info.bioinfweb.libralign.model.tokenset

Class BioJava3TokenSet<C extends org.biojava3.core.sequence.template.Compound>

java.lang.Object

java.util.AbstractCollection<E>

java.util.AbstractSet<C>

info.bioinfweb.libralign.model.tokenset.BioJava3TokenSet<C>

Type Parameters:

C - the compound type of the compounds contained in this set

All Implemented Interfaces:

TokenSet<C>, java.lang.Cloneable, java.lang.Iterable<C>, java.util.Collection<C>, java.util.Set<C>

public class BioJava3TokenSet<C extends org.biojava3.core.sequence.template.Compound>
extends java.util.AbstractSet<C>
implements TokenSet<C>

Implementation of TokenSet backed by a BioJava CompoundSet object.

Since:

0.4.0

Author:

Ben Stöver

Module:

info.bioinfweb.libralign.biojava3

Constructor Summary

Constructors

Constructor and Description
BioJava3TokenSet(BioJava3TokenSet<C> tokenSet) A constructor used to clone instances of this class.
BioJava3TokenSet(CharacterStateSetType type, org.biojava3.core.sequence.template.CompoundSet<C> compoundSet, boolean spaceForGap) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
BioJava3TokenSet<C>	clone() Clones this instance.
java.lang.String	descriptionByToken(C token) An description of the specified token (e.g.
org.biojava3.core.sequence.template.CompoundSet<C>	getCompoundSet() Returns the BioJava compound set that is viewed by this instance.
C	getGapToken() Returns the compound associated with AbstractTokenSet#DEFAULT_GAP_REPRESENTATION from the underlying BioJava token set using CompoundSet.getCompoundForString(String).
CharacterSymbolMeaning	getMeaning(C token) Returns the meaning of the specified symbol.
C	getMissingInformationToken() Returns the default object that represents an unknown position in this token set.
CharacterSymbolType	getSymbolType(C token) Returns the type of the specified token (symbol).
CharacterStateSetType	getType() Determines the type of tokens that are defined by this instance.
boolean	isGapToken(C token) Tests if the specified token represents a gap.
boolean	isMissingInformationToken(C 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.
java.util.Iterator<C>	iterator() Returns an unmodifiable iterator of the underlying BioJava compound set.
int	maxRepresentationLength() Calculates the maximal length of a representation returned by TokenSet.representationByToken(Object) of all tokens contained in this set.
java.lang.String	representationByToken(C token) Returns the representation string of the specified token that shall be displayed in an AlignmentArea or written into an alignment file.
boolean	representationLengthEqual() Checks if all representation strings returned by TokenSet.representationByToken(Object) have the same length.
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.
int	size()
C	tokenByKeyStroke(javax.swing.KeyStroke key) Returns the token from this set that is associated with the specified key stroke.
C	tokenByRepresentation(java.lang.String representation) Returns the token associated with the specified string representation used to display the token in an AlignmentArea or an alignment file.

Methods inherited from class java.util.AbstractSet

equals, hashCode, removeAll

Methods inherited from class java.util.AbstractCollection

add, addAll, clear, contains, containsAll, isEmpty, remove, retainAll, toArray, toArray, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Set

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

Methods inherited from interface java.util.Collection

parallelStream, removeIf, stream

Methods inherited from interface java.lang.Iterable

forEach

Constructor Detail

BioJava3TokenSet

public BioJava3TokenSet(BioJava3TokenSet<C> tokenSet)

A constructor used to clone instances of this class.

Parameters:

tokenSet - the instance to be cloned

BioJava3TokenSet

public BioJava3TokenSet(CharacterStateSetType type,
                        org.biojava3.core.sequence.template.CompoundSet<C> compoundSet,
                        boolean spaceForGap)

Creates a new instance of this class.

Parameters:

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

compoundSet - the BioJava compound set containing the compounds to be copied into the new instance

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

Throws:

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

Method Detail

getCompoundSet

public org.biojava3.core.sequence.template.CompoundSet<C> getCompoundSet()

Returns the BioJava compound set that is viewed by this instance.

Returns:

the underlying compound set instance

tokenByKeyStroke

public C 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<C extends org.biojava3.core.sequence.template.Compound>

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

iterator

public java.util.Iterator<C> iterator()

Returns an unmodifiable iterator of the underlying BioJava compound set.

Note that this iterator will return the elements of this set as they were when this method if called. If the set is modified later on, the iterator will not reflect such changes and will not throw a ConcurrentModificationException.

