info.bioinfweb.libralign.model.implementations

Class BioJava3SequenceAlignmentModel<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

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>

info.bioinfweb.libralign.model.implementations.AbstractUnmodifyableAlignmentModel<S,C>

info.bioinfweb.libralign.model.implementations.BioJava3SequenceAlignmentModel<S,C>

Type Parameters:

S - the type of BioJava sequence objects used by the underlying LightweightProfile

C - the compound type used by the underlying BioJava sequence objects

All Implemented Interfaces:

AlignmentModel<C>, SequenceAccess<S>, SequenceAccessAlignmentModel<S,C>

public class BioJava3SequenceAlignmentModel<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>
extends AbstractUnmodifyableAlignmentModel<S,C>
implements SequenceAccessAlignmentModel<S,C>

/** An implementation of AlignmentModel backed by a set of BioJava Sequence implementations. This class does not allow to write tokens (compounds) since this is not supported by the Sequence interface.

Although sequences may be added and removed from instances of this class, AbstractUndecoratedAlignmentModel.addSequence(String) will add null as a new sequence. The technical reason is that this class cannot create instance of the unknown type S. It would anyway not make much sense to use this method, since the new sequence could not be edited. If concrete new sequences shall be added, AbstractUnmodifyableAlignmentModel.addSequence(String, Object) should be used instead.

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
BioJava3SequenceAlignmentModel(org.biojava3.core.sequence.template.LightweightProfile<S,C> underlyingModel, java.lang.String namePrefix, CharacterStateSetType setType, boolean spaceForGap) Creates a new instance of this class and copies the sequences contained underlyingModel to it.
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) Creates a new instance of this class using its own ID manager.
BioJava3SequenceAlignmentModel(TokenSet<C> tokenSet, SequenceIDManager idManager, boolean reuseSequenceIDs) Creates a new instance of this class using a possibly shared ID manager.

Method Summary

Modifier and Type	Method and Description
protected 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.
int	getSequenceLength(java.lang.String sequenceID) Returns the length of the specified sequence.
C	getTokenAt(java.lang.String sequenceID, int index) Returns the token at the specified position.
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>	newInstanceFromProfile(org.biojava3.alignment.template.Profile<org.biojava3.core.sequence.template.Sequence<C>,C> underlyingModel, java.lang.String namePrefix, CharacterStateSetType setType, boolean spaceForGap) Creates a new instance of this class and copies the sequences contained underlyingModel to it.
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>	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.

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

addSequence, getSequence, getWriteType, insertTokenAt, insertTokensAt, removeTokenAt, removeTokensAt, replaceSequence, 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

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

addSequence, replaceSequence

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

addSequence, addSequence, appendToken, appendTokens, containsSequence, getChangeListeners, getID, getLabel, getMaxSequenceLength, getSequenceCount, getTokenSet, getWriteType, insertTokenAt, insertTokensAt, isSequencesReadOnly, isTokensReadOnly, removeSequence, removeTokenAt, removeTokensAt, renameSequence, sequenceIDIterator, sequenceIDsByName, sequenceNameByID, setID, setLabel, setTokenAt, setTokensAt, setTokenSet

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

getSequence

Constructor Detail

BioJava3SequenceAlignmentModel

public BioJava3SequenceAlignmentModel(TokenSet<C> tokenSet,
                                      SequenceIDManager idManager,
                                      boolean reuseSequenceIDs)

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

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.)

BioJava3SequenceAlignmentModel

public BioJava3SequenceAlignmentModel(TokenSet<C> tokenSet)

Creates a new instance of this class using its own ID manager.

Parameters:

tokenSet - the token set which is supported by the implementation

BioJava3SequenceAlignmentModel

public 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. Later changes in underlyingModel will not be reflected by the new instance.

