info.bioinfweb.libralign.model.implementations

Class AbstractUnmodifyableAlignmentModel<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>

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

Type Parameters:

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

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

All Implemented Interfaces:

AlignmentModel<T>, SequenceAccess<S>, SequenceAccessAlignmentModel<S,T>

Direct Known Subclasses:

BioJava3SequenceAlignmentModel, CharSequenceAlignmentModel

public abstract class AbstractUnmodifyableAlignmentModel<S,T>
extends AbstractMapBasedAlignmentModel<S,T>
implements SequenceAccessAlignmentModel<S,T>

Implements basic functionality for a map based alignment model that uses unmodifiable sequence objects as its underlying data source.

Since:

0.1.0

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
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.

Method Summary

Modifier and Type	Method and Description
java.lang.String	addSequence(java.lang.String sequenceName, S content) Adds a the specified sequence to the underlying data source and generates an ID for it.
S	getSequence(java.lang.String sequenceID) Returns the sequence object with the specified ID.
AlignmentModelWriteType	getWriteType() Returns a value that specifies if whole sequences or single tokens can be edited in the underlying data source.
void	insertTokenAt(java.lang.String sequenceID, int index, T token) Inserts a token at the specified position.
void	insertTokensAt(java.lang.String sequenceID, int beginIndex, java.util.Collection<? extends T> tokens) Inserts a sequence of tokens starting at the specified position.
void	removeTokenAt(java.lang.String sequenceID, int index) Removes the token at the specified position from the underlying data source.
void	removeTokensAt(java.lang.String sequenceID, int beginIndex, int endIndex) Removes the token inside the specified interval from the underlying data source.
S	replaceSequence(java.lang.String sequenceID, S content) Replaces the sequence object with the specified ID by the specified contents.
void	setTokenAt(java.lang.String sequenceID, int index, T token) Replaces the token at the specified position by the passed token.
void	setTokensAt(java.lang.String sequenceID, int beginIndex, java.util.Collection<? extends T> tokens) Replaces a sequence of tokens starting at the specified position.

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

containsSequence, createNewSequence, 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.AlignmentModel

addSequence, addSequence, appendToken, appendTokens, containsSequence, getChangeListeners, getID, getLabel, getMaxSequenceLength, getSequenceCount, getSequenceLength, getTokenAt, getTokenSet, isSequencesReadOnly, isTokensReadOnly, removeSequence, renameSequence, sequenceIDIterator, sequenceIDsByName, sequenceNameByID, setID, setLabel, setTokenSet

Constructor Detail

AbstractUnmodifyableAlignmentModel

public 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.

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

sequenceOrder - the list object defining the order of the sequences

AbstractUnmodifyableAlignmentModel

public 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.

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

AbstractUnmodifyableAlignmentModel

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

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

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

addSequence

public java.lang.String addSequence(java.lang.String sequenceName,
                                    S content)

Adds a the specified sequence to the underlying data source and generates an ID for it.

This method calls first AbstractUndecoratedAlignmentModel.addSequence(String) and than #setSequenceContent(int, Object) internally. Therefore two different events will be fired.

Note that since the sequences in this implementation are considered as unmutable it does not make sense to call AbstractUndecoratedAlignmentModel.addSequence(String) on an instance of this class unless you want to have an empty sequence in the alignment.

Specified by:

addSequence in interface SequenceAccessAlignmentModel<S,T>

Parameters:

sequenceName - the name of the new sequence

content - the sequence object to be added.

Returns:

the unique ID of the new sequence

Throws:

AlignmentSourceNotWritableException - This exception is not thrown by this implementation.

replaceSequence

public S replaceSequence(java.lang.String sequenceID,
                         S content)

Replaces the sequence object with the specified ID by the specified contents. Internally the current sequence is first removed from the underlying map and after that the new sequence is added using the same ID. Therefore two SequenceChangeEvents are fired, one for the removal and one for the insertion.

Between these two events the underlying map does not contain any sequence with the specified ID. For the case that event handlers of the first event add any new sequences to the map they have to make sure not to use the ID passed to this method (which might accidentally be created by a call of AbstractUndecoratedAlignmentModel.addSequence(String)), because the new contents would than be overwritten in the second step of this method.

It also has to be noted that there

Specified by:

replaceSequence in interface SequenceAccessAlignmentModel<S,T>

Parameters:

sequenceID - the ID of the sequence to be replaced

content - the new sequence object

Returns:

the previous sequence identified by the specified ID, or null if there was no sequence with the ID

getWriteType

public AlignmentModelWriteType getWriteType()

Description copied from interface: AlignmentModel

Returns a value that specifies if whole sequences or single tokens can be edited in the underlying data source. s

Specified by:

getWriteType in interface AlignmentModel<T>

Returns:

the write type of this data source

setTokenAt

public void setTokenAt(java.lang.String sequenceID,
                       int index,
                       T token)
                throws AlignmentSourceNotWritableException

Description copied from interface: AlignmentModel

Replaces the token at the specified position by the passed token.

