org.expasy.jpl.commons.collection.symbol.seq
Class MotifMatcher<T>

java.lang.Object
  org.expasy.jpl.commons.collection.symbol.seq.AbstractSequencePositioner<T>
      org.expasy.jpl.commons.collection.symbol.seq.MotifMatcher<T>

All Implemented Interfaces:

Iterable<Integer>, ExtraIterable<Integer>, IndexIterable, SequenceIterable<T>

public class MotifMatcher<T>
extends AbstractSequencePositioner<T>

This class allows to search a regular expression pattern all over a symbol sequence and store positions in its inner Iterator.

Version:

1.0

Author:

nikitin

Nested Class Summary

class

MotifMatcher.Iterator Inner iterator over pattern matching sequence positions.

Nested classes/interfaces inherited from interface org.expasy.jpl.commons.collection.ExtraIterable

ExtraIterable.AbstractExtraIterator<T>

Field Summary

protected Pattern	aminoAcidMotifPattern Motif searched on SymbolSequenceImpl object
protected String	symbolSequence String representation of SymbolSequenceImpl

Fields inherited from class org.expasy.jpl.commons.collection.symbol.seq.AbstractSequencePositioner

numberOfPositions, sequence

Constructor Summary

protected

MotifMatcher(String strPattern) Create an instance for a given pattern.

Method Summary

boolean	equals(Object o) equal instances have equal patterns.
Pattern	getPattern()
int	hashCode()
MotifMatcher.Iterator	iterator() Returns a JPL iterator over a set of elements of type T.
static <T> MotifMatcher<T>	newInstance(String pattern)
void	setSequence(SymbolSequence<T> sequence) Override setSequence() to convert byte sequence representation to String in order to use Java Regular Expression.

Methods inherited from class org.expasy.jpl.commons.collection.symbol.seq.AbstractSequencePositioner

getNumberOfSites, iterator

Methods inherited from class java.lang.Object

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

Field Detail

aminoAcidMotifPattern

protected Pattern aminoAcidMotifPattern

Motif searched on SymbolSequenceImpl object

symbolSequence

protected String symbolSequence

String representation of SymbolSequenceImpl

Constructor Detail

MotifMatcher

protected MotifMatcher(String strPattern)

Create an instance for a given pattern.

Parameters:

strPattern - the motif to search.

Throws:

RuntimeException - if regexp has a compilation error.

Method Detail

newInstance

public static <T> MotifMatcher<T> newInstance(String pattern)

setSequence

public void setSequence(SymbolSequence<T> sequence)

Override setSequence() to convert byte sequence representation to String in order to use Java Regular Expression.

Specified by:

setSequence in interface SequenceIterable<T>

Overrides:

setSequence in class AbstractSequencePositioner<T>

Parameters:

sequence - the sequence where motif search will be done.

getPattern

public final Pattern getPattern()

Returns:

the motif pattern

iterator

public MotifMatcher.Iterator iterator()

Description copied from interface: ExtraIterable

Returns a JPL iterator over a set of elements of type T.

Returns:

a JPL iterator.

equals

public boolean equals(Object o)

equal instances have equal patterns.

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object