Parameters:

namePrefix - the prefix to be used for sequence names in the new instance (Sequence names will contain this prefix followed by the index of the according sequence in the underlying model. Sequence names may be changes using AbstractUndecoratedAlignmentModel.renameSequence(String, String) later.)

underlyingModel - the BioJava class containing the sequences to be added to the new model

type - the token type of the new instance's token set (Only a discrete type would make sense for this class.)

spaceForGap - determines whether the space key shall be associated with gap symbol in the token set

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

Throws:

java.lang.NullPointerException - if underlyingModel, type or compoundSet are null

BioJava3SequenceAlignmentModel

public BioJava3SequenceAlignmentModel(org.biojava3.core.sequence.template.LightweightProfile<S,C> underlyingModel,
                                      java.lang.String namePrefix,
                                      CharacterStateSetType setType,
                                      boolean spaceForGap)

Creates a new instance of this class and copies the sequences contained underlyingModel to it. Later changes in underlyingModel will not be reflected by the new instance.

Parameters:

underlyingModel - the BioJava class containing the sequences to be added to the new model

namePrefix - the prefix to be used for sequence names in the new instance (Sequence names will contain this prefix followed by the index of the according sequence in the underlying model. Sequence names may be changes using AbstractUndecoratedAlignmentModel.renameSequence(String, String) later.)

type - the token type of the new instance's token set (Only a discrete type would make sense for this class.)

spaceForGap - determines whether the space key shall be associated with gap symbol in the token set

Throws:

java.lang.NullPointerException - if underlyingModel, type or compoundSet are null

Method Detail

newInstanceFromProfile

public 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> 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. Later changes in underlyingModel will not be reflected by the new instance.

Parameters:

underlyingModel - the BioJava class containing the sequences to be added to the new model

namePrefix - the prefix to be used for sequence names in the new instance (Sequence names will contain this prefix followed by the index of the according sequence in the underlying model. Sequence names may be changes using AbstractUndecoratedAlignmentModel.renameSequence(String, String) later.)

type - the token type of the new instance's token set (Only a discrete type would make sense for this class.)

spaceForGap - determines whether the space key shall be associated with gap symbol in the token set

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

Throws:

java.lang.NullPointerException - if underlyingModel, type or compoundSet are null

newInstanceFromProfile

public 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> newInstanceFromProfile(org.biojava3.alignment.template.Profile<org.biojava3.core.sequence.template.Sequence<C>,C> underlyingModel,
                                                                                                                                                                                                                                             java.lang.String namePrefix,
                                                                                                                                                                                                                                             CharacterStateSetType setType,
                                                                                                                                                                                                                                             boolean spaceForGap)

Creates a new instance of this class and copies the sequences contained underlyingModel to it. Later changes in underlyingModel will not be reflected by the new instance.

Parameters:

underlyingModel - the BioJava class containing the sequences to be added to the new model

namePrefix - the prefix to be used for sequence names in the new instance (Sequence names will contain this prefix followed by the index of the according sequence in the underlying model. Sequence names may be changes using AbstractUndecoratedAlignmentModel.renameSequence(String, String) later.)

type - the token type of the new instance's token set (Only a discrete type would make sense for this class.)

spaceForGap - determines whether the space key shall be associated with gap symbol in the token set

Throws:

java.lang.NullPointerException - if underlyingModel, type or compoundSet are null

createNewSequence

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

Description copied from class: AbstractMapBasedAlignmentModel

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.

Specified by:

createNewSequence in class AbstractMapBasedAlignmentModel<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

Parameters:

sequenceID - the ID the new sequence must have

sequenceName - the name the new sequence will have

Returns:

the new sequence object

getSequenceLength

public int getSequenceLength(java.lang.String sequenceID)

Description copied from interface: AlignmentModel

Returns the length of the specified sequence.

Specified by:

getSequenceLength in interface AlignmentModel<C extends org.biojava3.core.sequence.template.Compound>

Parameters:

sequenceID - the identifier the sequence in the alignment

Returns:

the length of the sequence or -1 if no sequence with the specified name exists

getTokenAt

public C getTokenAt(java.lang.String sequenceID,
                    int index)

Description copied from interface: AlignmentModel

Returns the token at the specified position.

Specified by:

getTokenAt in interface AlignmentModel<C extends org.biojava3.core.sequence.template.Compound>

Parameters:

sequenceID - the identifier the sequence where the token is contained

index - the index of the element contained in the specified sequence (The first element has the index 0.)

Returns:

the token to be displayed in the GUI alignment view