Specified by:

setTokenAt in interface AlignmentModel<T>

Parameters:

sequenceID - the identifier the sequence where the token is contained

index - the index of the element to be replaced (The first element has the index 0.)

token - the new token for the specified position

Throws:

AlignmentSourceNotWritableException - if the underlying data source is not writable for tokens

setTokensAt

public void setTokensAt(java.lang.String sequenceID,
                        int beginIndex,
                        java.util.Collection<? extends T> tokens)
                 throws AlignmentSourceNotWritableException

Description copied from interface: AlignmentModel

Replaces a sequence of tokens starting at the specified position. If the specified collection contains more tokens than the currently present in the sequence at the specified start position the additional tokens are appended.

Specified by:

setTokensAt in interface AlignmentModel<T>

Parameters:

sequenceID - the identifier the sequence where the token is contained

beginIndex - the index of the first element to be replaced (The first element in the sequence has the index 0.)

tokens - the new tokens for the specified position

Throws:

AlignmentSourceNotWritableException - if the underlying data source is not writable for tokens

See Also:

AlignmentModelUtils.charSequenceToTokenList(CharSequence, TokenSet)

insertTokenAt

public void insertTokenAt(java.lang.String sequenceID,
                          int index,
                          T token)
                   throws AlignmentSourceNotWritableException

Description copied from interface: AlignmentModel

Inserts a token at the specified position. All tokens located behind the specified index are moved by 1.

Specified by:

insertTokenAt in interface AlignmentModel<T>

Parameters:

sequenceID - the identifier the sequence in the alignment

index - the new index the inserted element will have (0 <= elementIndex < sequenceLength)

token - the token to be inserted

Throws:

AlignmentSourceNotWritableException - if the underlying data source is not writable for tokens

insertTokensAt

public void insertTokensAt(java.lang.String sequenceID,
                           int beginIndex,
                           java.util.Collection<? extends T> tokens)
                    throws AlignmentSourceNotWritableException

Description copied from interface: AlignmentModel

Inserts a sequence of tokens starting at the specified position. All tokens located behind the specified index are moved by the number of tokens that are contained in tokens.

Specified by:

insertTokensAt in interface AlignmentModel<T>

Parameters:

sequenceID - the identifier the sequence where the token is contained

beginIndex - the index of the first element to be replaced (The first element in the sequence has the index 0.)

tokens - the new tokens for the specified position

Throws:

AlignmentSourceNotWritableException - if the underlying data source is not writable for tokens

See Also:

AlignmentModelUtils.charSequenceToTokenList(CharSequence, TokenSet)

removeTokenAt

public void removeTokenAt(java.lang.String sequenceID,
                          int index)
                   throws AlignmentSourceNotWritableException

Description copied from interface: AlignmentModel

Removes the token at the specified position from the underlying data source.

Specified by:

removeTokenAt in interface AlignmentModel<T>

Parameters:

sequenceID - the identifier the sequence in the alignment

index - the index of the element to be removed (The first element has the index 0.)

Throws:

AlignmentSourceNotWritableException - if the underlying data source is not writable for tokens

removeTokensAt

public void removeTokensAt(java.lang.String sequenceID,
                           int beginIndex,
                           int endIndex)
                    throws AlignmentSourceNotWritableException

Description copied from interface: AlignmentModel

Removes the token inside the specified interval from the underlying data source. The subsequence to be removed begins at the specified beginIndex and extends to the token at index endIndex - 1). Thus the length of the subsequence is {@code endIndex - beginIndex}.

Specified by:

removeTokensAt in interface AlignmentModel<T>

Parameters:

sequenceID - the identifier the sequence in the alignment

beginIndex - the beginning index, inclusive

endIndex - the ending index, exclusive

Throws:

AlignmentSourceNotWritableException - if the underlying data source is not writable for tokens

getSequence

public S getSequence(java.lang.String sequenceID)

Description copied from interface: SequenceAccess

Returns the sequence object with the specified ID.

If the implementing class also implements SequenceDataAdapter the returned object can be a view or copy of a sequence in the underlying data source depending in the return value of SequenceDataAdapter.returnsCopies(). If SequenceAccessAlignmentModel is implemented the object used to store the sequence data is returned.

Specified by:

getSequence in interface SequenceAccess<S>

Parameters:

sequenceID - the ID of the sequence to be returned

Returns:

the sequence object as described above