info.bioinfweb.libralign.model.tokenset

Class CharacterTokenSet

java.lang.Object

java.util.AbstractCollection<E>

java.util.AbstractSet<E>

java.util.HashSet<T>

info.bioinfweb.libralign.model.tokenset.AbstractTokenSet<java.lang.Character>

info.bioinfweb.libralign.model.tokenset.CharacterTokenSet

All Implemented Interfaces:

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

public class CharacterTokenSet
extends AbstractTokenSet<java.lang.Character>

A token set consisting of characters.

Since:

0.1.0

Author:

Ben Stöver

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
CharacterTokenSet(CharacterStateSetType type) Creates a new empty instance of this class.
CharacterTokenSet(CharacterStateSetType type, java.lang.CharSequence tokens) Creates a new instance of this class where the initial tokens are determined by the characters in the specified character sequence.
CharacterTokenSet(CharacterTokenSet tokenSet) A constructor used to clone instances of this class.

Method Summary

Modifier and Type	Method and Description
CharacterTokenSet	clone() Clones this instance.
java.lang.String	descriptionByToken(java.lang.Character token) In this default implementation the description is equal the character itself.
int	maxRepresentationLength() Always returns one.
static CharacterTokenSet	newAminoAcidInstance(boolean distinguishCase) Returns a new instance of this class containing all amino acid tokens (one letter codes), including the gap token ('-') and ambiguity codes.
static CharacterTokenSet	newDNAInstance(boolean distinguishCase) Returns a new instance of this class containing all nucleotide tokens, including 'T' and not 'U', the gap token ('-') and all IUPAC ambiguity codes.
static CharacterTokenSet	newNucleotideInstance(boolean distinguishCase) Returns a new instance of this class containing all nucleotide tokens, including both 'T' and 'U', the gap token ('-') and all IUPAC ambiguity codes.
static CharacterTokenSet	newRNAInstance(boolean distinguishCase) Returns a new instance of this class containing all nucleotide tokens, including 'U' and not 'T', the gap token ('-') and all IUPAC ambiguity codes.
java.lang.String	representationByToken(java.lang.Character token) Returns the character itself.
boolean	representationLengthEqual() Always returns true.
java.lang.Character	tokenByRepresentation(java.lang.String representation) Returns the first character of representation if that character is contained in this set.

Methods inherited from class info.bioinfweb.libralign.model.tokenset.AbstractTokenSet

addSpaceKeyForGaps, getGapToken, getKeyMap, getMeaning, getMissingInformationToken, getSymbolType, getType, isGapToken, isMissingInformationToken, isSpaceForGap, setSpaceForGap, tokenByKeyStroke

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 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

CharacterTokenSet

public CharacterTokenSet(CharacterStateSetType type)

Creates a new empty instance of this class.

Parameters:

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

CharacterTokenSet

public CharacterTokenSet(CharacterStateSetType type,
                         java.lang.CharSequence tokens)

Creates a new instance of this class where the initial tokens are determined by the characters in the specified character sequence.

Parameters:

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

tokens - a sequence containing the tokens to be contained in this set

CharacterTokenSet

public CharacterTokenSet(CharacterTokenSet tokenSet)

A constructor used to clone instances of this class.

Parameters:

tokenSet - the instance to be cloned

Method Detail

newNucleotideInstance

public static CharacterTokenSet newNucleotideInstance(boolean distinguishCase)

Returns a new instance of this class containing all nucleotide tokens, including both 'T' and 'U', the gap token ('-') and all IUPAC ambiguity codes.

Returns:

the new instance

newDNAInstance

public static CharacterTokenSet newDNAInstance(boolean distinguishCase)

Returns a new instance of this class containing all nucleotide tokens, including 'T' and not 'U', the gap token ('-') and all IUPAC ambiguity codes.

Returns:

the new instance

newRNAInstance

public static CharacterTokenSet newRNAInstance(boolean distinguishCase)

Returns a new instance of this class containing all nucleotide tokens, including 'U' and not 'T', the gap token ('-') and all IUPAC ambiguity codes.

Returns:

the new instance

newAminoAcidInstance

public static CharacterTokenSet newAminoAcidInstance(boolean distinguishCase)

Returns a new instance of this class containing all amino acid tokens (one letter codes), including the gap token ('-') and ambiguity codes.

The returned instance can also be used to take up molecular character data from a stream, where the character type (amino acid or nucleotide) is not known, because all nucleotide characters and ambiguity codes are also contained in the amino acid token set. (That is not the case the other way around.)

Returns:

the new instance

representationByToken

public java.lang.String representationByToken(java.lang.Character token)

Returns the character itself.

Parameters:

token - the token associated with the representation

Returns:

a string consisting only of the character token

tokenByRepresentation

public java.lang.Character tokenByRepresentation(java.lang.String representation)

Returns the first character of representation if that character is contained in this set.

Parameters:

representation - the string representation of the token (This would usually be the token itself in this class.)

Returns:

the token or null if no according token is contained in this set

See Also:

TokenSet.tokenByRepresentation(java.lang.String)

maxRepresentationLength

public int maxRepresentationLength()

Always returns one. Overwrite this method if you overwrite representationByToken(Character).

Returns:

1

representationLengthEqual

public boolean representationLengthEqual()

Always returns true. Overwrite this method if you overwrite representationByToken(Character).

Returns:

true

descriptionByToken

public java.lang.String descriptionByToken(java.lang.Character token)

In this default implementation the description is equal the character itself. Overwrite this method if you want to provide a more detailed description.

Parameters:

token - the token that shall be described

Returns:

a string consisting only of the character token

clone

public CharacterTokenSet clone()

Clones this instance.

Specified by:

clone in interface TokenSet<java.lang.Character>

Specified by:

clone in class AbstractTokenSet<java.lang.Character>

Returns:

a deep copy of this object