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

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

All Implemented Interfaces:

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

Direct Known Subclasses:

MotifMatcher

public abstract class AbstractSequencePositioner<T>
extends Object
implements SequenceIterable<T>

This class provides a skeletal implementation of the PositionIterable interface, to minimize the effort required to implement this interface. To implement a JPL positioner on a Sequence, the programmer needs only to extend this class and provide implementations for the iterator. (The iterator returned by the iterator method must implement the foundNextPosition() method).

Version:

1.0

Author:

nikitin

Nested Class Summary

class

AbstractSequencePositioner.Iterator This inner class provides implementations for next() and hasNext() needed from Iterator interface.

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

ExtraIterable.AbstractExtraIterator<T>

Field Summary

protected int	numberOfPositions
protected SymbolSequence<T>	sequence Iterator will iterate over found positions on this sequence.

Constructor Summary

AbstractSequencePositioner()

Method Summary

int	getNumberOfSites() get number of positions
IndexIterable.Iterator	iterator(SymbolSequence<T> sequence) coupling sequence with iterator
void	setSequence(SymbolSequence<T> sequence) Set the sequence for future searches.

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.expasy.jpl.commons.collection.IndexIterable

iterator

Field Detail

sequence

protected SymbolSequence<T> sequence

Iterator will iterate over found positions on this sequence.

numberOfPositions

protected int numberOfPositions

Constructor Detail

AbstractSequencePositioner

public AbstractSequencePositioner()

Method Detail

setSequence

public void setSequence(SymbolSequence<T> sequence)

Set the sequence for future searches.

Specified by:

setSequence in interface SequenceIterable<T>

Parameters:

sequence - the sequence where motif search will be done.

Throws:

IllegalArgumentException - if sequence is not defined.

getNumberOfSites

public int getNumberOfSites()

Description copied from interface: SequenceIterable

get number of positions

Specified by:

getNumberOfSites in interface SequenceIterable<T>

iterator

public IndexIterable.Iterator iterator(SymbolSequence<T> sequence)

Description copied from interface: SequenceIterable

coupling sequence with iterator

Specified by:

iterator in interface SequenceIterable<T>