info.bioinfweb.libralign.model.tokenset

Class TokenSetTools

java.lang.Object

info.bioinfweb.libralign.model.tokenset.TokenSetTools

public class TokenSetTools
extends java.lang.Object

Provides tool methods useful for implementing TokenSet.

Since:

0.1.0

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
TokenSetTools()

Method Summary

Modifier and Type	Method and Description
static <T> CharacterSymbolMeaning	getMeaning(TokenSet<T> tokenSet, T token) Determines the meaning of the specified token as defined by TokenSet.getMeaning(Object).
static <T> CharacterSymbolType	getSymbolType(TokenSet<T> tokenSet, T token) Returns CharacterSymbolType.UNCERTAIN for all missing information tokens.
static <T> boolean	isGapToken(TokenSet<T> tokenSet, T token) Tests if the specified token represents a gap in the specified token set.
static <T> boolean	isMissingInformationToken(TokenSet<T> tokenSet, T token) Tests if the specified token represents missing data in the specified token set.
static int	maxRepresentationLength(TokenSet tokenSet) Calculates the maximal length of a representation returned by #representationByToken(Object) of all tokens contained in the specified set.
static boolean	representationLengthEqual(TokenSet tokenSet) Checks if all representation strings returned by #representationByToken(Object) have the same length.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

TokenSetTools

public TokenSetTools()

Method Detail

maxRepresentationLength

public static int maxRepresentationLength(TokenSet tokenSet)

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

Parameters:

tokenSet - the set to be examined

Returns:

Since all representations must be at least one character long the returned string should have a length >= 1.

representationLengthEqual

public static boolean representationLengthEqual(TokenSet tokenSet)

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

Parameters:

tokenSet - the set to be examined

Returns:

true if all lengths are equal, false otherwise

isGapToken

public static <T> boolean isGapToken(TokenSet<T> tokenSet,
                                     T token)

Tests if the specified token represents a gap in the specified token set.

Parameters:

tokenSet - the token set containing the specified token

token - the token to be tested

Returns:

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

isMissingInformationToken

public static <T> boolean isMissingInformationToken(TokenSet<T> tokenSet,
                                                    T token)

Tests if the specified token represents missing data in the specified token set.

Parameters:

tokenSet - the token set containing the specified token

token - the token to be tested

Returns:

true if the specified token is recognized as a missing data symbol, false otherwise.

getSymbolType

public static <T> CharacterSymbolType getSymbolType(TokenSet<T> tokenSet,
                                                    T token)

Returns CharacterSymbolType.UNCERTAIN for all missing information tokens. If TokenSet.getType() of tokenSet 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.

Parameters:

tokenSet - the token set containing the specified token

token - the token to be tested

Returns:

the symbol type

getMeaning

public static <T> CharacterSymbolMeaning getMeaning(TokenSet<T> tokenSet,
                                                    T token)

Determines the meaning of the specified token as defined by TokenSet.getMeaning(Object).

This default implementation will return CharacterSymbolMeaning.GAP for all tokens which are positively tested by TokenSet.isGapToken(Object) and CharacterSymbolMeaning.MISSING for all tokens which are positively tested by TokenSet.isMissingInformationToken(Object). In all other cases CharacterSymbolMeaning.CHARACTER_STATE is returned.

Parameters:

tokenSet - the token set containing the specified token

token - the token to be tested

Returns:

the symbol meaning