info.bioinfweb.libralign.model.tokenset

Class AbstractTokenSet<T>

java.lang.Object

java.util.AbstractCollection<E>

java.util.AbstractSet<E>

java.util.HashSet<T>

info.bioinfweb.libralign.model.tokenset.AbstractTokenSet<T>

Type Parameters:

T - the type of token to be stored in this set

All Implemented Interfaces:

TokenSet<T>, java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<T>, java.util.Collection<T>, java.util.Set<T>

Direct Known Subclasses:

CharacterTokenSet, DefaultTokenSet

public abstract class AbstractTokenSet<T>
extends java.util.HashSet<T>
implements TokenSet<T>

An abstract implementation of TokenSet that provides a TreeMap used to map key characters to tokens and inherits from HashSet so also tokens that do not implement Comparable are supported.

Since the implemented functionality of this class assumes discrete token values, #isContinuous() always returns false.

Since:

0.1.0

Author:

Ben Stöver

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
AbstractTokenSet(CharacterStateSetType type) Creates a new empty instance of this class.
AbstractTokenSet(CharacterStateSetType type, AbstractTokenSet<T> source) Copy constructor that copies all elements the contents of the key map from source to the new instance.

Method Summary

Modifier and Type	Method and Description
protected void	addSpaceKeyForGaps()
abstract AbstractTokenSet<T>	clone() Inherited classes have to overwrite this method and create a deep copy of getKeyMap().
T	getGapToken() Returns the default object that represents a gap in this token set.
protected java.util.Map<javax.swing.KeyStroke,T>	getKeyMap() Returns the mapping from key characters to tokens.
CharacterSymbolMeaning	getMeaning(T token) Returns the meaning of the specified symbol.
T	getMissingInformationToken() Returns the default object that represents an unknown position in this token set.
CharacterSymbolType	getSymbolType(T token) This default implementation returns CharacterSymbolType.UNCERTAIN for all missing information tokens.
CharacterStateSetType	getType() Determines the type of tokens that are defined by this instance.
boolean	isGapToken(T token) Default implementation that tests of the string representation of the specified token is equal to "".
boolean	isMissingInformationToken(T token) Tests if the specified token represents an unknown position (usually '?').
boolean	isSpaceForGap() Determines whether TokenSet.tokenByKeyStroke(KeyStroke) shall return the gap token, if the space bar is pressed, even if that key stroke is not associated with that token.
void	setSpaceForGap(boolean spaceForGap) Allows to specify whether TokenSet.tokenByKeyStroke(KeyStroke) shall return the gap token, if the space bar is pressed, even if that key stroke is not associated with that token.
T	tokenByKeyStroke(javax.swing.KeyStroke key) Returns the token from this set that is associated with the specified key stroke.

Methods inherited from class java.util.HashSet

add, clear, contains, isEmpty, iterator, remove, size, spliterator

Methods inherited from class java.util.AbstractSet

equals, hashCode, removeAll

Methods inherited from class java.util.AbstractCollection

addAll, containsAll, retainAll, toArray, toArray, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface info.bioinfweb.libralign.model.tokenset.TokenSet

descriptionByToken, maxRepresentationLength, representationByToken, representationLengthEqual, tokenByRepresentation

Methods inherited from interface java.util.Set

add, addAll, clear, contains, containsAll, equals, hashCode, isEmpty, iterator, remove, removeAll, retainAll, size, spliterator, toArray, toArray

Methods inherited from interface java.util.Collection

parallelStream, removeIf, stream

Methods inherited from interface java.lang.Iterable

forEach

Constructor Detail

AbstractTokenSet

public AbstractTokenSet(CharacterStateSetType type)

Creates a new empty instance of this class.

AbstractTokenSet

public AbstractTokenSet(CharacterStateSetType type,
                        AbstractTokenSet<T> source)

Copy constructor that copies all elements the contents of the key map from source to the new instance.

Parameters:

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

source - the source instance to be cloned

Method Detail

getType

public CharacterStateSetType getType()

Description copied from interface: TokenSet

Determines the type of tokens that are defined by this instance.

Specified by:

getType in interface TokenSet<T>

Returns:

the token set type

tokenByKeyStroke

public T tokenByKeyStroke(javax.swing.KeyStroke key)

Description copied from interface: TokenSet

Returns the token from this set that is associated with the specified key stroke. This key can be pressed to insert the specified token into an AlignmentArea.

