Uses of Class
info.bioinfweb.libralign.model.implementations.SequenceIDManager

Packages that use SequenceIDManager

Package	Description
info.bioinfweb.libralign.model.factory	Contains factory classes to create instances of implementations of AlignmentModel.
info.bioinfweb.libralign.model.implementations	Contains common implementations of AlignmentModel which are part of LibrAlign.

Uses of SequenceIDManager in info.bioinfweb.libralign.model.factory

Methods in info.bioinfweb.libralign.model.factory that return SequenceIDManager

Modifier and Type	Method and Description
SequenceIDManager	AbstractAlignmentModelFactory.getSharedIDManager() Returns the sequence ID manager that is shared among all model instances created by this factory.

Constructors in info.bioinfweb.libralign.model.factory with parameters of type SequenceIDManager

Constructor and Description
AbstractAlignmentModelFactory(SequenceIDManager sharedIDManager, boolean reuseSequenceIDs, T defaultToken) Creates a new instance of this class using a shared sequence ID manager.
BioPolymerCharAlignmentModelFactory(SequenceIDManager sharedIDManager, boolean reuseSequenceIDs, java.lang.Character defaultToken, boolean distinguishCase) Creates a new instance of this class using a shared sequence ID manager.

Uses of SequenceIDManager in info.bioinfweb.libralign.model.implementations

Methods in info.bioinfweb.libralign.model.implementations that return SequenceIDManager

Modifier and Type	Method and Description
protected SequenceIDManager	AbstractUndecoratedAlignmentModel.getIDManager()

Methods in info.bioinfweb.libralign.model.implementations with parameters of type SequenceIDManager

Modifier and Type	Method and Description
static <C extends org.biojava3.core.sequence.template.Compound> BioJava3SequenceAlignmentModel<org.biojava3.alignment.template.AlignedSequence<? extends org.biojava3.core.sequence.template.Sequence<C>,C>,C>	BioJava3SequenceAlignmentModel.newInstanceFromProfile(org.biojava3.alignment.template.Profile<org.biojava3.core.sequence.template.Sequence<C>,C> underlyingModel, java.lang.String namePrefix, CharacterStateSetType setType, boolean spaceForGap, SequenceIDManager idManager, boolean reuseSequenceIDs) Creates a new instance of this class and copies the sequences contained underlyingModel to it.

Constructors in info.bioinfweb.libralign.model.implementations with parameters of type SequenceIDManager

Constructor and Description
AbstractListAlignmentModel(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.
AbstractListAlignmentModel(TokenSet<T> tokenSet, SequenceIDManager idManager, boolean reuseSequenceIDs, int initialCapacity, boolean useMaxLength) Creates a new instance of this class.
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.
AbstractUndecoratedAlignmentModel(TokenSet<T> tokenSet, SequenceIDManager idManager, boolean reuseSequenceIDs) Creates a new instance of this class.
AbstractUnmodifyableAlignmentModel(TokenSet<T> tokenSet, SequenceIDManager idManager, boolean reuseSequenceIDs) Creates a new instance of this class relying on a TreeMap.
AbstractUnmodifyableAlignmentModel(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 and list implementation.
AbstractUnmodifyableAlignmentModel(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.
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.
BioJava3SequenceAlignmentModel(org.biojava3.core.sequence.template.LightweightProfile<S,C> underlyingModel, java.lang.String namePrefix, CharacterStateSetType setType, boolean spaceForGap, SequenceIDManager idManager) Creates a new instance of this class and copies the sequences contained underlyingModel to it.
BioJava3SequenceAlignmentModel(TokenSet<C> tokenSet, SequenceIDManager idManager, boolean reuseSequenceIDs) Creates a new instance of this class using a possibly shared ID manager.
CharSequenceAlignmentModel(TokenSet<java.lang.Character> tokenSet, SequenceIDManager idManager, boolean reuseSequenceIDs) Creates a new instance of this class using a possibly shared ID manager.
PackedAlignmentModel(TokenSet<T> tokenSet, SequenceIDManager idManager, boolean reuseSequenceIDs) Creates a new instance of this class with the maximum number of different tokens that is equal to the number of tokens in the specified set.
PackedAlignmentModel(TokenSet<T> tokenSet, SequenceIDManager idManager, boolean reuseSequenceIDs, int minTokenCount) Creates a new instance of this class.