info.bioinfweb.libralign.model.implementations.decorate

Class DelegatedAlignmentModelView<T>

java.lang.Object

info.bioinfweb.libralign.model.adapters.AbstractBasicAlignmentModelView<T>

info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView<T>

Type Parameters:

T - the token type of the underlying and the viewed model

All Implemented Interfaces:

AlignmentModel<T>, AlignmentModelView<T,T>, BasicAlignmentModelView<T>

public abstract class DelegatedAlignmentModelView<T>
extends AbstractBasicAlignmentModelView<T>
implements AlignmentModelView<T,T>

Implementation of AlignmentModelView that delegates all methods to the underlying model and uses the same token type as the underlying model. Inherited classes can overwrite single delegated methods to change the behavior.

Note that getChangeListeners() also delegates to the underlying model and therefore modifying this list, actually modifies the listener list of the underlying model.

This class is marked as abstract, since it does not behave different then the underlying model, if no method is overwritten or added in inherited classes.

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
DelegatedAlignmentModelView(AlignmentModel<T> underlyingModel)

Method Summary

Modifier and Type	Method and Description
java.lang.String	addSequence(java.lang.String sequenceName) Adds a new empty sequence to the underlying data source and generates an ID for it.
java.lang.String	addSequence(java.lang.String sequenceName, java.lang.String sequenceID) Adds a new empty sequence to the underlying data source assigning the specified ID to it.
void	appendToken(java.lang.String sequenceID, T token) Appends a token at the end of the sequence.
void	appendTokens(java.lang.String sequenceID, java.util.Collection<? extends T> tokens) Appends a sequence of tokens starting at the end of the current sequence.
boolean	containsSequence(java.lang.String sequenceID) Checks if a sequence associated with the specified unique identifier is contained in this model.
java.util.Set<AlignmentModelChangeListener>	getChangeListeners() Returns all change listeners currently attached to this object.
java.lang.String	getID() Some implementations may specify string identifying an alignment, which is then returned by this method.
java.lang.String	getLabel() Returns a string labeling this alignment.
int	getMaxSequenceLength() Returns the length of the longest sequence in the alignment which is equivalent to the length of the alignment.
int	getSequenceCount() Returns the number of sequences in the underlying data source.
int	getSequenceLength(java.lang.String sequenceID) Returns the length of the specified sequence.
T	getTokenAt(java.lang.String sequenceID, int index) Returns the token at the specified position.
TokenSet<T>	getTokenSet() Returns the token set which is supported by the implementation.
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.
boolean	isSequencesReadOnly() Checks of whole sequences can be changed in the underlying data source
boolean	isTokensReadOnly() Checks of tokens can be changed in the underlying data source
boolean	removeSequence(java.lang.String sequenceID) Removes the specified sequence from the underlying data source.
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.
java.lang.String	renameSequence(java.lang.String sequenceID, java.lang.String newSequenceName) Renames a sequence in the underlying data source.
java.util.Iterator<java.lang.String>	sequenceIDIterator() Returns an iterator over unique IDs of all sequences contained in the underlying data source in the order they are stored in this model.
java.util.Set<java.lang.String>	sequenceIDsByName(java.lang.String sequenceName) Returns the set of unique sequence IDs associated with the specified name.
java.lang.String	sequenceNameByID(java.lang.String sequenceID) Returns the sequence name (that would be visible to the application user) associated with the specified unique ID.
void	setID(java.lang.String id) Allows to specify a new ID for this alignment.
void	setLabel(java.lang.String label) Allows to specify a new label for this alignment.
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.
void	setTokenSet(TokenSet<T> set) Replaces the current token set with the specified one.

Methods inherited from class info.bioinfweb.libralign.model.adapters.AbstractBasicAlignmentModelView

getUnderlyingModel, setUnderlyingModel

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.BasicAlignmentModelView

getUnderlyingModel

Constructor Detail

DelegatedAlignmentModelView

public DelegatedAlignmentModelView(AlignmentModel<T> underlyingModel)

Method Detail

getID

public java.lang.String getID()

Description copied from interface: AlignmentModel

Some implementations may specify string identifying an alignment, which is then returned by this method. Such string IDs will usually be unique in some context and immutable.

