY

Constructor Summary

Constructors

Constructor and Description
ArrayListAlignmentModel(TokenSet<T> tokenSet) Creates a new instance of this class using AbstractListAlignmentModel.DEFAULT_INITIAL_CAPACITY as the initial capacity which is only used if it is lower than AbstractUndecoratedAlignmentModel.getMaxSequenceLength() to create new sequence array lists.
ArrayListAlignmentModel(TokenSet<T> tokenSet, SequenceIDManager idManager, boolean reuseSequenceIDs) Creates a new instance of this class using AbstractListAlignmentModel.DEFAULT_INITIAL_CAPACITY as the initial capacity which is only used if it is lower than AbstractUndecoratedAlignmentModel.getMaxSequenceLength() to create new sequence array lists.
ArrayListAlignmentModel(TokenSet<T> tokenSet, SequenceIDManager idManager, boolean reuseSequenceIDs, int initialCapacity, boolean useMaxLength) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
protected java.util.List<T>	createNewSequence(java.lang.String sequenceID, java.lang.String sequenceName, int initialCapacity) This method is called by #createNewSequence(int, String) and must be implemented by inherited classes.

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

createNewSequence, getInitialCapacity, getSequence, getSequenceLength, getTokenAt, getWriteType, insertTokenAt, insertTokensAt, isUseMaxLength, removeTokenAt, removeTokensAt, setTokenAt, setTokensAt

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

containsSequence, doAddSequence, doRemoveSequence, getSequenceCount, getSequenceMap, getSequenceOrder, sequenceIDIterator

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

Constructor Detail

ArrayListAlignmentModel

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

Creates a new instance of this class using AbstractListAlignmentModel.DEFAULT_INITIAL_CAPACITY as the initial capacity which is only used if it is lower than AbstractUndecoratedAlignmentModel.getMaxSequenceLength() to create new sequence array lists.

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.)

ArrayListAlignmentModel

public ArrayListAlignmentModel(TokenSet<T> tokenSet)

Creates a new instance of this class using AbstractListAlignmentModel.DEFAULT_INITIAL_CAPACITY as the initial capacity which is only used if it is lower than AbstractUndecoratedAlignmentModel.getMaxSequenceLength() to create new sequence array lists. The returned instance uses its own ID manager.

Parameters:

tokenSet - the token set which is supported by the implementation

ArrayListAlignmentModel

public ArrayListAlignmentModel(TokenSet<T> tokenSet,
                               SequenceIDManager idManager,
                               boolean reuseSequenceIDs,
                               int initialCapacity,
                               boolean useMaxLength)

Creates a new instance of this class.

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.)

initialCapacity - the initial capacity newly generated array lists will have

useMaxLength - Specify true here if initialCapacity shall only be used if it is lower than AbstractUndecoratedAlignmentModel.getMaxSequenceLength() to create new sequence array lists.

Method Detail

createNewSequence

protected java.util.List<T> createNewSequence(java.lang.String sequenceID,
                                              java.lang.String sequenceName,
                                              int initialCapacity)

Description copied from class: AbstractListAlignmentModel

This method is called by #createNewSequence(int, String) and must be implemented by inherited classes. In contrast to #createNewSequence(int, String) it provides an additional parameter specifying the initial capacity the returned list object shall have. This parameter value if set depending on the return values of AbstractListAlignmentModel.isUseMaxLength() either to a fixed value as specified by AbstractListAlignmentModel.getInitialCapacity() or by the maximum length of other sequences in this provider if any of these contain more elements than AbstractListAlignmentModel.getInitialCapacity().

Specified by:

createNewSequence in class AbstractListAlignmentModel<T>

Parameters:

sequenceID - the ID the new sequence must have

sequenceName - the name the new sequence will have

initialCapacity - the initial capacity the returned list object shall have

Returns:

the new sequence object