com.milaboratory.core.sequence

Class Wildcard

java.lang.Object

com.milaboratory.core.sequence.Wildcard

public final class Wildcard
extends Object

Representation of a wildcard symbol.

Method Summary

Methods

Modifier and Type	Method and Description
int	basicSize() Returns a number of basic letters that matches this wildcard.
long	getBasicMask() Returns basicMask representation of the wildcard.
byte	getCode() Returns alphabet code.
byte	getMatchingCode(int i) Returns i-th code that this wildcard matches.
char	getSymbol() Returns a wildcard letter.
byte	getUniformlyDistributedBasicCode(long seed) Returns uniformly distributed element (nucleotide or amino acid et cetera) corresponding to this wildcard.
boolean	intersectsWith(Wildcard otherWildcard) Returns true if set of symbols represented by this wildcard intersects with set of symbols represented by otherWildcard.
boolean	isBasic() Returns true if and only if this wildcards has only one matching letter, so it represents definite letter and formally it is not a wildcard.
boolean	matches(byte code) Returns whether this wildcard contains specified element (nucleotide or amino acid etc.).
int	size() Returns a number of letters (including wildcards) that matches this wildcard.

Methods inherited from class java.lang.Object

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

Method Detail

getSymbol

public char getSymbol()

Returns a wildcard letter.

Returns:

wildcard letter

getBasicMask

public long getBasicMask()

Returns basicMask representation of the wildcard. Wildcard bit basicMask is a long integer where: (basicMask >>> i) & 1 == 1, if wildcard includes i-th code

Returns:

basicMask representation of the wildcard

basicSize

public int basicSize()

Returns a number of basic letters that matches this wildcard. For example, for nucleotide wildcard 'R' the corresponding nucleotides are A and G, so the basicSize is 2.

Returns:

number of basic letters corresponding to this wildcard

size

public int size()

Returns a number of letters (including wildcards) that matches this wildcard. For example, for nucleotide wildcard 'R' the corresponding nucleotides and wildcards are A, G, N, R, S, W, K, M, B, D and V, so the size is 11.

Returns:

number of basic letters corresponding to this wildcard

isBasic

public boolean isBasic()

Returns true if and only if this wildcards has only one matching letter, so it represents definite letter and formally it is not a wildcard.

Returns:

true if and only if this wildcards has only one matching letter, so it represents definite letter and formally it is not a wildcard

getMatchingCode

public byte getMatchingCode(int i)

Returns i-th code that this wildcard matches.

Parameters:

i - index of letter

Returns:

i-th code that this wildcard matches

getCode

public byte getCode()

Returns alphabet code.

Returns:

alphabet code

matches

public boolean matches(byte code)

Returns whether this wildcard contains specified element (nucleotide or amino acid etc.).

Parameters:

code - binary code of element

Returns:

true if this wildcard contains specified element and false otherwise

intersectsWith

public boolean intersectsWith(Wildcard otherWildcard)

Returns true if set of symbols represented by this wildcard intersects with set of symbols represented by otherWildcard.

Parameters:

otherWildcard - other wildcard

Returns:

true if set of symbols represented by this wildcard intersects with set of symbols represented by otherWildcard

getUniformlyDistributedBasicCode

public byte getUniformlyDistributedBasicCode(long seed)

Returns uniformly distributed element (nucleotide or amino acid et cetera) corresponding to this wildcard. Note: for same seeds the result will be the same.

Parameters:

seed - seed

Returns:

uniformly distributed symbol corresponding to this wildcard