Note that the key character is only used by AlignmentArea if it does not collide with a default keyboard action. (Usually the key character can be any lower or upper case letter or digit.)

Specified by:

tokenByKeyStroke in interface TokenSet<T>

Parameters:

key - the key stroke (key code and shift mask) the user can press to insert the returned token into an AlignmentArea

Returns:

the associated token (sequence element) or null if none is defined

getKeyMap

protected java.util.Map<javax.swing.KeyStroke,T> getKeyMap()

Returns the mapping from key characters to tokens.

Returns:

an instance of TreeMap in the current implementation (Note that this might change in future versions.)

isGapToken

public boolean isGapToken(T token)

Default implementation that tests of the string representation of the specified token is equal to "".

Specified by:

isGapToken in interface TokenSet<T>

Parameters:

token - the token to be tested

Returns:

true if the specified token is recognized as a gap, false otherwise.

See Also:

TokenSet.isGapToken(java.lang.Object)

getGapToken

public T getGapToken()

Description copied from interface: TokenSet

Returns the default object that represents a gap in this token set.

Specified by:

getGapToken in interface TokenSet<T>

Returns:

the according gap object (Implementations may create a new instance with every call of this method or always return the same instance. In general gap objects should not have any mutable object specific properties to avoid problems if the same instance if located at multiple positions in an alignment.)

isSpaceForGap

public boolean isSpaceForGap()

Description copied from interface: TokenSet

Determines whether TokenSet.tokenByKeyStroke(KeyStroke) shall return the gap token, if the space bar is pressed, even if that key stroke is not associated with that token.

Specified by:

isSpaceForGap in interface TokenSet<T>

Returns:

true if the gap token shall always be returned, false otherwise.

setSpaceForGap

public void setSpaceForGap(boolean spaceForGap)

Description copied from interface: TokenSet

Allows to specify whether TokenSet.tokenByKeyStroke(KeyStroke) shall return the gap token, if the space bar is pressed, even if that key stroke is not associated with that token.

Specified by:

setSpaceForGap in interface TokenSet<T>

Parameters:

spaceForGap - Specify true here, if the gap token shall always be returned, false otherwise.

isMissingInformationToken

public boolean isMissingInformationToken(T token)

Description copied from interface: TokenSet

Tests if the specified token represents an unknown position (usually '?'). This method is e.g. used by data areas to determine the positions of gaps.

Note that it's legal to have multiple tokens to be considered as unknown symbols, but one of them must be defined as the default. When alignments are written to files, some formats may accept only one

Specified by:

isMissingInformationToken in interface TokenSet<T>

Parameters:

token - the token to be tested

Returns:

true if the specified token is recognized as an unknown position, false otherwise.

getMissingInformationToken

public T getMissingInformationToken()

Description copied from interface: TokenSet

Returns the default object that represents an unknown position in this token set.

Specified by:

getMissingInformationToken in interface TokenSet<T>

Returns:

the according object (Implementations may create a new instance with every call of this method or always return the same instance. In general objects should not have any mutable object specific properties to avoid problems if the same instance if located at multiple positions in an alignment.)

getSymbolType

public CharacterSymbolType getSymbolType(T token)

This default implementation returns CharacterSymbolType.UNCERTAIN for all missing information tokens. If getType() specifies a nucleotide or amino acid token set, CharacterSymbolType.UNCERTAIN is returned for all tokens which have a IUPAC ambiguity code string representation (as returned by TokenSet.representationByToken(Object)). In all other cases CharacterSymbolType.ATOMIC_STATE is returned.

Inherited classes should overwrite this method, if other uncertain or any polymorphic tokens are present.

Specified by:

getSymbolType in interface TokenSet<T>

Parameters:

token - the symbol to be tested

Returns:

the type of the specified symbol

getMeaning

public CharacterSymbolMeaning getMeaning(T token)

Description copied from interface: TokenSet

Returns the meaning of the specified symbol. (Note that LibrAlign models will usually not contain match tokens directly).

Specified by:

getMeaning in interface TokenSet<T>

Parameters:

token - the token to determine the meaning from

Returns:

the meaning of the specified token

clone

public abstract AbstractTokenSet<T> clone()

Inherited classes have to overwrite this method and create a deep copy of getKeyMap().

Specified by:

clone in interface TokenSet<T>

Overrides:

clone in class java.util.HashSet<T>

Returns:

an identical token set

addSpaceKeyForGaps

protected void addSpaceKeyForGaps()