Specified by:

iterator in interface java.lang.Iterable<C extends org.biojava3.core.sequence.template.Compound>

Specified by:

iterator in interface java.util.Collection<C extends org.biojava3.core.sequence.template.Compound>

Specified by:

iterator in interface java.util.Set<C extends org.biojava3.core.sequence.template.Compound>

Specified by:

iterator in class java.util.AbstractCollection<C extends org.biojava3.core.sequence.template.Compound>

Returns:

the iterator

size

public int size()

Specified by:

size in interface java.util.Collection<C extends org.biojava3.core.sequence.template.Compound>

Specified by:

size in interface java.util.Set<C extends org.biojava3.core.sequence.template.Compound>

Specified by:

size in class java.util.AbstractCollection<C extends org.biojava3.core.sequence.template.Compound>

representationByToken

public java.lang.String representationByToken(C token)

Description copied from interface: TokenSet

Returns the representation string of the specified token that shall be displayed in an AlignmentArea or written into an alignment file.

Note that some CharSequenceAdapters and StringAdapters only use the first character of the returned string to represent a token.

Specified by:

representationByToken in interface TokenSet<C extends org.biojava3.core.sequence.template.Compound>

Parameters:

token - the token associated with the representation

Returns:

a string which is at least one character long an empty string if no token in this set has the specified representation

tokenByRepresentation

public C tokenByRepresentation(java.lang.String representation)

Description copied from interface: TokenSet

Returns the token associated with the specified string representation used to display the token in an AlignmentArea or an alignment file.

Specified by:

tokenByRepresentation in interface TokenSet<C extends org.biojava3.core.sequence.template.Compound>

Parameters:

representation - the string representation of the token

Returns:

the according token or null if none is defined

maxRepresentationLength

public int maxRepresentationLength()

Description copied from interface: TokenSet

Calculates the maximal length of a representation returned by TokenSet.representationByToken(Object) of all tokens contained in this set.

Specified by:

maxRepresentationLength in interface TokenSet<C extends org.biojava3.core.sequence.template.Compound>

Returns:

a value >= 1 (since all representations must be at least one character long)

representationLengthEqual

public boolean representationLengthEqual()

Description copied from interface: TokenSet

Checks if all representation strings returned by TokenSet.representationByToken(Object) have the same length.

Specified by:

representationLengthEqual in interface TokenSet<C extends org.biojava3.core.sequence.template.Compound>

Returns:

true if all lengths are equal, false otherwise

descriptionByToken

public java.lang.String descriptionByToken(C token)

Description copied from interface: TokenSet

An description of the specified token (e.g. the full name of the compound like "Adenine").

Specified by:

descriptionByToken in interface TokenSet<C extends org.biojava3.core.sequence.template.Compound>

Parameters:

token - the token that shall be described

Returns:

a string containing no line breaks

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<C extends org.biojava3.core.sequence.template.Compound>

Returns:

the token set type

isGapToken

public boolean isGapToken(C token)

Description copied from interface: TokenSet

Tests if the specified token represents a gap. 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 gaps, but one of them must be defined as the default gap tokens. When alignments are written to files (e.g. using JPhyloIO), some formats may accept only one of these tokens as a gap and the others may be represented as additional character states.

Specified by:

isGapToken in interface TokenSet<C extends org.biojava3.core.sequence.template.Compound>

Parameters:

token - the token to be tested

Returns:

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

getGapToken

public C getGapToken()

Returns the compound associated with AbstractTokenSet#DEFAULT_GAP_REPRESENTATION from the underlying BioJava token set using CompoundSet.getCompoundForString(String).

Specified by:

getGapToken in interface TokenSet<C extends org.biojava3.core.sequence.template.Compound>

Returns:

the gap token or null if the underlying BioJava token set does contain a representation for AbstractTokenSet#DEFAULT_GAP_REPRESENTATION

See Also:

TokenSet.getGapToken()

isMissingInformationToken

public boolean isMissingInformationToken(C 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<C extends org.biojava3.core.sequence.template.Compound>

Parameters:

token - the token to be tested

Returns:

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

getMissingInformationToken

public C 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<C extends org.biojava3.core.sequence.template.Compound>

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(C token)

Description copied from interface: TokenSet

Returns the type of the specified token (symbol). Symbols can either represent an atomic token or a polymorphic state or a set of tokens, if the the position is uncertain.

Specified by:

getSymbolType in interface TokenSet<C extends org.biojava3.core.sequence.template.Compound>

Parameters:

token - the symbol to be tested

Returns:

the type of the specified symbol

getMeaning

public CharacterSymbolMeaning getMeaning(C 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<C extends org.biojava3.core.sequence.template.Compound>

Parameters:

token - the token to determine the meaning from

Returns:

the meaning of the specified token

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<C extends org.biojava3.core.sequence.template.Compound>

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<C extends org.biojava3.core.sequence.template.Compound>

Parameters:

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

clone

public BioJava3TokenSet<C> clone()

Clones this instance.

Specified by:

clone in interface TokenSet<C extends org.biojava3.core.sequence.template.Compound>

Overrides:

clone in class java.lang.Object

Returns:

a deep copy of this object