Specified by:

getID in interface AlignmentModel<T>

Returns:

the ID of this alignment or null if none is assigned

setID

public void setID(java.lang.String id)

Description copied from interface: AlignmentModel

Allows to specify a new ID for this alignment.

Specified by:

setID in interface AlignmentModel<T>

Parameters:

id - the new ID

getLabel

public java.lang.String getLabel()

Description copied from interface: AlignmentModel

Returns a string labeling this alignment.

Specified by:

getLabel in interface AlignmentModel<T>

Returns:

the name or title of this alignment

setLabel

public void setLabel(java.lang.String label)
              throws java.lang.UnsupportedOperationException

Description copied from interface: AlignmentModel

Allows to specify a new label for this alignment.

Specified by:

setLabel in interface AlignmentModel<T>

Parameters:

label - the new label

Throws:

java.lang.UnsupportedOperationException - if this implementation does not allow to change labels

getTokenSet

public TokenSet<T> getTokenSet()

Description copied from interface: AlignmentModel

Returns the token set which is supported by the implementation.

Specified by:

getTokenSet in interface AlignmentModel<T>

Returns:

a token set containing all valid tokens

setTokenSet

public void setTokenSet(TokenSet<T> set)
                 throws java.lang.UnsupportedOperationException,
                        java.lang.IllegalArgumentException

Description copied from interface: AlignmentModel

Replaces the current token set with the specified one.

Specified by:

setTokenSet in interface AlignmentModel<T>

Parameters:

set - the new token set to be used

Throws:

java.lang.UnsupportedOperationException - if this implementation does not support changing token sets during runtime

java.lang.IllegalArgumentException - if the specified token set is not a valid replacement for the previous one (in some does way does not fulfill the needs of the implementation)

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<T>

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

getMaxSequenceLength

public int getMaxSequenceLength()

Description copied from interface: AlignmentModel

Returns the length of the longest sequence in the alignment which is equivalent to the length of the alignment.

Note that this value represents the number of compounds of the specified data type. If e.g. a DNA data source is viewed as amino acid data this method would still return the number of nucleotides in the longest sequence.

Specified by:

getMaxSequenceLength in interface AlignmentModel<T>

Returns:

the number of columns in the alignment or 0 if there are not sequences contained in the underlying data source

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

isTokensReadOnly

public boolean isTokensReadOnly()

Description copied from interface: AlignmentModel

Checks of tokens can be changed in the underlying data source

Specified by:

isTokensReadOnly in interface AlignmentModel<T>

Returns:

true if token can be written or removed, false otherwise

isSequencesReadOnly

public boolean isSequencesReadOnly()

Description copied from interface: AlignmentModel

Checks of whole sequences can be changed in the underlying data source

Specified by:

isSequencesReadOnly in interface AlignmentModel<T>

Returns:

true if sequences can be written, renamed or removed, false otherwise

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.

Specified by:

containsSequence in interface AlignmentModel<T>

Parameters:

sequenceID - the ID of the sequence to checked on

Returns:

true if an according sequence was found, false otherwise

sequenceIDsByName

public java.util.Set<java.lang.String> sequenceIDsByName(java.lang.String sequenceName)

Description copied from interface: AlignmentModel

Returns the set of unique sequence IDs associated with the specified name.

Specified by:

sequenceIDsByName in interface AlignmentModel<T>

Parameters:

sequenceName - the name of the sequence that would be visible to the application user

Returns:

the set of sequence IDs (The returned set maybe unmodifiable (depending on the implementation) and empty if no sequence with the specified name is present in this model.)

sequenceNameByID

public java.lang.String sequenceNameByID(java.lang.String sequenceID)

Description copied from interface: AlignmentModel

Returns the sequence name (that would be visible to the application user) associated with the specified unique ID.

