com.milaboratory.core.motif

Class Motif<S extends Sequence<S>>

java.lang.Object

com.milaboratory.core.motif.Motif<S>

Type Parameters:

S - base sequence type

All Implemented Interfaces:

Serializable

public final class Motif<S extends Sequence<S>>
extends Object
implements Serializable

Data structure for efficient exact and fuzzy matching/searching of sequences (wildcard-aware).

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
Motif(S sequence) Creates motif from sequence.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	allows(byte code, int position)
boolean	equals(Object o)
BitapPattern	getBitapPattern()
int	hashCode()
boolean	matches(S sequence, int from)
Motif<S>	or(Motif<S> other) Returns per-position or of two motifs.
int	size()

Methods inherited from class java.lang.Object

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

Constructor Detail

Motif

public Motif(S sequence)

Creates motif from sequence.

Parameters:

sequence - sequence

Method Detail

or

public Motif<S> or(Motif<S> other)

Returns per-position or of two motifs.

e.g. ATGC or TTCC = WTSC

Parameters:

other -

Returns:

getBitapPattern

public BitapPattern getBitapPattern()

size

public int size()

allows

public boolean allows(byte code,
             int position)

matches

public boolean matches(S sequence,
              int from)

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object