Specified by:

sequenceNameByID in interface AlignmentModel<T>

Parameters:

sequenceID - the unique unmodifiable ID the sequence is identified by

Returns:

the sequence name or null if no sequence with this ID is contained in this model

addSequence

public java.lang.String addSequence(java.lang.String sequenceName)
                             throws AlignmentSourceNotWritableException

Description copied from interface: AlignmentModel

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

Specified by:

addSequence in interface AlignmentModel<T>

Parameters:

sequenceName - the name of the new sequence

Returns:

the unique ID of the new sequence

Throws:

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

addSequence

public java.lang.String addSequence(java.lang.String sequenceName,
                                    java.lang.String sequenceID)
                             throws AlignmentSourceNotWritableException,
                                    java.lang.IllegalArgumentException

Description copied from interface: AlignmentModel

Adds a new empty sequence to the underlying data source assigning the specified ID to it.

Specified by:

addSequence in interface AlignmentModel<T>

Parameters:

sequenceName - the name of the new sequence

sequenceID - the ID the new sequence shall have

Returns:

the unique ID of the new sequence (identical with sequenceID)

Throws:

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

java.lang.IllegalArgumentException - if a sequence with the specified ID is already present in this model

removeSequence

public boolean removeSequence(java.lang.String sequenceID)
                       throws AlignmentSourceNotWritableException

Description copied from interface: AlignmentModel

Removes the specified sequence from the underlying data source.

Specified by:

removeSequence in interface AlignmentModel<T>

Parameters:

sequenceID - the unique ID of the sequence to be removed

Returns:

true if an sequence with the specified ID was removed, false if no sequence with the specified ID was contained in this model

Throws:

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

renameSequence

public java.lang.String renameSequence(java.lang.String sequenceID,
                                       java.lang.String newSequenceName)
                                throws AlignmentSourceNotWritableException,
                                       SequenceNotFoundException

Description copied from interface: AlignmentModel

Renames a sequence in the underlying data source.

Specified by:

renameSequence in interface AlignmentModel<T>

Parameters:

sequenceID - the ID of the sequence to be renamed

newSequenceName - the new name the sequence shall have

Returns:

the name the sequence had until now

Throws:

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

SequenceNotFoundException - if a sequence with the specified ID is not present the underlying data source

sequenceIDIterator

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

Description copied from interface: AlignmentModel

Returns an iterator over unique IDs of all sequences contained in the underlying data source in the order they are stored in this model.

Specified by:

sequenceIDIterator in interface AlignmentModel<T>

Returns:

an iterator over the IDs

getSequenceCount

public int getSequenceCount()

Description copied from interface: AlignmentModel

Returns the number of sequences in the underlying data source.

Specified by:

getSequenceCount in interface AlignmentModel<T>

getChangeListeners

public java.util.Set<AlignmentModelChangeListener> getChangeListeners()

Description copied from interface: AlignmentModel

Returns all change listeners currently attached to this object. This collection is writable and should also be used to add or remove listeners.

This method returns the same object in every call. Therefore changes made to different references always affect all references.

Specified by:

getChangeListeners in interface AlignmentModel<T>

Returns:

a collection object containing the listeners

getTokenAt

public T 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<T>

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

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)

appendToken

public void appendToken(java.lang.String sequenceID,
                        T token)
                 throws AlignmentSourceNotWritableException

Description copied from interface: AlignmentModel

Appends a token at the end of the sequence.

Specified by:

appendToken in interface AlignmentModel<T>

Parameters:

sequenceID - the identifier the sequence in the alignment

token - the token to be inserted

Throws:

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

appendTokens

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

Description copied from interface: AlignmentModel

Appends a sequence of tokens starting at the end of the current sequence.

Specified by:

appendTokens in interface AlignmentModel<T>

Parameters:

sequenceID - the identifier the sequence where the token is contained

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